# page private for now


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

 * Finding over-representation of transcription factor binding sites in group of genes/pathways found dysregulated in gene expression data 
== TOOLS THAT USE TRANSCRIPTION FACTOR MOTIFS ==

=== 1) 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

{{attachment:opossum3.png}}

 * tip if you use Mozilla Firefox (e.g. 30.0) webbrowser: it can take more than 5 min to get the results back from the oPOSSUM server, in this case you need to change the default response timeout (which is 300s = 5 mins):
   * open Firefox
   * in the address bar, enter about:config and accept the warning message
   * set network.http.response.timeout to 0(no response time out or a time of your choice e.g 3000 for 3000 seconds)
   * reopen Firefox and launch oPOSSUM 3.0

=== 2) PSCAN: http://159.149.109.9/pscan/ ===
 * need Refseq as gene identifier
== TOOLS THAT USE ENCODE CHIP-seq DATA ==
=== ENCODE ChIP-Seq Significance Tool: http://encodeqt.stanford.edu/hyper/ ===
{{attachment:encode_chip_seq_significance_tool.png}}
=== CSAN: (as PSCAn but using chip-seq data): http://159.149.109.9/cscan/ ===
{{attachment:CSCAN.png}}
=== GET THE GENES NEARBY ChIP-SEQ ENCODE DATA and LOOK AT THE MAP OVERLAP using EnrichmentMap POST-ANALYSIS ===
{{attachment:fromENCODE.png}}


= TOOL THAT USES MOTIF DISCOVERY , MOTIF DATABASE and ENCODE CHIP_seq =
== iRegulon ==
 * http://iregulon.aertslab.org/
 * published in July 2014 : PMID:25058159
 * tested (./)
 * Cytoscape 3 app
 * input is a gene list (official gene symbol)
 * need to create first a network (see tutorial: import network from table) , then to select nodes (genes) of interest) and run the iRegulon app.


= additional references =
  * Wyeth Wasserman lab: http://www.cisreg.ca/
  * blog: http://gettinggeneticsdone.blogspot.ca/2013/06/encode-chip-seq-significance-tool-which.html
  * [[CancerStemCellProject/VeroniqueVoisin/AdditionalResources/CHIP_seq | link to ChIP-seq basics]]