Princeton Protein Orthology Database (P-POD) Help: Search Terms

This page describes the different types of search terms that can be used to retrieve proteins in P-POD. Currently, you can search by several different types of protein identifiers and descriptions (see below). Searches may be performed using UniProt, NCBI or ENSEMBL gene IDs, although it should be noted that not all of these types of IDs are available for all organisms in the current version of P-POD. Multiple identifiers may be entered with IDs separated by pipes ( (e.g. RAS1|RAS2) and wild card searches are also permitted (e.g. RAS*). In addition, you can search for disease-related information via OMIM phenotype records (# symbol, e.g. #256840). The OMIM ID (without the # symbol) can be entered at the bottom of the search page.

Valid Search Terms for Gene/Protein Search of the "Reference Genome Annotation Project" Data Set

The search terms that can be used in the search of the Reference Genome Annotation Project data set consist of columns 2, 3, 10 and 11 of the gene association file provided by the Gene Ontology (GO) consortium; for more information on these files, see the GO documentation. The same search terms apply for the updated Heinicke et al (2007) data set. However, please note that at this time only UniProt IDs (e.g.Q8II45) can be entered for Plasmodium falciparum queries. Examples for each species are:

Species (GO File) DB_Object_ID (Column 2) DB_Object_Symbol (Column 3) DB_Object_Name (Column 10) Synonym (Column 11)
Arabidopsis thaliana (gene_association.tair) 2032758 AT1G72830 AT1G72830 HAP2C
Caenorhabditis elegans (gene_association.wb) WBGene00022121 cogc-3 wwp-1 Y71F9AM.4
Danio rerio (gene_association.zfin) ZDB-GENE-990415-72 fgf8a fibroblast growth factor 8 a
Dictyostelium discoideum (gene_association.dictyBase) DDB_G0274021 rnrB ribonucleoside-diphosphate reductase Actr10
Drosophila melanogaster (gene_association.fb) FBgn0000490 dpp decapentaplegic Activin-A-receptor-25D
Escherichia coli P0A6C5
Gallus gallus (gene_association.goa_chicken) Q5F433 PRAF3_CHICK PRA1 family protein 3 IPI00597483
Homo sapiens (gene_association.goa_human) A4D0S4 LAMB4_HUMAN Laminin subunit IPI00295437
Mus musculus (gene_association.mgi) MGI:1349215 Abcd1 ATP-binding cassette, sub-family D ALDP
Rattus norvegicus (gene_association.rgd) 3728 Snap25 synaptosomal-associated protein 25
Saccharomyces cerevisiae (gene_association.sgd) S000000003 CDC28 Translation elongation factor 1 beta YAL003W
Schizosaccharomyces pombe (gene_association.GeneDB_Spombe) SPBC28F2.07 zta1 NADPH quinone oxidoreductase SPCC285.01c

Valid Identifiers for the "Archive of Heinicke et al 2007" Data Set

See Archived information from Heinicke et al (2007) PLoS ONE 2:e766. for search terms that can be used for this data set.

Additional information