And our sermon title this morning is Fit for Godliness, Fit for Godliness. And we are studying 1 Timothy chapter 2 and now we come to verses 8 through 15. We've been looking at verses 1 through 7 and the exhortation there from Paul to Timothy to pray. And so now we're moving on, moving through this practical exhortation in 1 Timothy chapter 2 and we come to verses 8 through 15 today. Now, this is the purpose of 1 Timothy, the purpose for Paul's writing to Timothy because he says in chapter 3 is so that we ought to know, so that we can know how we are to conduct ourselves in the house of God, which is the church of God, the church of the living God, the pillar and ground of the truth. This letter began in chapter 1 with a charge to Timothy. Deal with the false teachers, deal with the false teaching, charge some that they don't teach any divergent doctrines. In other words, clean up what's going on in Ephesus. False teachers and false teaching in Ephesus were having such an impact that life and doctrine in Ephesus were under attack, they were under assault. And we'd already seen in chapter 1 how many had suffered shipwreck of their faith, how we lost Hymenaeus and Alexander and certainly many of their followers had found themselves cast on the rocks apart from Christ as a result of following after this false doctrine. And so this is a serious charge and in a sense understanding that and understanding this concept, this context, the letter to Timothy from Paul here is a polemic. In other words, it's an argument, it's a heated argument against false teaching and error in Ephesus. It's Paul's correction, if you will, of wrong thinking and wrong behavior. Now if we think about it that way, if you think about Paul in his letter to Timothy, correcting wrong behavior, correcting wrong thinking, that in looking at Paul's exhortations, we can reconstruct, if you will, what is going on in Ephesus at this time. That's a good way to approach Bible study. You look at the context and you can determine what's happening contextually in their situation at their time. We also have plenty of historical information to help us. We're going to look at that as well. Now, very important to understand that as we move into verses 8 through 15 here. We need to know from the context how these verses applied to those who were in Ephesus so that we can have a good and firm and solid understanding of how these verses apply in our context today. Many, many, many will take verses 8 through 15, especially 9 through 15 and completely disregard these verses as culturally irrelevant or out of date. They're just an anachronism of a bygone age and have no application for us today. Now, the Bible says that all of Scripture is breathed out by God and is given and is profitable for instruction. All Scripture is profitable, well, except for 9 through 15, right? Enough. All Scripture is profitable. Here there is application from verses 9 to 15 that will specifically apply to our context today. And the reason that we want to take time to walk through this is that there is a powerful tide of cultural influence that not only swept through Ephesus at this time, swept through the known world at this time, but also there's a powerful cultural tide that sweeps through our context today. And we need, if we're going to stand confidently in God's Word, if we're going to stand against that tide and stem that tide, we've got to be able to be confident in our understanding of what these passages, what these verses are saying to us so that we can obey the Lord, so that we can be faithful to Him in what we find here. There are many of those that would discredit or discount what is being said, and they use that as an excuse to disobey God. And they do that to their own destruction. There are valuable, valuable lessons to be learned, lest we think that's for ladies only in verses 9 to 15. Men, that's also for you. There are valuable principles that you can apply from this text here and we want to be faithful to God in this. Now, the very heart of this passage as we get into these verses, we find a, it's a treasure trove of truth from God's Word. There's a lot packed, as we found with many of these passages, there's a lot packed in here. There's a lot of truth to look through. It is very clear. It's very straightforward. For the most part, it's very easy to understand. You can read the text and pretty obviously see for yourself what it's talking about. But this text, especially verses 9 to 15, are at the same time wrapped in controversy, wrapped in conflict, in confusion. And who is the author of confusion? Satan is the author of confusion. He's wrapped in confusion. Even as it was when this letter would have first arrived in Ephesus in the first century. They would have had difficulty with this also. This is a passage that may not be hard to understand, but as Peter says in 2 Peter 3 16, it's one of those that many who are untaught and unstable will twist to their own destruction as they do the rest of the scriptures. You might say to yourself, that's a strong statement. We're talking about modesty, basically, in verses 9 to 15. And we can twist these passages, these verses, to our own destruction. Absolutely you can. Absolutely you can. At the end of the day, this passage is about submission to authority. It's about submission. Specifically, the authority that God has ordained from creation for our good and God's glory. It is about submission, submission to His Word. Submission to Him, to Christ, to God, and submission to His Word so fully that it impacts how you dress, how you conduct yourself, how you interact with the members of the opposite sex, how you express what is inwardly in your heart. It has everything to do, everything to do with denying yourself, taking up your cross daily and following Him, which is a call to salvation, a call to discipleship, a call to submit to the Lordship of Jesus Christ. The reason that this passage, these verses are often twisted because of our flesh because our hearts are deceitful, because of our self-will, our self-indulgence, our pride. At the root of it all, it's submission to authority. It's submission for both men and women. It's submission. And it's at the heart of whether or not we will submit to and live for Him. If you claim to be a Christian, you've said, I've submitted to the Lordship of Jesus Christ. If you're not submitted to the Lordship of Jesus Christ and as a fruit of genuine saving faith, you are obeying Him, you're not a Christian. When the Lord saves, the Lord gives a man a new heart, and as a fruit of that new heart, as a fruit of that new nature, that new creation in Christ then obeys the Lord, submits to His Lordship. He treasures His Word and he seeks hard in following after Christ, taking up His cross and denying Himself. Wicked men would rather twist the words of Almighty God, rather than submit to them, rather than to humble themselves to them and joyfully obey them. Think about it for a moment. In our context today, in our culture, in our society, why does the idea of submission draw such a vitriolic or hostile response from most people? What does that say about us? What does that say about your flesh? When you hear the word submission and you bristle against it, what does that say about you? It speaks volumes about you. Even as a genuine Christian, we can sometimes have difficulty submitting ourselves to authority. Our flesh just wants to rail against it. Our flesh wants to question it. Our flesh wants to deny it. Our flesh wants to run the opposite direction. We know that from childhood, right? In rejecting the authority of our parents. Throughout Scripture, Scripture is replete. Throughout Scripture, there's the call of God for all of us, men, women, children, all of us to submit to authority. We are all under authority. And authority is God's gift to us on this planet while we're here on this side of eternity so that we can learn how we submit to our ultimate authority, who is God. All authority is given by God. This submission from the heart is a mark of genuine saving faith. If you are unsubmissive in heart, your ultimate unsubmissiveness is against God himself. This whole passage is really with respect to submission. At the end of our study in chapter 2 verses 8 through 15, we pray that the only question that will remain will be whether or not you will joyfully submit to the Word of God, or if you will join those who twist it and rebel against it to their own destruction. You've got to ask yourself that question. This today will be an introduction of sorts. We're going to take a look beginning in chapter 2 verse 8 and give you an introduction of sorts to what will hopefully be several sermons on this issue to help both ladies and men in our church learn the truths that God has contained in this passage for our good and for his glory. And so let's dig in together and let's begin looking at chapter 2 here. At this time in Ephesus, Paul and Timothy were faced with cultural pressures that began to influence behavior in the church. That's not new. There are always cultural pressures that influence the church. Always. From that time until now, and there will always be cultural pressures that influence the church and influence behavior in the church. The primary concern of this passage in response to these pressures was the behavior specifically of women and their role, their biblical role in the church. This crops up or gets attested to in a couple of different ways. One, this mainly had to do with their attitudes, with their dress and their conduct in public, specifically public worship and under public teaching. But now two, because Christian lifestyles are always under scrutiny by an outside eye, right? By the outside world. Paul also has in mind here the perceptions of believing outsiders as well. One, this influence in the church with respect to attitudes, dress, their conduct in public worship. But also we have in concern here the testimony of the Christian to a lost and dying world. For those who profess godliness as it says in verse 10, your life is to be a testimony. You are to be, as the verse says, fit for godliness. In Ezekiel 36, verse 23, God doesn't set you apart or sanctify you for your sake, he says there. It's something important for us to understand. He doesn't save you necessarily in that sense. He doesn't sanctify you, make you holy, conform you into the image of Christ, give you that heart holiness that is in association or in concord or in cord with godliness in order for your sake, in order for you personally, for your own good necessarily in that sense. The Lord sanctifies you as it says in Ezekiel 36 for his name's sake, for his sake, for his honor, for his glory. And he says there that the nations will know that he is the Lord when he is hallowed in you before their eyes. The Lord God is to be hallowed in you before the eyes of a lost world. They are to see the effects. God's mighty work in you of conversion, they're to see that in your life. You're to be a testimony to God. In that sense, you are set apart from sin. You're set apart from the world. If you're here today, you claim the name of Christ, you are set apart from sin. If you're here today, you claim the name of Christ and you're not set apart from sin, you're not a Christian. When the Lord God saves, he sets you apart from the world. He separates you from sin.  