PPI logo P. s. pv. tomato DC3000 P. s. pv. phaseolicola 1448A
Key to the Pto DC3000 - Plant Interaction data

genome resources
home page

Return to the Pto DC3000 - Plant Interaction page

While the Pto DC3000-Plant Interaction tables at this site have been developed using the principles of Gene Ontology annotation, certain fields have been added or formatted differently to enhance accessibility of the data to the P. syringae research community. Explanations of the different fields are given below.

GO term:
The term used to capture information on the gene products
The unique identifier with which the GO database can be searched for other gene products annotated to the term in question

Refers to the three different ontologies within GO:

C = Cellular Component
F = Molecular Function
P = Biological Process

Reference and associated PubMed ID:
Refers to a representative publication where evidence for the term assignment is shown.

1. Identity of homolog for similarity-based annotations. In cases where evidence is inferred from sequence similarity, the "with" field is used to identify homolog on which the annotation is based. For example, if an effector was characterized in P. syringae maculicola ES4326, GO annotations for the homologous effector from P. syringae tomato DC3000 will specify the identify of the homolog from Pma ES4326 in the "with" field

2. Identity of other genes mutagenized. In cases where an annotation is based on mutation of multiple gene products, identities of the additionally mutagenized genes are shown in the "with" field. For example, if the annotation is based on a double mutation, one of which is the gene being annotated, the identifier for the second mutated gene would be placed in the "with" field.

3. Identity of interacting gene products. For terms reflecting binding, this field specifies the identity of the bound gene product. NOTE: For the purposes of the Pto DC3000-Plant Interaction model, interacting gene products derived from the host are placed in the "host interaction" field

Evidence code

Indicates the nature of the evidence on which the annotation is based. Evidence codes used for the GO-based model of Pto DC3000-Plant Interactions include those listed below. A complete listing of GO evidence codes with in-depth explanations can be found at Guide to GO Evidence Codes

1. Experimental

IDA = Inferred from direct assay
IPI = inferred from physical interaction
IGI = inferred from genetic interaction
IMP = inferred from mutant phenotype
IEP = inferred from expression pattern

IC = inferred by curator

2. Bioinformatic

ISS = inferred from sequence or structural similarity
IGC = inferred from genomic context

NOTE ON ISS ANNOTATIONS: for genes annotated with the ISS evidence code, the identity of the ortholog from which the annotation was inferred is shown in the "with" field and the publication is that which documents similarity with the gene product being annotated

Host ID

Identity of the host organism (if any) on which the annotation is based:

A thal = Arabidopsis thaliana (cultivar specified where indicated in the publication)
N tab xanthi = Nicotiana tabaci xanthi
N benth = Nicotiana benthimiana
S lyco = tomato (cultivar given where specified)
S pimp =
wild tomato
S cerevisiae = yeast
Glycine max = soybean
P vulgaris = common bean

NOTE FOR USERS OF THE GO DATABASE: In the GO database, taxa are identified by their ID numbers .

Host interaction

Identity of host proteins and pathways with which the pathogen interacts. To maximize the amount of information about the plant interaction, this field includes not only the host proteins directly bound but also genes or processes that are up or downregulated which would not be normally included in GO annotations


Magdalen Lindeberg
PPI Project Coordinator
Dept Plant Pathology
Cornell University