{"action":"created","issue":{"url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/64","labels_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/64/labels{/name}","comments_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/64/comments","events_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/64/events","html_url":"https://github.com/BgeeDB/expression-annotations/issues/64","id":111826624,"number":64,"title":"GTEx normality - Current status","user":{"login":"aechchiki","id":13200013,"avatar_url":"https://avatars.githubusercontent.com/u/13200013?v=3","gravatar_id":"","url":"https://api.github.com/users/aechchiki","html_url":"https://github.com/aechchiki","followers_url":"https://api.github.com/users/aechchiki/followers","following_url":"https://api.github.com/users/aechchiki/following{/other_user}","gists_url":"https://api.github.com/users/aechchiki/gists{/gist_id}","starred_url":"https://api.github.com/users/aechchiki/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aechchiki/subscriptions","organizations_url":"https://api.github.com/users/aechchiki/orgs","repos_url":"https://api.github.com/users/aechchiki/repos","events_url":"https://api.github.com/users/aechchiki/events{/privacy}","received_events_url":"https://api.github.com/users/aechchiki/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/BgeeDB/expression-annotations/labels/GTEx","name":"GTEx","color":"fad8c7"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-10-16T12:59:44Z","updated_at":"2015-10-19T13:25:28Z","closed_at":null,"body":"Following information on cause of death (#55), serology information (#54) and medical history (#61), @mimiblis and I would like to report the following status for the current 571 GTEx subjects (AME: 283 + ANE: 288 ) :\r\n- YES: 166 (AME: 70 + ANE: 96) -> ~ 29%\r\n- NO:  123 (AME: 73 + ANE: 50) -> ~ 22%\r\n- PENDING: 284 (AME: 140 + ANE: 144) -> ~49%\r\n\r\n\r\nAmong the \"PENDING\" patients, we report the following cases (% are calculated on the whole dataset): \r\n- diabetis: 71 (AME: 69 + ANE: 2) -> ~12% \r\n- dementia: 57 (AME: 4 + ANE: 53) -> ~10%\r\n- arthritis: 34 (AME: 33 + ANE: 1) -> ~ 6%\r\n- infections (fungal/bacterial/opportunistic): 36 (AME: 25 + ANE:11) -> ~ 6%\r\n- cancer/non-metastatic cancer detection: 22 (AME: 14 + ANE: 8) -> ~4%\r\n- gonhorea: 9 (ANE) -> ~2%\r\n- schizophrenia: 9 (AME)  -> ~2%\r\n- ascites: 11 (AME: 7 + ANE; 4) -> ~2%\r\n- parkinson: 1 (AME) -> <1%\r\n- alzheimer: 2 (ANE) -> < 1%\r\n- sepsis: 7 (AME) ->  ~1%\r\n- cellulites: 3 (AME) -> <1%\r\n- sclerosis: 2 (AME) -> <1%\r\n- osteomyelitis: 4 (AME) -> ~1%\r\n- heart disease (not cause of death, column DF-DG): 118 (47 AME + 71 ANE) --> ~21%\r\n- chronic resp disease: 106 (52 ANE + 54 AME) --> ~19%\r\n\r\nObviously, we cannot discard all those cited \"PENDING\" patients (this would mean, excluding more than 90% of the \"PENDING\"!). \r\n\r\n\r\nWe think that a good compromise would be to:\r\n-  completely discard subjects with: cancer, sclerosis, gonhorrea, sepsis, infections. Tthis would mean: 82 subjects (~30% of the current \"pending\", aka15% of the whole ) tagged as \"NO\".\r\n- discard brain and nervous tissue from subjects with: dementia, alzheimer, parkinson.  \r\n- discard liver tissue from subjects with: ascites.\r\n- discard bone tissue from subjects with: osteomyelitis.\r\n- discard skin tissue from subjects with: cellulites.\r\n\r\nFurthermore:\r\n- discard heart tissue from subjects with: heart disease (NOT heart failure!)\r\n- discard lungs tissue from subjects with: pneumonia, chronic respiratory disease\r\n- discard brain tissue from subjects with: AVC and hardy scale 3 or 4 (as we already discussed)\r\n- discard liver tissue from subjects with: liver disease \r\n- discard kidney tissue from subjects with: renal disease/failure\r\n\r\nWe still don't know how to deal with subjects suffering from diabetes and arthritis. We cannot discard them all for sure (too many! ~37% of \"pending\", aka ~19% of the whole! )\r\n\r\n\r\nWaiting for your advice ;)"},"comment":{"url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/comments/149212345","html_url":"https://github.com/BgeeDB/expression-annotations/issues/64#issuecomment-149212345","issue_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/64","id":149212345,"user":{"login":"aechchiki","id":13200013,"avatar_url":"https://avatars.githubusercontent.com/u/13200013?v=3","gravatar_id":"","url":"https://api.github.com/users/aechchiki","html_url":"https://github.com/aechchiki","followers_url":"https://api.github.com/users/aechchiki/followers","following_url":"https://api.github.com/users/aechchiki/following{/other_user}","gists_url":"https://api.github.com/users/aechchiki/gists{/gist_id}","starred_url":"https://api.github.com/users/aechchiki/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aechchiki/subscriptions","organizations_url":"https://api.github.com/users/aechchiki/orgs","repos_url":"https://api.github.com/users/aechchiki/repos","events_url":"https://api.github.com/users/aechchiki/events{/privacy}","received_events_url":"https://api.github.com/users/aechchiki/received_events","type":"User","site_admin":false},"created_at":"2015-10-19T13:25:28Z","updated_at":"2015-10-19T13:25:28Z","body":"Follow-up of Bgee meeting today: \r\n- discard subjects suffering from diabetes type I (autoimmune disease); \r\n- we're gonna examine \"pending\" subjects case by case, next week (with Anne and Marc): be sure the info on every subject is well reported in the \"Explanation for status\" column "}}