You're to be that testimony to Christ that we know from history and from experience. There will always be cultural pressures that will assault that testimony. There always will be. For the church as a whole, for us as a body, there are cultural pressures that assault the church. But for you individually, if you claim the name of Christ, you're going to have to stand against the fiery darts of the wicked one. There will be cultural pressure attacking and assaulting you. We have to stand against that. The enemy is going to make sure of that. We're not ignorant of his schemes, but it's how you respond to that pressure that makes all the difference. And if we respond to that pressure with submissiveness to God's word, with care, with how we apply God's word, then we can be safe if we depend on God for that. It makes all the difference how you respond to it. In Scripture, we see several examples of this cultural oppression. There was the culturally oppressed church here in Ephesus, very obvious. There was the culturally oppressed church in Corinth. We look in Revelation. We see the compromising church in Pergamus, the corrupt church in Thyatira. The dead church in Sardis. The lukewarm church in Laodicea and so on. What amazes me is not the cultural oppression against the churches, but the fact that the professing church so easily caves into the pressure. The professing church is caving in all the time. You have pressure today to ordain women in roles of pastoral leadership in the church. Listen, a church with a woman pastor has no pastor. The word of God is very clear on this. It goes beyond that. Today, there's great pressure in the body of Christ to ordain homosexuals in the ministry. There's constant pressure from the culture to be tolerant, to be ecumenical, to give up doctrine for the sake of peace, to give up that which we are to contend earnestly for so that we can have some false sham unity that is abominable in the eyes of God. There's constant pressure from the culture around us to deny the faith. And we see churches capitulating to this pressure all the time. Jesus Christ is the only way to heaven. No one comes to the Father except through me, Christ said. We see cultural pressure constantly to be perceived as loving and gracious. And so churches abandon the word of God and they start preaching to felt needs. They exalt the need of man over the glory of God and forsake the preaching against sin. Forsake preaching against hell, against judgment, against justice, against wrath. The very things that we need to know in order to be right with God. They forsake the preaching of God's attributes in that sense for the sake of tickling someone's ears or giving the people what they want to hear. No repentance. There's certainly under pressure from the culture, the professing Christian is, to fall into sin and deceit. To live a sinful life despite your profession. There always will always be pressure from the world that stands in opposition to God's people. Our heartfelt commitment here, our vow to the Lord here, if you're a member of this church, is to stand in opposition to that oppression. To stand, vow to the Lord that by his grace we will hold fast to his word and that we will not compromise with the trappings of this wicked world, but that we will stand strong against that cultural pressure and stand for him. We will not compromise with the spirit of the age. We're going to preach his word and be faithful to him. This is what churches need to do. This is what individuals need to do. If you're a Christian, you must do that. Churches and Christians, professing Christians all the time, cave in so easily to the pressure. Just a little bit of persecution, a little bit of name calling, and you're caving into the pressure. We're not to cave in. The cultural pressure and emphasis here led the women there to rebel basically in one of two primary ways. One through external dress, which is an expression of internal attitudes. External dress, which is an expression of internal attitudes. Now listen, God is concerned with a heart. God is concerned with a heart, but it's the fruit of that heart that is visible oftentimes in the way that we dress, in the way that we conduct ourselves. In deportment is the old word, talking of behavior in manners, in the way that we live. External dress is an expression of internal attitudes. But two, they rebelled through abandoning the God-given role of women in the church. Let me ask you, are these issues, issues that we see even in the church today? Amen. We see these in the church. Do we from time to time even see these issues in our church? Yes. So is this teaching here from verses 8 to 15, is this teaching culturally relevant in our context today? Yeah, you better believe it is. It's very relevant. We have a lot to learn from this. We see these even today. There's nothing new under the sun, right? Such as this common demand, same problems they were facing. It's just repackaged. We have the same problems today. We need to hit this head-on and obey the Lord in these areas. And these verses have much to teach us. Men, they have much to teach you as well, so don't check out. So with this in mind, what is a godly pastor then to do? Paul is exhorting Timothy. What is Timothy to do in Ephesus? What's Paul to do? Well, Paul, as he is supposed to do in faithfulness to the Lord, begins to set forth expectations governing the behavior of women in Ephesus. And in doing so, Paul incurs the wrath of women for all the ages. He's been assaulted for centuries over this. George Bernard Shaw said that Paul is the eternal enemy of women. Is that true here? No. This is for your good, ladies, and for God's glory. And men, again, there's a lot here for you to apply. You need to apply these passages also. This is for our good and the Lord's glory. Do you cave into this pressure? No. You preach, thus saith the Lord, and you keep pressing forward. If, as it will, you can just see it. Can't you just see inexorably? We're just leading to this complete lack of tolerance, this complete hatred of Christianity, and everything that Christianity stands for. Can't you see it that at some point, preaching roles in the church, preaching modesty is going to be hate speech, right? We're going to run us out of town on a spit. We don't cave into that pressure. You preach, thus saith the Lord. The Bible's clear that sodomy is abominable in the eyes of God, and you preach that, whether others consider it to be hate speech or not. As this is the word of God, and we're to submit to the word of God. At the end of this passage, with the Lord's help, we're going to have a very clear understanding, and again, this is just a, what a gift from God, these verses. We're going to have a clear understanding of modesty, a clear understanding of biblical attitudes about sexual purity, sexual immorality, biblical attitudes toward authority, biblical attitudes with how we're to conduct ourselves as members of the opposite sex, our attitudes toward the roles that God has given us. This is intensely practical and intensely clear, and so we're going to reap a lot as we sow through this passage. Men, again, there's a lot here that you can apply. Receive with meekness the implanted word, which is able to save your soul. Engage with these verses, and allow the spirit of God to convict you of sin, to apply these truths to your heart, that you can live by them, and allow the Lord to sanctify you through it. This has everything to do with our sanctification. Allow the Lord to work and pray that he does. All right? Well, let's begin. Let's look at verse 8. We'll begin here in verse 8, and again, this will take us a couple of weeks, but let's begin here with Paul's brief instruction in one verse here to men. Verse 8, I desire therefore that the men pray everywhere, lifting up holy hands without wrath, without doubting. Now, this here, he begins, I desire. That the desire there is linked to the previous passage. In the previous passage, we looked at Paul's exhortation to Timothy that we should pray for all men, because in verse 4, God desires that all men be saved. Here we see this exhortation continued with Paul's desiring to Timothy that men pray everywhere, lifting up holy hands without wrath and doubting. This word for desire is the word bulimai. In verse 4, God says, I desire, fellow, I wish that all men be saved. It's a wish, a want, a desire on the part of God that all men be saved. This is important for us to understand here in verse 8 that bulimai is a desire. I desire or I want here for men to pray, but that's a want. That's a desire with intention, with an annotated thought, with a determined resolve. In other words, bulimai here is to be viewed as a command. It's to be viewed as a command. It's not the idea that he wishes, it's the idea that he commands that all men pray everywhere, lifting up holy hands without wrath and doubting. That everywhere, so we understand, refers back to in a sense the six alls that we saw in the last passage. There's a universal or an all-encompassing to this command. We're to pray everywhere. Men are to pray in every church. This is specifically talking about public prayer and the prayer that goes on in worship. But we're to pray everywhere. And everywhere that there's a church and everywhere that we are to pray publicly, all men everywhere to pray. We're to pray in this way. Now he says, lifting up holy hands. As we saw before, this was a common posture for prayer. Men stood while they prayed. People often lifted their eyes and prayed out loud, and they prayed by lifting hands. Let me ask you, knowing what we know from Scripture, is God concerned with the posture of your prayer? No. God is concerned with the heart. Here, if you look at this, this command, bulamai, I desire, I command therefore that men pray everywhere lifting up the emphasis on holy hands. The holiness. Is God concerned with the hands? No, God's concerned with the quality of those hands. The internal, if you will, nature of those hands that are expressed in this posture that we see. God is concerned with the inward reality. God is concerned with the heart. This is heart holiness. It's seen heart holiness in one sense in the fact that it is devoid of wrath and doubting, devoid of anger. It was possible at this time in Ephesus. There was so much contention going on with these false teachers that strife erupted in the church. This church was an assaulted church. It was in chaos. It was having difficulty. So there was strife going on. The word doubting there comes from chapter one. It literally means contention. They were to pray without this anger, without this strife, without this contention, without this disturbance in our hearts. We're to lift up holy hands. That is a pure heart. That is holy living. That is heart holiness. Again, God is concerned with the heart. The fruit of that is clean hands. The fruit of that is righteous living.  And we know that that also expresses inward reality, don't we?  We also know that dirty hands or unclean hands were an expression of uncleanness inwardly. These are to be clean hands and a pure heart. God is concerned with the quality of the hands, with the cleanness of the heart, not hear the posture. That is always the case. If you have claimed the name of Christ you've said I've turned for my sin. You've said I've left a life lived for myself and I have turned in faith alone to Christ.  Here, now think about it, in exhorting the men to pray lifting up holy hands what God is saying through this passage is that the prayer of men with dirty hands is unacceptable. The prayer of the wicked isn't heard by God the Bible says that we are to live in accord with our profession. When you profess the name of Christ you turn from your sin. Jesus Christ came into the world to save sinners but he came to save them from their sin, not in their sin. Worship from an impure heart. Worship from a heart that has not been transformed by Christ. Worship from a haughty, unrepentant heart is an abomination to God. The sacrifices of God are a broken heart and a contrite spirit. We are to repent before the Lord. We are to have holy hands. Now let me ask you, can you make your own hands holy? No. You have no righteousness of your own. You can't just clean your life up and expect that your worship is acceptable. I need to get back to reading my Bible. I just need to get back to church. I need to get back to doing this, that or the other thing. I need to quit drinking or I need to quit cussing chewing and going with the girls who are doing. I need to clean my life up.  