2012-12-07
Marina Lizio (marina.lizio@riken.jp)
Pathway enrichment analysis done by (edimont@hsph.harvard.edu) and co-expression cluster analysis done by (j.k.baillie@ed.ac.uk). Enrichment analysis done by (arner@gsc.riken.jp)
This folder contains results on co-expression modules.

*hg19_co-expression_modules.tar.gz archive contains all human co-expression modules. For each co-expression module, a file with the name of the module displays all significantly enriched pathways(<5% FDR) and their associated pvalue, FDR, nGenes (number of genes in the module that belong to a pathway), nPathway (number of total genes in a pathway).
*mm9_co-expression_modules.tar.gz archive for all mouse co-expression modules.
*hg19_co-expression_GOstats.tar.gz is an archive containing a tab-separated file with GOstat enrichment analysis for each human sample. For each file, GO_id, GO_term, pvalue and entrez_geneid are reported. The last column is a list of all significantly enriched entrez gene ids.

2014-02-21
Additional data on coexpression for both human mouse was added.
*mm9_co-expression_GOstats.tar.gz is an archive containing a tab-separated file with GOstat enrichment analysis for each mouse sample.
*{hg19|mm9}.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz files contain scores for overrepresented known JASPAR motifs.
*coexpression_DPI_cluster_scores_median_mouse_Oct9_2012.txt.gz is the median expression values for all mouse samples per coexpression cluster.
*coexpression_DPI_cluster_scores_median_human_Aug3_2012.txt.gz is the median expression values for all human samples per coexpression cluster.
*{hg19|mm9}.novel_motif.coexpression_clusters_overrepresentation.txt.gz files contain scores for overrepresented novel motifs.
*ENCODE_TF_ChIP-seq_peak_enrichment_coexprclusterencode.filtered.csv.gz is a file containing the enrichment of ENCODE transcription factors ChIP_seq peak signal for each co-expression cluster.