Time-courses gene class list

This list collects groups of genes with functions relevant for the time-courses analysis.

Useful links for gene class lists

GSEA @ Broad institute: MsigDB gene sets http://www.broadinstitute.org/gsea/downloads.jsp

Pathway Commons http://www.pathwaycommons.org/pc/#

Epigenetic Regulation

Here is a file with 3 sheets of gene lists, all generated using the MeSHOP procedure ( http://meshop.oicr.on.ca/meshop/index.html ). MeSHOPs are a measure of over-representation of MeSH annotations for a set of articles. In this case, I looked across all of the available genes (where each gene is represented by a set of articles) and reported those genes with an enrichment score of p<0.001 for any of the three terms: nucleosomes, histones and DNA methylation. The File:EpigeneticsLists MeSHOPs 20121113.xls is attached.

Known early response genes

Mariko Okada: Here is a potential list to survey early responsive genes. This is on MCF-7 cells, but it will be useful to start from here.

Analysis of this paper is described here; http://www.ncbi.nlm.nih.gov/pubmed/17142811

A similar work has been also done by Eric Lander; http://www.ncbi.nlm.nih.gov/pubmed/10380925

File:Genelist-2006-01-16-with-fc2.xls

Kojiro Yano:A module of negative feedback regulators defines growth factor signaling. (from Amit et al Nat Genet. 2007 Apr;39(4):503-12.)

File:Amit 2007 Nat Genet EGF HeLa.txt List of genes whose expression peaked within 120 mins of EGF stimulus in HeLa cells.

File:Amit 2007 Nat Genet EGF MCF10A.txt List of genes whose expression peaked within 120 mins of EGF stimulus in MCF10A cells.

File:Amit 2007 Nat Genet serum MCF10A.txt List of genes whose expression peaked within 120 mins of serum stimulus in MCF10A cells.

NB. Also look here: Time-courses_resources#List_of_early_response_marker_genes

Stem cell markers

Kojiro Yano: There is a comprehensive review of murine stem cell markers (ALTEX. 2010;27(1):17-42).

File:Altex 1 10 Leist Markers mEScells.txt List of mES cell markers.

File:Altex 1 10 Leist Markers mNScells.txt List of mNS cell markers.