You need Christ. You need a new life. You need a new heart. You need to be transformed by God and then worship from that transformed heart. If the Lord gives you a new heart, you will be clean, as he said to the disciples, indeed. You'll be clean. You'll be new. And that will inevitably lead to clean conduct, clean living, clean hands. That's the pure heart, the clean hands that God is talking about there. Worship of God in is simply unacceptably Him. That's why baptism, why the Lord's Supper, why self-examination is so important. We're to examine ourselves. We're to be pure. Live a holy life before Him. We need Christ. That's verse 8. Now in verse 9 here Paul begins to exhort Timothy with respect to the ladies in Ephesus. And in verses 9 through 15 looking at this passage verses 9 to 15, 6 verses here are just a beautifully arranged table. A beautifully arranged table. And you have place settings all over the table. Place settings of modesty. Place settings of self-control. Place settings of submission. Of humility. Of roles in the church. These beautiful place settings around the table. And you have a glorious centerpiece right in the middle of the table. And that's verse 10. I want you to look at that with me. Verse 10. Here Paul says to Timothy proper for women professing godliness with good works. Here's this beautifully set table. And we've got modesty and self-control and adornment and apparel and submission and humility and roles and authority. All these place settings around with this beautiful centerpiece which is fitting which is proper for women professing godliness with good works. Here this becomes a basis if you will for self-examination through this passage. This verse 10 this centerpiece is a challenge on the part of the apostle Paul to the ladies in Ephesus and to us to self-examine ourselves with respect to the things that are being taught here. It speaks of that which is proper or fitting for women professing godliness. It's where we get the title of the sermon from. Fit for godliness. The word here for proper means fitting or fit. Here's the test ladies. If we're going to view this as our centerpiece this is the challenge from Paul then here's the test. If a woman is making a claim to godliness or a profession of faith saying you're Christian then your whole life must be brought under the reality of that claim. Men the same applies to you doesn't it. If a man is making a claim to godliness making a profession of faith saying that you're in Christ claiming to be a Christian then your whole life men will be brought under the reality of that claim. That means the way that you dress here. We're going to see that. The way that you conduct yourself the way that you interact with those of the opposite sex.   You're still living in your sin. This is a challenge to you as well. If you are going to make a claim to Christ if you're going to make a claim to godliness then you must turn from your sin abandon that life of sin despise it reject it do away with it. Can't you feel the weight of it right aren't you sick and tired of living in sin. The way the transgressor the Bible says is hard. Pleasure in sin is fleeting pleasure and then the guilt comes. The condemnation comes and eventually the judgment comes. Turn from your sin abandon that life to make a claim for godliness you put your faith and trust in Christ alone to save you. You have no works that are going to commend you to God you can't do enough good you can't help enough old ladies across the street. You can't do it you must be wrapped in the righteousness of Christ you must have another's righteousness he has to clean your hands he has to clean your heart. But if you're going to make a claim to godliness if you're going to claim to be a Christian you've got to turn from your sin and put all of your hope all of your trust in Christ alone to save you. Anyone making that claim to godliness is going to submit everything that they are to him it's a submission of everything you are to a submission to all that he is. Now there are those things here if you're going to make that claim if we're going to use this as a test verse 10 then there are clearly those things in scripture which are proper that we'll discuss and that necessitates that there are those things which are improper and we'll tie those to these issues the way that you dress the way that you conduct yourself the way that you interact with members of the opposite sex your attitudes about intimacy sexual immorality authority submission roles there are those things which are proper and obviously there are those things which are not attitudes which are not proper conduct which is not proper dress which is not proper the Lord in this challenge in verse 10 the Lord in this centerpiece is calling professing Christians specifically here professing Christian women to give proof or to give evidence of their claim to godliness in these things to give evidence to give proof it's very interesting in verse 10 there the word for professing means literally promising you are when you come to Christ you are promising to be fit for godliness you're making a promise you're making a covenant with God like Job said I made a covenant with my eyes when you come to Christ you're making a covenant with your life to submit all things to be fit for godliness the Lord is concerned with His name and you're a testimony of His name you're to be fit for godliness that word means promising and you're making a promise to be godly in these areas as we look through these verses and going through this series we're going to take this centerpiece and we're going to look at each of those areas that the passage specifically addresses as we go through the series so we'll cover these points together you may want to jot these down one today we'll begin looking at outwardly fit for godliness remember the title of the sermon is fit for godliness one is outwardly fit for godliness two from these passages these verses here we're going to look at what it looks like to be inwardly fit for godliness outwardly fit for godliness and inwardly fit for godliness go so closely together you're going to see that as we walk through this verses very closely tied together but once outwardly fit for godliness for godliness, you'll be effectively fit for godliness. We'll see that, effectively fit for godliness. We see from God's word, and it's specifically here in these verses, that the Lord has deliberately fit you for godliness. Deliberately fit you for godliness. And then especially with respect to the role of women, the Lord has gloriously, ladies, has gloriously fit you for godliness. So outwardly fit for godliness, inwardly fit for godliness. Effectively fit, deliberately fit, and gloriously fit. As we go through each one of these points, each of those areas will build on the issues or the areas that have come before, and we'll inform our understanding of those. And this should, I'm praying, please be in prayer with me. This will have a dramatic impact on how we view these things. We'll have dramatic fruit in our church. Ultimately, dramatic fruit for the glory of God and for the conversion of souls. This is, these verses are God's gift to you. Just in a cursory hearing of these verses, are these verses oppressive, repressive? No, these verses, ladies, are liberating. These verses are God's good for you. They are glorious. And I want you to see that as we walk through here. Let's take a look at point one. Outwardly fit for godliness. Let's look at verse nine together. Here, after the exhortation of men, Paul says to Timothy in the church, in like manner also, that the women adorn themselves in modest apparel with propriety and moderation, not with braided hair or gold or pearls or costly clothing, all right? Good principle in Bible study. As you get into the word of God, you move on from milk to solid food, you're gonna study intently the word of God. First principle here is to study your context, to learn your context. From the position that Paul is taking here, we can reconstruct the problems going on in Ephesus and the problems specifically with respect to sexual impurity in this church. In chapter five, verse two, we see the women exhorted to maintain purity. In chapter five, verse six, the Bible says she who lives in pleasure is dead while she lives. That word for pleasure there means to live self-indulgently. You're living for your own self-will. In chapter five, verse 11, there are younger widows in this church at Ephesus who have grown wanton against Christ.  In second Timothy, chapter three, verse six, there are gullible women in the church who are led away by various lusts. Again, an issue of sexual impurity. And then here, in first Timothy, chapter two, verse nine, there's an issue here of sexual purity and beginning specifically with the way that the women in the church display themselves. They're displaying themselves sensually and they are acting and dressing immodestly. Now, there's possibly two answers for this in terms of reconstructing the context at the time. One is that as we see in chapter five, they have those gullible women who are being led away by various lusts, potentially under the influence of false teachers in Ephesus and false teaching that is going on and these women are being led away by false teachers in false teaching within the church at Ephesus. That's a possibility. I think more likely is the emergence of an outside cultural influence on the church at Ephesus, not unlike the outside cultural influence that we have on the church today. This came in the form of what commentators call the Roman woman. We know from experience, from history, a recent experience, recent history, the impact of feminism on the church, the impact of the sexual revolution on the ways that people think, the ways that people act, the ways that people look at and interpret the word of God. We see those influences in our day and age. In this time, in the first entry in Ephesus, when this letter was written, there was this emerging cultural influence from outside the church called the Roman woman. What commentators today are calling the Roman woman and basically it's just a repackaged sexual revolution, a repackaged feminism, that there was this intent on the part of basically lost women, pagan women, in culture at the time to reject normal conceptions of modesty or normal conceptions of the way that women were to be. They were rejecting those and pushing forward their new desire to exert influence or to take authority for themselves. We see that in our day and age, right? See that all the time against the word of God. But that's what happened. That was what was happening at this time as well. This is, in either way, regardless of whether it came from within or without, these are the things that are not fitting here in Ephesus, not fitting for women who are professing godliness. And remember, as we go through, this was in the context, if you will, of public worship, of public prayer and affects their public testimony. Now at the beginning of verse nine, Paul begins with in like manner also. That's why I said that that word bulimai in verse eight is so important because the in like manner also points back to that command on the part of Paul. It picks up the force of that command. And so now ladies and men too, everything that we see in verses nine through 15 is going to come to us not in the form of a wish, not in the form of a preference or of an opinion on the part of Paul, as many would like to say, but in the form of a command by the Holy Spirit through the pen of Paul to us. It is a command from God that we are to obey. And it says here in like manner also that the women are to adorn themselves in modest apparel. This adorning themselves, interesting word. It's a Greek word, cosmene, meaning to adorn. It comes from the same root word that we get the word cosmos, world in Greek from. The word world literally meant an ordered system or an ordered arrangement. And so in this sense, cosmene for adorn yourselves, adorn yourself or to put yourself in good order. It's to put you in a well order, to put things in proper order. It's where we get our word cosmetic from. You're to arrange yourself properly, to put yourself in good order, good or proper order. Now the reference here specifically is to outward clothing or