# page private for now


= Find over represented transcription factor motifs in co-expressed genes =

 * Finding over-representation of transcription factor binding sites in group of genes/pathways found dysregulated in gene expression data 


== Wyeth Wasserman lab: http://www.cisreg.ca/ ==

==== oPOSSUM (tested, 3.0) (http://www.cisreg.ca/oPOSSUM/) ====
     * help: http://opossum.cisreg.ca/oPOSSUM3/help.html
     * web tool (no account necessary)
     * the method has 3 steps:
       * phylogenetic footprinting to find regions in the non coding DNA (promoter regions) that are conserved between species
       * detection of transcription factor motifs using the JASPAR database (JASPAR PSSMs: position specific scoring matrices)
       * 2 statistics methods (Fisher's score and Z score) to evaluate over-represented binding sites compared to background
       * tips:
        * select potential transcription factor candidates by generating a Z score / Fisher's plot: select the transcription factors that emerged from the cloud
        * look at the %GC content - Z score to see if you have a %gC content bias: if any, run the GC_compo tool (http://opossum.cisreg.ca/GC_compo/) to select an appropriate background set and use the Sequence-based Single Site Analysis tool

== PSCAN: http://159.149.109.9/pscan/ ==

== using ENCODE CHIP-seq ==
== CSAN: (as PSCAn but using chip-seq data): http://159.149.109.9/cscan/ ==
http://encodeqt.stanford.edu/hyper/

 * blog: http://gettinggeneticsdone.blogspot.ca/2013/06/encode-chip-seq-significance-tool-which.html