Human Expression Resources
The Genome Sciences Centre has begun collecting publicly available data for large-scale global co-expression analyses. Oligonucleotide probe intensities, cDNA microarray hybridization ratios, or SAGE tag counts are used to calculate expression similarity metrics (e.g. Pearson Correlation) between each gene. Expression data (raw intensities, ratios, or counts) or co-expression data (pearson distances) will be made available on request or through the supplementary data page (see below). Please contact Obi Griffith at obig@bcgsc.ca if you have any questions.
Publications
Obi L. Griffith, Erin D. Pleasance, Debra L. Fulton, Mehrdad Oveisi, Martin Ester, Asim Sidiqui and Steven J.M. Jones. 2005. Assessment and Integration of Publicly Available SAGE, cDNA Microarray, and Oligonucleotide Microarray Expression Data for Global Coexpression Analyses. Genomics. 86(4):476-488
Pubmed Abstract
Full text at Genomics
Supplementary Materials
High-confidence Coexpression Data for cisRED
A set of the highest confidence coexpressed gene pairs were chosen from the three datasets using the following criteria. These co-expression links are being used by the Genome Sciences Centre Gene Regulation (Informatics) Team to predict human regulatory elements as part of the cisRED project (www.cisred.org). Note: A gene pair may be present in the list multiple times if it passes more than one of the following criteria.
Homo sapiens data
High-confidence Human Coexpression Criteria (version 1):
32923 coexpressed gene pairs for 5562 genes- Minimum Common Experiments (MCE): Affy;cDNA:100, SAGE:25
- Individual pearson cutoff: r >= 0.8
- Combined pearson cutoff: r_avg >= 0.65
- Pearson cutoff with GO confirmation: r>= 0.65
Downloads
High-confidence Human Coexpression Criteria (version 2):
92472 coexpressed gene pairs for 7447 genes- Minimum Common Experiments (MCE): 100
- Individual pearson cutoff: r >= 0.8
- Combined pearson cutoff: r_avg >= 0.65
- TMM: TMM_score >= 7
- ArrayProspector: AP_score >= 0.7
Downloads
Mus musculus data
High-confidence Mouse Coexpression Criteria (version 1):
92478 coexpressed gene pairs for 5070 genes- Minimum Common Experiments (MCE): 100
- Individual pearson cutoff: r >= 0.8
- Combined pearson cutoff: r_avg >= 0.65