apparel. Your outward clothing is to be well ordered or in proper order. The opposite to this word is chaos. And which is out of order. It is confused. It's to become chaotic. Now in that sense, you've got instruction, right? In both directions. One is you don't want to go to church chaotic. Again, we're talking about public worship. You're not to go and this is internal and external. We're not to arrange ourselves chaotically. And don't we see that? I mean, sometimes you just got to walk through the mall to see some chaos going on with the way people arrange or order themselves today. We're not to be chaotic in our appearance. We're to be well ordered. You're to arrange yourself. In other words, that has the connotation doesn't it of care, of taking care with how you arrange yourself, how you order yourself, how you adorn yourself. These women were to adorn themselves. We're to adorn ourselves in modest apparel. We're to take care with that. Now it says here, modest apparel. That word apparel we want to take a look at for a moment. Dress, outer dress, outer clothing, at this time would basically communicate one of two ideas, right? Basically it was there to communicate one of two ideas. The first idea that apparel clothing would communicate was modesty or dignity. This was common, so you know, at the time. Unlike today, we would say today culturally that most of our apparel that we see is immodest, is undignified, right? That's the cultural trend. However, at this time, at this point in time, the cultural trend was, the cultural pressure was modest. Was to be dignified in your dress, right? And it communicated that for most women and especially wives, this was the common approach to dress. It was to communicate modesty and to communicate dignity, especially to communicate respect to your husband, respect to your mother, respect to your father. The acceptable garment at this time was called a stola. It's a robe, all right? It had a lot of material to it. It was designed to conceal the body. It was designed to cover the body, not designed to reveal. And again, this wearing of the stola, this robe-like garment was for the respect of a husband, of the respect of others that you would come in contact with. Respect to your brothers and sisters in the church. Again, speaking of worship here, respect to the Lord. It was designed to, and this is important, designed to conceal the body, all right? So that's one idea that dress, outward dress would communicate. The second idea that dress would communicate was promiscuous availability. Promiscuous availability or an overt subversion, a disrespect of authority. When we say promiscuous, we're talking about sexual impurity, sexual immorality. You made yourself, by your dress, sexually or sensually available to someone else. It communicated promiscuous availability. Now, that was becoming very common at the time for the Roman woman. The article of clothing that communicated this was not the stola, but the toga. The toga was a colorful garment, far less material, and it was designed, designed for the purpose of revealing the body, not concealing the body, all right? You see motive there, don't you? You see intent. In one, the motive, the intent is to conceal. In the other, the motive or the intent is to reveal. This clothing was common for prostitute. At that time, day and age, that clothing, that revealing clothing, was considered a shameful form of advertising. It was advertising, advertising a very specific thing. At the end of verse nine, Paul gives some specifics here with this clothing. He says, not with braided hair or gold or pearls or costly clothing. We have at the beginning of verse nine here, this inference of revealing the body versus concealing the body. All of this together, you have to understand, in the context of the first century, communicated.  That's what you were communicating. You're communicating availability, such that juvenile. It's a guy that wrote here. I found this quote, thought it was very interesting. There is nothing, he says, that a woman will not permit herself to do, and he's writing at this time, at the time that the letter from Paul to Timothy was written. There's nothing that a woman will not permit herself to do, nothing that she deems shameful when she encircles her neck with green emeralds and fastens huge pearls to her elongated ears. So now what's being communicated there? Is it wrong to have a set of pearl earrings? Okay, no, we're gonna talk about that. Is it wrong to get a gold ring or a gold necklace as a gift though? But now at this time, what adorning yourself extravagantly in that way, or what adorning yourself in revealing fashion communicated was there's nothing too shameful for you. Nothing that you would deem shameful, nothing that you would restrict yourself from doing, such that you were sexually or sensually available. It was the dress that communicated that heart. And that's very important to understand here. That was the two ideas that dress communicated. Now, in other words, for you here today, and to make quick application of this, and we'll make more application as the weeks go by, I'm not concerned with representing Christ here, so I'll dress however I wanna dress. I'm not concerned with being fit for godliness, and so I won't take any consideration to how I adorn myself, as the scripture says. The motivation behind this second form of clothing was to draw attention to yourself, was to draw attention away from everyone else, often it had the effect of drawing the attention of another woman's husband, and to draw attention to yourself. Today, it's not as much extravagance that does that, as it is revealing clothing. Revealing clothing draws attention to yourself, and there's an interesting contrast here. At this time in Ephesus, and we see this also in Corinth, the issue, if you will, were the women in the church rejecting cultural norms for dress and accepting this new Roman woman kind of approach to dress, all right? Today in our context, it's the opposite. It's the accepting of cultural norms for dress, and a rejecting of what would be considered biblical approach to that issue. In that day and age, clothing became a way that women would exalt themselves and subvert authority. In today's culture, we've completely changed, completely changed the idea of what beauty is, right? Today, beauty is synonymous with sensual. Beauty is synonymous with sexy. Beauty is synonymous with revealing the body, not concealing the body. It's no longer the hidden person of the heart. It is the revealed external body of a woman. Many times today, women just don't know the difference. Men, same issue, many men just don't know the difference, and we dress immodestly as defined by the scripture, all right? Talking about outward godliness here, outward fit, outwardly fit for godliness is first point. That notion, all right, is meaningless apart from the heart. Is God concerned with the article of clothing on your body? Only to the degree that he is concerned with how that expresses an inward reality, an inward attitude, an inward heart truth. The Lord is concerned with the heart, and it's interesting, go back to chapter two, look at verse nine, there's a word here that is used that the Holy Spirit chooses very specifically, and I love this, in like manner also, that the women adorn themselves in modest apparel. That word there for apparel is the word katastale in Greek. Katastale literally means down, it's a compound word, down robe, it talks about this stola, this large robe, this robe that the women wore at the time. But it also carries the idea of an inward reality that goes along with that, and it's very interesting here. It means literally the idea of keeping something in check to be reserved or to operate with restraint. The word is an outward word expressing the clothing, but also has with it the inward reality, or the inward understanding of restraint or reserved, or keeping yourself in check, self-control. This word, or the dress here that we're talking about, this exhortation from Paul to Timothy, has carried with it throughout this verse, is going to carry with it a sexual or a sensual connotation, all right? Restraint in clothing is to be accompanied by a restraint in your attitude. In other words, restraint and attitude should impact what you wear. The issue in the heart should impact how you adorn yourself. Those two things have to go together. And the old word that we use for that is deportment, deportment or comportment. Deportment speaks to your behavior, your manners, the level to which you conduct yourself with respect. Again, it's carefully chosen by the Holy Spirit. Let me give you an example of where we see that word, that concept in scripture.  It reminds me of Proverbs 31, where Solomon says that strength and honor are her clothing. You have this concept of outward apparel matched with an inward reality. Here we see that in 1 Peter chapter three, verse three through six. Where here Peter says, do not let your adornment be merely outward, arranging the hair, wearing gold or putting on fine apparel. There's that word apparel. Rather, let it be the hidden person of the heart with the incorruptible beauty of a gentle and quiet spirit which is very precious in the sight of God. For in this manner, in former times, the holy women who trusted in God also adorned themselves, being submissive to their own husbands as Sarah obeyed Abraham, calling him Lord, whose daughters you are if you do good and are not afraid with any terror. In other words, if you've got a Christian woman who has a heart on fire for God, she's humble to the word of God, she loves the Lord. She is fervent for the Lord. She desires from the heart to live for him. She's bringing her thinking and her conduct under the authority of God's word. You don't have to worry about how she dresses because that dress is an outward expression of an inward reality that's already there. The dress is going to fall into place. Strengthen, honor her clothing, and she expresses that in the way that she outwardly adorns or apparels herself. Now that saying that, the Holy Spirit using this word to convey this meaning means that your clothing, ladies, because again, we're talking about outwardly fit for Godliness. We'll get on to inwardly fit here soon. Your clothing will reflect a deeper set of values.  If you claim to be a Christian and yet your clothing is not reflecting Christian values, there's a disconnect. Clothing is to reflect Christian values. It is to be rejecting of the popular culture. It's to stand opposed to the popular culture, opposed to that influence. And you gotta think about it. Who is dressing you? Are you being dressed in that sense, adorned by the word of God? Fit for Godliness or is Paris dressing you? Is Vogue dressing you? Is New York dressing you? Is the culture dressing you? Who's dressing you? You must have a valuation. In order for this to be understood and true in your life to have a good biblical understanding of this, as a Christian woman, and guys, you can apply this to yourself as a Christian man, you must have a different valuation of beauty than the world has. It has to be different. The world's valuation of beauty is so opposed to God's valuation of beauty. It must be different. If you think to yourself, well, I think this looks beautiful. Because of what you see in magazines or on TV or in the movies or what you see everybody wearing around the mall or wherever, listen, you're gonna be swept into that way of thinking.  You need to allow the word of God. You need to allow God to inform you of what is beautiful. And that is tied very closely to sexual immorality. Let's look at another example quickly together, Isaiah chapter three. I wanna give you a negative example of this. The Lord in the Old Testament rebuked Israel for it too. So, let's we think that this is only a New Testament issue? Lord rebuked Israel for it too. And we've got to see the negative example here as well so we can come to grips with this.  