Evaluating Regulatory Motifs in Gene Promoters
Author Information
Author(s): Meng Guofeng, Mosig Axel, Vingron Martin
Primary Institution: CAS-MPG Partner Institute and Key Laboratory for Computational Biology
Hypothesis
Do co-expressed genes share common regulatory motifs in mammals?
Conclusion
Functional regulatory motifs are over-represented in sets of differentially expressed genes and can be detected using computational methods.
Supporting Evidence
- 25 out of 33 experiments showed significant over-representation of transcription factor binding sites.
- De novo predictions also recovered motifs similar to target matrices in about 73% of cases.
- The study confirmed that computational methods can detect over-represented motifs in gene promoters.
Takeaway
The study found that genes that are turned on or off together often have similar control sequences, and we can find these sequences using computer programs.
Methodology
The study analyzed microarray experiments from the ArrayExpress database to check for over-representation of transcription factor binding sites in differentially expressed genes using the oPOSSUM tool.
Potential Biases
Potential biases may arise from the selection of experiments and the quality of microarray data.
Limitations
The study focused only on experiments where the identity of the transcription factor was known, which may limit the generalizability of the findings.
Participant Demographics
The study analyzed data from human and mouse experiments.
Statistical Information
P-Value
p<0.05
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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