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Data collection description: summary of the data sources |
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| Data type |
Description |
Representation |
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| 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 |
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| Tag counts at quality 0.99 cut-off from 139 SAGE libraries for 16,726 genes [45] |
Average and total tag counts |
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| 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 |
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| 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 |
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| 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 |
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gcRMA, robust multi-array analysis with background adjustment for GC content of probes; OMIM, Online Mendelian Inheritance in Man; OPHID, Online Predicted Human Interaction Database; SAGE, serial analysis of gene expression. | ||
Peña-Castillo et al. Genome Biology 2008 9(Suppl 1):S2 doi:10.1186/gb-2008-9-s1-s2 |
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