It's very important that we understand how these things fit together. In Isaiah chapter three, look at verse 16. Isaiah chapter three, verse 16. Here, moreover the Lord says, because the daughters of Zion are, what is that word? Hotty, prideful, self-willed, calling attention to themselves, wanting to draw attention to themselves, are prideful. Because the daughters of Zion are hotty and walked with outstretched necks, and here it is, wanton eyes, pointing to sexual immorality, the sensual reasons that we dress the way we do, walking and mincing as they go, making a jingling with their feet, they had anklets on their ankles. Verse 17, therefore the Lord will strike them with a scab. The crown of the head of the daughters of Zion and the Lord will uncover, and here it is again, this inference to sexual immorality, he'll uncover their secret parts. He'll bear their shame, so to speak. Verse 18, in that day, the Lord will take away the finery, the jingling anklets, the scarves and the crescents. By the way, who gave those things to them? The Lord God did. Remember, I think it's Ezekiel 16, when the baby struggling in its blood, the Lord cleaned the baby, washed the baby, cared for the baby, gave her a ring for her nose, right?  The Lord provided these, but these women in Israel at this time, used what the Lord gave as a blessing and turned it into a curse.  Look at verse 19, the pendants, the bracelets and the veils, the headdresses, the leg ornaments and the headbands, the perfume boxes, the charms and the rings, the nose jewels, the festal apparel and the mantles, the outer garments, the purses, wow, man. The mirrors, the finelin and the turbines and the robes, right? And so it shall be, instead of a sweet smell, which it once may have been, there will be a stench. There'll be judgment here for doing this, instead of a sash, a rope. Again, is God concerned with the outward apparel? God's concerned with the outward apparel to the degree that it expresses an inward corruption, an inward wickedness. It's the heart that matters to God. Instead of well-set hair, baldness. Instead of a rich robe, a girding of sackcloth and branding instead of beauty. Your men shall fall by the sword and you're mighty in the war. This is judgment of God. This is, again, a negative example. We must be careful to honor God in the outward expressions of our inner faith, our inner godliness. I saw this quote by John Chrysostom. I thought this was very appropriate and something to consider and please consider it carefully. Here's what Chrysostom said. You carry your snare everywhere and spread your nets in all places. Now he's talking specifically, ladies, here to you. Men can do this as well, right? You carry your snare. You have a snare that you carry everywhere, he says, and spread your nets in all places. You allege that you never invited others to sin. You did not, indeed, by your words, but you have done so by your dress and by your deportment. When you have made another sin in his heart, how can you be innocent? Tell me, whom does this world condemn? Whom do judges punish? Those who drink poison or those who prepare it and administer the fatal potion? You have prepared the abominable cup. You have given the death-dealing drink and you are more criminal than are those who poison the body. You murder not the body, but the soul and it is not to enemies you do this, nor are you urged on by any imaginary necessity nor provoked by injury, but out of foolish vanity and pride. This is a dangerous thing. This is something that was going on in Ephesus, but I would submit to you, this goes on all over the place in professing churches today. It's something that we must take to heart. Ultimately here, this is about coming well-ordered, well-arranged for worship. We must be fit for Godliness. Again, all of this depends on the heart. All of this depends on the heart. You can be outwardly modest and inwardly like a ravenous wolf. Again, it is the heart. It's not saying that you must come to church in a burlap sack or slovenly or indifferent, but properly with the right motive, with the right heart. It's not saying that everyone should come to church on a three-piece suit with a pocket watch or that you need to wear your prom dress. You have to dress nicely with the right heart, expressing that which is communicated from the heart. We know that 1 Samuel, right? 1 Samuel 16, 7 says that God does not look on the outward appearance, but God looks on the heart. God looks on the heart. How do I know that I'm dressed right? How do you know? How do you know if you're dressed right? Examine your heart. Check your heart. Labor to avoid sensual attention. Labor to avoid communicating something sensually. Show me a woman whose heart is fit for godliness and you don't have to worry about what she dresses. Examine your heart, examine your motives and the heart will dictate that outward expression. Let's pray together. Father in heaven, Lord God, I thank you Lord for this practical teaching, God, from your word. Just amazed at you, Lord, at the economy of words with which you teach us. Got amazed by the Holy Spirit at your choice of words and how carefully framed and how beautifully communicative they are in teaching us about these things. God, you are so genius for it. Brilliant, omnipotent, all wise. God, and we worship you and praise you for that. God, thank you for this. Thank you for your help in understanding these things. God, I pray for soft hearts in response to this. God, I pray for humility. I pray for great care. Lord, we want to be a sexually pure church. We don't want to allow Satan to have a foothold in our church with respect to sexual immorality. We want to be pure before you. God, set apart from sin, worshiping you, praising you. God, as your word that you be worshiped with a pure heart and with clean hands and by your spirit, according to your grace and mercy, God, help us to do this for your glory. Help us to do this, Lord, as a testimony to those who are outside.  We want to draw a line in the sand, God, a stake in the ground and fend off those fiery darts of the wicked one that we might be a genuine trophy, God, of your grace and mercy to us. This is for your namesake so that those nations will see you, God, hallowed in our eyes that we might be worthy of the calling with which you've called us. Thank you for this time. Thank you for these dear brothers and sisters. God, what a joy it is to serve alongside them. And I pray that you would bless them, bless the labor of their hands in your vineyard, God, and continue to bless and preserve this church to the salvation of souls and for your everlasting praise and worship. In Jesus' name, amen.


This lecture is part of a Canadian Bioinformatics Workshop and is made available under the Creative Commons. Welcome to Module 1, Introduction to Pathway and Network Analysis of GeneLists, as part of the Pathway and Network Analysis of OMEX Data Workshop. In Module 1, I'm going to provide you a brief introduction to Pathway and Network Analysis and some background information about gene lists and pathways that are going to be required for the rest of the workshop. So the basis of this workshop is helping people interpret gene lists. And the general idea is that you perform some kind of experiment where you get thousands of genes that result and then you want to know how to interpret those. Typically, any kind of genome scale analysis or OMEX, such as genomics, proteomics, RNA-seq, transcriptomics, etc., produces lots of information like this. And one of the main ways that people interpret this data is by trying to understand some mechanistic story that pulls these things together. So if we want to know what's interesting about the thousands of genes that were resulted from our transcriptomics experiment, we might ask if they are enriched in known pathways, complexes, or functions. So this picture represents a transcriptomics experiment, and once you have collected the raw data, you might rank or cluster it to generate a gene list. And then in this course, we want to compare that gene list to prior knowledge about cellular processes using various analysis tools and ideally find some new interesting discovery. Pathway Network Analysis saves time compared to the traditional approach if you had hundreds or thousands of genes and you wanted to interpret them manually. You'd have to look each one up, understand its function, and understand the relationship of the functions of all the genes on your list to try and figure out if there are particular mechanisms that were in common and that might be interesting to highlight. And so this approach traditionally is very time-consuming. Pathway Network Analysis helps gain mechanistic insight into omics data in a more automated way. For instance, we could identify a master regulator, drug targets, or characterizing pathways that are active in a sample. And any type of analysis that involves pathway or network information is a type of pathway or network analysis. Pathway Network Analysis is most commonly applied to help interpret lists of genes, and the most popular type is pathway enrichment analysis, but there are many others that are useful and will be covering pathway enrichment analysis and a number of others as part of this workshop. The benefits of pathway analysis compared to analyzing information at the transcript or protein level one by one is that considering the data in the context of pathways usually makes it easier to interpret because we're working with familiar concepts like the cell cycle. We identify possible causal mechanisms, which is useful, especially if we're interested in therapeutically targeting those mechanisms. We can use pathway and network analysis to predict new roles for genes that we don't know the function of. And pathway and network analysis helps improve statistical power, which will cover more in the workshop, and it might also lead to more reproducible results. For instance, if we do multiple experiments on multiple samples, we might get different gene expression profiles or signatures for each sample or condition, but they might all affect the same pathways, and so looking at the level of genes, we might not see exact replication of the signatures across conditions, but looking at the level of pathways, we might see replication of pathways across the conditions. And pathway and network analysis also facilitates integration of multiple data types in a multi-omics approach. I mentioned pathway and network analysis. What are pathways and how are they different from networks? Pathways are usually detailed, high-confidence models of a biological process, usually formed with steps. We might have biochemical reactions as part of the pathway. Usually the models are developed based on many years of study and many publications. So for instance, the EGF receptor pathway or metabolism are examples. Networks, on the other hand, are sets of relationships between genes of different types. For instance, we could have genes activating each other or binding each other, and they represent a more simplified view of cellular logic, frequently they're noisier, and they often come from large-scale genome-wide assays, like co-expression relationships for transcriptomics or large-scale protein interaction screens. There are many types of pathway and network analysis, for instance enrichment of fixed gene sets, so this could answer the question of what biological processes are altered in my sample. DeNovo subnetwork construction and clustering usually answers questions like what pathways are altered in this sample, and it's not limited to known pathways that could also identify new pathways. It can also be used to, for instance, identify clinically relevant tumor subtypes. And pathway-based modeling is more advanced and can help identify if there are particular molecules that are important or critical in a pathway given the data that you've collected. The general pathway analysis workflow is summarized here. So first we collect some genomics data, for instance gene expression data. This workshop uses gene expression data extensively, although the concepts that we'll cover are applicable