Criteria for IDA, IEP, ISS, IGC, RCA, and IEA assignment in PAMGO_MGG

PAMGO_MGG curators; 2008

This GO reference describes the criteria used in assigning the evidence codes of IDA (ECO:0000314), IEP (ECO:0000270), ISS (ECO:0000250), IGC (ECO_0000317), RCA (ECO:0000245) and IEA (ECO:0000501) to annotate gene products from PAMGO_MGG. Standard BLASTP from NCBI was used (http://www.ncbi.nih.gov/blast) to iteratively search reciprocal best hits and thus identify orthologs between predicted proteins of Magnaporthe grisea and GO proteins from multiple organisms with published association to GO terms. The alignments were manually reviewed for those hits with e-value equal to zero and with 80% or better coverage of both query and subject sequences, and for those hits with e<=10^-20, pid >=35 and sequence coverage >=80%. Furthermore, experimental or reviewed data from literature and other sources were incorporated into the GO annotation. IDA was assigned to an annotation if normal function of its gene was determined through transfections into a cell line and overexpression. IEP was assigned to an annotation if according to microarray experiments, its gene was upregulated in a biological process and the fold change was equal to or bigger than 10, or if according to Massively Parallel Signature Sequencing (MPSS), its gene was upregulated only in a certain biological process and the fold change was equal to or bigger than 10. ISS was assigned to an annotation if the entry at the With_column was experimentally characterized and the pairwise alignments were manually reviewed. IGC was assigned to an annotation if it based on comparison and analysis of gene location and structure, clustering of genes, and phylogenetic reconstruction of these genes. RCA was assigned to an annotation if it based on integrated computational analysis of whole genome microarray data, and matches to InterPro, pfam, and COG etc. IEA was assigned to an annotation if its function assignment based on computational work, and no manual review was done.