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Supplementary material for manuscript,

"BioMoby services to support clustering of co-regulated genes based on similarity of promoter configurations".
 
 
  The co-expressed genes promoter analysis pipeline was assessed on a set of genes that was extracted from Thompson et al. (2002).
This study reports the identification of a group of co-expressed Human genes, the PDEF module, that they found mainly expressed in tissue extracted from breast and ovarian cancers.

The PDEF module:
  • PDEF
  • H2AFO
  • PSMD7
  • NUCKS
  • FLJ10111
  • SQSTM1
They also report another set of genes expressed during pregnancy:
  • ENSG00000183668 (PSG9)
  • PSG3
  • PSG6
  • PAPPA
  • CSH1
  • CYP19
  • ADAM12
  • PSG5
  • TFPI2
  • PSG2
For the purpose of our analysis, we have combined together the genes of both modules.

If you would like to repeat our analysis, you can use either our Web submission page or the Taverna software with the Workflow implemented
with a list of gene identifiers input.
  • Input for the Data submission Web page:
  • XML Input Document for the Taverna Workflow:
  • The parameter settings are the following:
    • promoter sequence extraction from Ensembl: species=homo_sapiens; upstream_length=500; downstream_length=0
    • MatScan: database=jaspar; threshold=0.85
    • TF-alignment: &alpha=0.5; &lambda=0.1; &mu=0.1
    • SOTA: distance=euclidean; resource_threshold=35
    • Multiple TF-alignment: &alpha=0.5; &lambda=0.1; &mu=0.1; Y=-10; c=100

     
  • Results