to other types of genomics data. But transcriptomics data or gene expression data is a very good example type of data to cover for this workshop, because it's popular and it's highly informative frequently. So once we've collected our genomics data, we normalize and score it. For instance we can compute differential expression between two conditions, and this generates some kind of gene list. And then we want to learn about the underlying mechanism that this gene list might be telling us about using pathway and network analysis. And to break this box out a little bit more, pathway and network analysis usually starts by running analyses and visualization methods that help us identify interesting pathways and networks. And once we've found one that's interesting, we can focus in on it to better understand molecular mechanism and eventually develop a publication quality model. So this workflow, the simplified workflow that I just showed you, is actually more complicated. We can use that workflow to analyze many different types of data, shown in blue at the top. This middle level shows us how we might process the data. Ultimately all of these processing steps result in a gene list that we can interpret using pathway analysis or network analysis. And here's the mechanistic drill down box. So we'll be going over these in more detail in the workshop and some more detail in the coming slides. So where did gene lists come from? There are many types of genomics data types and there are many ways to get gene lists from these data types and the gene lists have different meanings. For instance molecular profiling like measuring all the mRNA transcripts or protein levels in a sample can help us identify molecules that are important for our sample and this generates a gene list. We might also get some quantification of these, which generates a gene list plus the quantification values. And we can also rank, if we have many samples, we can rank and cluster them using biostatistical methods that generate a ranking or a clustering and these can also generate gene lists like the set of genes that are associated with a cluster. Another type of omics data is interactomics. For instance we can measure protein interactions, microRNA targets, transcription factor binding sites and frequently these interaction measuring methods provide lists of genes that are targeted by a protein or microRNA or a transcription factor. A genetic screen like a CRISPR screen can also provide a list of genes and genome-wide association studies can identify genes that are linked to SNPs that are associated with a phenotype of interest. These methods generates a gene list but the gene lists frequently mean different things based on the methods and you can think of other examples that might be relevant to your own work. So as I mentioned, gene lists have a meaning and you have to understand that meaning to understand how to interpret them. So frequently a gene list might relate to a biological system where we then want to understand protein complexes, pathways or physical interactions that are part of that biological system. A particular screen might identify a list of genes that's related to a gene function or a molecular function like protein kinases. It could identify a list of genes that's related to a similar cell or tissue location or a chromosomal location. So clearly these lists of genes have very different meanings. Again we need to understand that meaning to understand how to interpret the gene list. Okay, so the first part of this larger, more detailed workflow is this blue layer here which covers many different types of omics data that can be converted into gene lists. We talked about gene expression data and protein expression data, those are very similar. DNA methylation is similar but we might need to score methylation of gene promoters to get a gene list or link methylation groups to genes. Similarly microRNAs, if we measure their expression we have to link them to other genes using known or predicted targets. Protein binding to DNA or RNA, for instance with chromatidamine or precipitation, again we have to identify target genes because we might identify a region of the genome that is bound by a protein of interest but that might not be a gene. It might be near a gene or it could be quite far from a gene so additional work is required to identify target genes. Mapping protein interactions directly identifies a set of genes that interacts with the bait protein for instance and looking at mutations from whole genome sequencing or exome sequencing identifies a set of variants which can also be linked to genes through various different means. So before analysis, when we have data from any one of these methods we need to be aware that we need to normalize and do a proper background adjustment and proper quality control to avoid giving too much noise to the pathway analysis methods. Any kind of statistics that will increase signal and reduce noise is important. We need to consider how many genes result from this. We don't want to generate a single list filled with the entire genome. It needs to be more specific and we also need to make sure that the gene identifiers are compatible with the software that we're using and we'll talk about that more later. In general these days many genomics data types are handled by core facilities and those facilities typically have standard workflows that they apply to the data and they give you the result which can then be directly input into pathway network analyses. Sometimes people run their own analyses in their lab frequently and their work established workflows are available for these too and occasionally there's new genomics data types and the workflows might not be established and then you need to know something about how those workflows work or what the latest is in that area to figure out how to apply those workflows to your data. But again the general way of working with this data especially for something like gene expression data typically those are measured by a core facility and you'll just get the result as a gene list. So these types of established methods process the raw data and convert it into a gene list using various different strategies. Once you have a gene list hopefully what was part of the experimental design is asking the question of what you want to accomplish with this gene list. For instance you might want to summarize the processes or other aspects of gene function. You might want to compare two different samples or two different types of samples. You might want to identify a controller for a process like a transcription factor that you could then over express or knock out to test its causal nature. You could find new pathways or new pathway members and discover new aspects of gene function. You can correlate a disease or a phenotype with information from your gene list or you can find a drug that targets genes in your list. Okay so the green boxes here relate to pathway and network analysis. Pathway is on the left and networks on the right. We'll cover more detail about those in the workshop but I just wanted to introduce one very basic type of pathway analysis called pathway enrichment analysis and then I will tell you more about some background information that's important for just understanding how these types of analyses work. So a standard pathway enrichment analysis considers a list of genes from your experiment. For instance all the genes that are down-regulated in a brain cancer cell line and that's represented by this blue circle. And then we compare this blue circle, the genes in this blue circle with known pathways. So we might have a list of genes that are associated with a pathway or a neurotransmitter signaling. This might have 100 genes in it and we ask the question, what's the overlap of the neurotransmitter genes with my list? And you calculate some overlap and then given the information about all the genes in your list and the size of this overlap you can compute a p-value using a standard statistical test like a chi-square test or Fisher's exact test and you're wondering if there are more neurotransmitter signaling genes in this case in my list than I would expect by chance. Given the size of the neurotransmitter signaling pathway and the size of the genome. So if the neurotransmitter signaling pathway is only 1% of the genome and I see 5% of my genes in my gene list are part of the neurotransmitter signaling pathway, that's more than I expect. And I can get a calculate a p-value for that. So we do this with many pathways. So we test neurotransmitter signaling and then hundreds or thousands of other pathways. Once we're done we need to do some multiple testing correction because we want to avoid false discovery from just trying many pathways. And in the end we might develop some kind of hypothesis that drug-sensitive sensitivity and brain cancer is related to reduced neurotransmitter signaling. So pathway enrichment analysis as I've described it requires two things the gene list that you provide from your experiment and also a set of pathways which have to come from a database. And we compare these two and we find enriched pathways for instance using techniques such as GSEA and G Profiler. So to understand some background information about pathway enrichment analysis I'm going to tell you about gene identifiers to understand how gene lists work and I'll also talk about places where we get pathway information and other gene annotation like the genontology and other sources. So first I'll talk about the gene list. So a gene list is a list of genes and the important concept to understand is that a list of genes is not just a list of names but it's a list of unique identifiers that allows to understand unambiguously what genes we're just talking about. Identifiers or IDs are ideally unique stable names or numbers that help track database records. For instance the social insurance number or an entree gene ID. Gene and protein information is stored in many different databases and thus genes have many different identifiers. There are records for genes, DNA, RNA and protein so each gene might have corresponding records and a database of DNA sequences or RNA sequences and each of those records in those databases or entries in those databases would have a different identifier associated with it. So it's important to recognize the correct record type or entry type. For instance the entree gene database doesn't store information about sequence. They link to sequence in other databases where you might have DNA regions, RNA transcripts or protein sequences. For instance in the rough seek database which does store sequence. So it's important to know that as I mentioned that you need to use some standard identifier if you want to unambiguously share and have other systems like pathway analysis methods understand your genes. You can't just use colloquial names for genes as they just won't be recognized. Some common identifiers there are many are listed here. The red ones are ones that are frequently encountered. Entree gene that I bolded here is one that we recommend because it's quite stable. We also have species specific information for instance for human. There's a human genome naming commission and the human genome organization and it standardizes gene symbols which are different from gene names. So a gene symbol again is an identifier which means that it's globally unique and it should be unambiguous which means that there shouldn't be two genes with the same name. This is not the case for regular gene names that you might see in the literature. Similarly other organisms have other standard gene naming systems associated with them. So there are many different identifiers and sometimes we need to work with them to convert one to the other. You might have entree gene IDs that are useful for pathway analysis methods but you want to visualize you want to see the list as gene symbols which are more easy to read. There are software tools that recognize these identifiers although not every tool recognizes every identifier and you may