From: A critical assessment of Mus musculusgene function prediction using integrated genomic evidence
Data type | Description | Representation |
---|---|---|
Gene expression | Expression data from oligonucleotide arrays for 13,566 genes across 55 mouse tissues (Zhang et al. [21]) | Median-subtracted, arcsinh intensity measurements |
 | Expression data from Affymetrix arrays for 18,208 genes across 61 mouse tissues (Su et al. [44]) | gcRMA-condensed intensity measurements |
 | Tag counts at quality 0.99 cut-off from 139 SAGE libraries for 16,726 genes [45] | Average and total tag counts |
Sequence patterns | Protein sequence pattern annotations from Pfam-A (release 19) for 15,569 genes with 3,133 protein families [46] | Binary annotation patterns |
 | Protein sequence pattern annotations from InterPro (release 12.1) for 16,965 genes with 5,404 sequence patterns [47] | Binary annotation patterns |
Protein interactions | Protein-protein interactions from OPHID for 7,125 genes [28] (downloaded on 20 April 2006) | Binary interaction patterns and shortest path between genes |
Phenotypes | Phenotype annotations from MGI for 3,439 genes with 33 phenotypes [48] (downloaded on 21 February 2006 from [49]) | Binary annotation patterns |
Conservation profile | Conservation pattern from Ensembl (v38) for 15,939 genes across 18 species [50] | Binary conservation patterns and conservation scores |
 | Conservation pattern from Inparanoid (v4.0) for 15,703 genes across 21 species [51] | Binary conservation patterns and Inparanoid scores |
Disease associations | Disease associations from OMIM for 1,938 genes to 2,488 diseases/phenotypes [52, 53] (downloaded on 6 June 2006 from [54]) | Binary annotation patterns |