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
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:
They also report another set of genes expressed during pregnancy:
For the purpose of our analysis, we have combined together
the genes of both modules.
- ENSG00000183668 (PSG9)
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