need to map your gene list identifiers to some standard identifiers or between two different sets as I've mentioned. So there's different reasons to do this identifier mapping. The main one is converting database name numbers like integers that are associated with entree gene ID to human readable names or to convert between these when you need to use and put your gene list into a tool that only recognizes some of these. One example identifier mapping service which is quite useful is to convert this URL so you can input some genes or official names or identifiers and you can choose the type of output identifier from a very long list and when you click run it will say that these genes are also called this name or this identifier in a given database. I selected entree gene I selected ensemble genes as my target database here. So G convert is a useful tool for mapping identifiers if you need it. You have to be aware of the US are missing identifier mappings so here I entered oct4, ddt, and h3, f3a so oct4 is not recognized this may not be an official gene symbol even though it's a well known gene name and actually that's correct it is not an official gene symbol so if you use this it will not be recognized by tools that only recognize official gene symbols. The ddt gene is mapped to two different genes on the genome and if you look at the description you can see that one is the real gene that we might think of that's well known. Another gene is a novel protein that is some kind of read through through this open reading frame and so it probably is is duplicated because of uncertain genome annotation in that region of the genome. Here's another example h3, f3a which is a histone a type of histone and this one gene corresponds to two different proteins and or two different gene names this one gene symbol corresponds to two different names and two different genes and it's very closely related histones so sometimes you might see this and these might be linked because perhaps they have identical protein sequences or they might have identical gene sequences but have slightly different promoters for instance. So when you're working with identifiers like long lists of genes you have to be aware that there are some challenges and you need to be very careful to avoid errors so you always have to make sure that you're working with correct identifiers and that you map these correctly because if you make a mistake then instead of thinking you'll have one gene you'll actually have another gene in your list and that will enter into your analyses and then be wrong. So I mentioned gene name ambiguity if you have a so all of these names are names of the official gene symbol TP53 you should never use any of these not good identifiers and some of these terms might point to more than one gene and you can make mistakes in your gene list if you use them. There's also errors that are frequently introduced by spreadsheets like Excel so Oct4 example that I mentioned if you have that in your list is changed frequently to October 4th you've probably seen this if you've worked with Excel a lot and gene names there's a lot of different gene names that are converted to dates and the way to avoid this is to paste this text or to select the format of the cells that you paste to as text not general. So you might have problems reaching 100% because of some of these challenges so you might also have different databases database versions that might not recognize 100% of the genes that you have in your list and so you could if you want to reach 100% coverage do additional work using multiple sources of gene identifiers to increase coverage and you might have to do some of that work manually. Gene name errors are widespread in the scientific literature there's a paper about that, an interesting paper and there's also an interesting paper trying to quantify the problem with mistaken identifiers and how gene name errors can be introduced when using Excel in bioinformatics. Just to give you a bit of a warning of the importance of this here's an example that was quite unfortunate where a paper was published in Nature in 2003 that proposed that HES1 is a target of a given microRNA and what they found was that the gene termed human homologue of HES1 HES1 is not the same as the transcriptional repressor Harriet Hanser of Split which is also called HES1. So when they did all of their searching for HES1 they didn't realize that there's two genes both called HES1 and they made a mistake and actually it resulted in completely wrong information in their paper and a retraction. So general recommendations with working with gene lists for proteins and genes is to map everything to entree gene IDs or official gene symbols using a spreadsheet to make sure it's all working correctly. If you want to reach 100% coverage you might need to manually curate missing mappings using multiple resources and be very careful of Excel auto conversions especially when you're pasting a large gene list because when you paste a large gene list you don't see all of the conversions that are happening off screen so it's important to make sure that you are careful to remember to format cells as text before pasting or past as text. This assumes that you're working with proteins and genes and it doesn't and it recommends to map everything to genes and the reason for this is that the era of genomics and all of the pathway analysis methods that we will cover in this course and pretty much all of them that exist don't consider splice forms so they don't differentiate between two different forms of a gene at the protein level they're obviously different and they could have totally different functions and the gene level we don't know that because we just refer to them as a given gene and unfortunately currently most tools just work at the gene level and so it's important to understand that protein specific or isoform specific information is not captured by the majority of tools. So what have we learned in this section? Genes and products have attributes and attributes have many identifiers. Genomics often require some understanding of these identifiers and potentially conversion from one type to another. There are useful identifier mapping services available and whenever you can use standard commonly used identifiers to reduce ID mapping challenges in your workflow. So now coming back to pathway enrichment analysis and requirements we talked about gene lists. Now we're going to talk about pathways. Pathways and other gene function attributes are used in pathway enrichment analysis. There are lots of information available on databases. A good source of pathway information is gene ontology, biological processes terms. Also pathway databases like Reactome which we'll learn about in a workshop. But there are many other types of annotations associated with genes. For instance molecular function and cellular location chromosome position, disease association transcription factors that bind a set of genes and many others. So these all represent ways of annotating genes and you can all represent many of these as sets of genes. Like a set of genes with a given molecular function, like a protein kinase. So this information in this workshop we're going to be mostly focused on pathways but there is a lot of additional information about genes that we can use similarly to pathways in pathway enrichment analysis methods. Okay so talking about pathways first I'm going to talk about the gene ontology. The gene ontology or GO is a set of biological phrases or terms which are applied to genes like protein kinase, apoptosis or membrane. This gene ontology is also a dictionary so each term has a definition associated with it and it's actually quite useful for teaching because tens of thousands of biological terms have nice definitions in this ontology. I've mentioned the word ontology, gene ontology and ontology is a formal system for describing knowledge so usually ontologies have a couple of different features. So one feature is that terms are frequently related to each other which I'll explain in a bit. You also have a standard way of naming terms and this is more information about gene ontology is available at the project homepage. So gene ontology is structured in a hierarchy the terms are these boxes here and the relationships between terms vary but two examples are ISA and part of relationships so we might see for instance B cell apoptosis is a type of apoptosis which is a type of program cell death which is a type of cell death this is a type of physiological process etc all the way up to a very general part of the hierarchy. B cell apoptosis is also part of B cell homeostasis which is a type of immune cell homeostasis. So you get the idea of how these different relationships here have different meanings and the advantage of organizing all of these terms in this hierarchy is that it describes multiple levels of detail about gene function. Terms can have more than one parent or child and that sometimes complicates gene ontology analysis but it's just important to understand that. So gene ontology covers three different aspects of gene function cellular component branch or aspect of the ontology covers where genes are located in the cell the molecular function branch or aspect covers molecular functions like enzyme functions and the biological process aspect covers pathways like cell division or more general path more general processes. So gene ontology is actually composed of two parts the first part are terms which I talked about just now Go terms are added manually by editors at various different annotation groups worldwide they're added by request and experts help with major redevelopment the gene ontology terms there are many of them there are over 44,000 terms currently in the ontology this grows over time so it is evolving although over the past few years it's remained relatively stable they've covered a lot of the known concepts in biology the second part of gene ontology are annotations so this is a particularly interesting part of gene ontology that we use for pathway enrichment analysis this links terms to genes so annotations take a term and they connect it to a gene using an association usually trained curators of genome databases do this they're known as these links between genes and terms in the ontology are known as gene associations or Go annotations multiple annotations are possible per gene and frequently genes have many different terms associated with them some gene ontology annotations created automatically without human review and this tends to be lesser quality and so it's important to understand that there's two types of annotation which I'll explain more in a bit so because of this hierarchy and because multiple terms can be associated to a gene a given gene once it's associated to a term automatically associates that gene to all of the other terms that are the parent of that term that we associate to and so that's one way of generating a lot of additional terms that are associated with a gene as I mentioned there are two major sources of annotation manual which are curated by scientists and these are very high quality although their time consuming to create so there are fewer of them relatively another type of manual annotation are computational analysis methods which generate a lot of annotation automatically but then the results are reviewed by people and filtered to just keep the ones that make sense so electronic annotation is generally annotation derived without human validation frequently computational prediction the accuracy here varies some computational methods are extremely accurate like computational methods that predict transmembrane regions and protein sequences are more than 95% accurate reaching 99% frequently but others are lower quality so in general this is frequently treated as lower quality than the manual evidence sources so a key point is to be aware of the annotation origin we can understand the annotation origin because each annotation when a term is linked to a gene is associated with an evidence code there are lots