Identifying Signaling Pathways from Gene Expression Data
Author Information
Author(s): Liu Yingchun, Ringnér Markus
Primary Institution: Lund University
Hypothesis
Can gene expression signatures be used to identify deregulated signaling pathways?
Conclusion
The study presents a method that successfully identifies relevant signaling pathways from gene expression signatures.
Supporting Evidence
- The method identified expected pathways for oncogenic gene signatures.
- It provides additional information complementary to existing methods like EASE and GSEA.
- The study highlights the importance of regulatory motif analysis in pathway identification.
Takeaway
The researchers found a way to see which cell signaling pathways are broken by looking at gene activity patterns.
Methodology
The method involves extracting signaling pathways from the TRANSPATH database and analyzing gene expression signatures for enrichment of transcription factor binding sites.
Potential Biases
Potential bias from incomplete knowledge of target genes for transcription factors.
Limitations
The method may introduce false positives due to reliance on putative transcription factor binding sites.
Statistical Information
P-Value
<0.001
Digital Object Identifier (DOI)
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