of different evidence codes like the ones listed here all of the ones in red are manual or human curated or reviewed and the one that's not is called IEA or inferred from electronic annotation all major eukaryotic model organism species and human are covered by gene ontology annotations many bacterial and parasite species are covered and new species annotations are always in development there's a current list of official go annotations that can be downloaded from the gene ontology website and you can always map gene ontology terms by from a close species to a new species that's not annotated if you were working with a genome that's not available does not have standard gene ontology annotations available so just to spend more time on understanding the relationship of gene ontology to these different species so one point to be aware of is that well gene ontology annotations are available for many species not species are covered the same at the same level so some species have many more annotations than others so for instance human has the most annotations orange here is non-experimental and blue is experimental so there's over 200,000 terms that are associated with genes that come from primary experimental sources and if we look at mouse there's quite a lot but chicken doesn't have that many it's mostly non-experimental which might be computational sources and you can see how some species have far fewer annotations also might have smaller genomes but you can see the variability and the difference between experimental and non-experimental annotations as well as the number of annotations there are many contributing databases just to list a few most small organism databases and major genome databases and protein databases like Unibrow to contribute a lot to the gene ontology project gene ontology has too many terms for some uses so people don't do this very much anymore but imagine you wanted to create a pie chart of gene functions to summarize at a very broad level your genes you might only want to show a few high level gene ontology terms and so Go Slim is developed as an official reduced set of Go terms that are available in generic form or for plants or yeast and you can map your genes you can map your Go terms to Slim terms if you want a very compressed small set of generic terms there are many software tools available that allow you to browse the gene ontology browse gene associations and use gene ontology in different types of analyses the website that I recommend if you're interested in browsing the gene ontology and its annotations is called Quick Go from the European Bioinformatics Institute it's a very nice website and it gives you lots of information about gene ontology gene ontology just to so you're aware is one of many types of ontologies anyone can create an ontology themselves by standardizing terms in their relationships and I just wanted to give you a sense that there's more than one type of ontology usually in the process we only come across the gene ontology but occasionally we come across other ontologies like a tissue type ontology or cell type ontology okay so that covers gene ontology I next want to briefly cover pathway databases so pathway databases store information about biological pathways and more detail than gene ontology there are hundreds of pathway databases that exist there's also databases that are derived from pathways and large meta databases like pathwaycommons.org which collects major databases and unifies them into one single portal we'll go over pathway databases in more detail and cover databases like Reactome in the workshop pathways you can derive pathway information from gene ontology biological processes pathway databases like Reactome that I mentioned and I mentioned Pathguide as a way for you to go and browse pathway databases that exist there's many other types of annotations that I mentioned and you can get these usually from genome browsers so one that I like is Ensemble Ensemble is a genome browser that pulls information from many different sources and one that's great is Entrez Gene from the US NIH National Center for Biotechnology information if you're working with a model organism those databases usually are the best sources of gene attributes for those genomes and there are many others that we could discuss during lab time in the workshop just as an example of how to use Ensemble Biomart so Ensemble is a genome database that stores lots of information about genes Biomart is a query tool that Ensemble makes available to allow convenient access to gene list annotation first you select your genome then you select some filters and select attributes to download and then you can download that information I'm going to give you a demo of Ensemble Biomart because I find that it's not very intuitive the first time you visit it but just a few pointers can get you on the right track so I can access Ensemble Biomart from the Ensemble homepage at the top here I'm going to click on Biomart sometimes Biomart takes a while you have to wait some number of half a minute sometimes for it to do its job so the first thing we do is choose a database because I'm interested in genes I'm going to choose Ensemble Genes database version 100 then I'm going to choose a data set I'm interested in human so I'm going to choose human genes once I choose that a set of filters loads here and I can click on filters and have to wait for it to finish loading I can click on filters and I can ask for all the genes that are in a given region like all the genes on chromosome 1 if I want to click that if I want to know that my query is recognized and properly created I can click the count button here and it will count up the genes that match my query so in this case there are 5,475 genes on chromosome 1 I'm going to uncheck that and I'm going to ask for a specific set of genes so I'm going to limit my genes to ones with gene symbols that are a couple that I'm going to add here again just to check that all of my genes are recognized I've entered 2 genes I'm going to click count and the count should be 2 out of all the genes that are in the database and that is correct so now I've verified that Biomart recognizes the input that I've added in the filter section I can then click on the attributes section there's lots of different attributes I can download so I can download features of genes like different types of identifiers I can download information about gene structures like the exon start and end positions I can download sequence information like the peptide region or the 5.UTR region and I'm going to go back to features here and download and select to download the gene stable identifier but I'm not going to download these other things and I'm going to scroll down to external identifiers and I'm going to ask for the go term name and the evidence code and also the gene symbol when I'm finished selecting features I can click results and the results will show me an example result and you can use this to make sure that the information that you've requested is there in the right columns so here I'm getting a lot of different gene ontology terms for TP53 and then I can download everything to a file in different formats I can choose to unique results because sometimes these results are duplicated and when I'm finished I press go to download all the information and then I can load it up in a spreadsheet and work with it so let's get back to our presentation that's Ensembl Biomart so what have we learned pathways and other gene attributes and databases exist and there are many different types we can get pathway information from gene ontology and pathway databases gene ontology is a classification system and dictionary for biological concepts there are many types of annotations contributed by different groups we can allow more than one annotation term per gene some genomes are annotated better than others annotation comes from manual and electronic sources and gene ontology can be simplified for certain uses using ghost slim and many other gene attributes are available from genome databases like Ensembl so coming back to the pathway analysis workflow just to remind everyone that we've been in this background lecture we've been talking about the identifiers that we're using at these steps here where we collect genomics data the results will use some kind of gene identifier to label genes we'll probably keep those during the normalization and scoring approach and we'll probably keep those making to create a gene list and then we might clean our gene list to make sure that all the gene identifiers are correct in preparation for analyzing them with a more detailed workflow so that's it for the lab for this lecture this lab is made available if you want to practice working with gene identifiers and attributes learning about G Profiler and Biomart you can use the Integrated Assignment Gene List or your own gene list to play with the G Convert System and G Profiler or use Ensembl Biomart I highly recommend just familiarizing yourself with those tools because they're very useful I use them regularly a few times a week that is the end of our lecture the main point again of this lecture is to bring everyone up to the same speed on some very basic concepts that we that everyone will need for the main workshop thanks for your attention


Okay, so I haven't watched this yet, but a lot of the folks on Twitter that I follow are talking about this So this is from Jason Campbell.  This sounds amazing like we have to listen to what he has to say to get the full context But I would absolutely love nothing more than to be part robot That would be awesome if we could upgrade ourselves in some way I think that'd be great because I feel like as human beings. We are flawed. We could use an upgrade I mean we have one hole to breathe and eat with which means we could potentially die if we get choked Even dolphins have a separate eating hole and a separate breathing hole. That should be part of our upgrade On top of that, I feel like we should do a patch to make our Bladders last longer if he's serious about this then I don't know why somebody wouldn't want this future Who wouldn't want to live in a sci-fi future where we're kind of part robots?    Well, I can choose any gender Why can't I just have like an exoskeleton of some sort of machine around me? Why not wouldn't that be dope? I would love that. Fuck. Yeah If I could have a mech suit or something or a fucking. I don't know robot arm Why not? Why is that so bad?  What a simpleton Along this is documented. This is proven. This is where silicon valley is going This is why they're so insistent on this transgender thing because if you stop being a man Then maybe you could stop being a human being maybe you can kind of just plug into some sort of machine This is where their control their profit motive is coming down the stream. There's a ton of literature about this I'm by I'm far from the first person to comment on it, but I'm just kind of connecting the dots Name the literature. I would love to explore this idea that Being transgender is a gateway into being cyborgs. Does anyone remember? During the gay marriage debate that america was having People would jump to the most dumbest most hyperbolic conclusion about where society would go if we dared to accept same-sex marriages I remember people saying well, you know, if we let people marry someone of the same sex Then what's to stop them from marrying dogs or toasters? What if I want to marry this phone? We allowed people to marry people of the same sex and Society hasn't fallen apart. I mean to be clear it is falling apart But not because of same-sex marriage to be clear It's because of capitalism late-stage capitalism But the fear mongering it's so hyperbolic that I feel like they undermine their own arguments and they don't even realize it Who believes this who believes that being transgender is going to lead to people being cyborgs? Nobody believes this not even a five-year-old would hear this and think that it's compelling You might like what is the agenda here?  It's microscopic.