oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes
By Shannan J. Ho Sui, J. Mortimer, David J. Arenillas, J. Brumm, C. J. Walsh, B. Kennedy, Wyeth W. Wasserman. Nucleic Acids Research, 2005
394 citations recorded by the source corpus.
Targeted transcript profiling studies can identify sets of co-expressed genes; however, identification of the underlying functional mechanism(s) is a significant challenge. Established methods for the analysis of gene annotations, particularly those based on the Gene Ontology, can identify functional linkages between genes. Similar methods for the identification of over-represented transcription factor binding sites (TFBSs) have been successful in yeast, but extension to human genomics has largely proved ineffective. Creation of a system for the efficient identification of common regulatory mechanisms in a subset of co-expressed human genes promises to break a roadblock in functional genomics research. We have developed an integrated system that searches for evidence of co-regulation by one or more transcription factors (TFs). oPOSSUM combines a pre-computed database of conserved TFBSs in human and mouse promoters with statistical methods for identification of sites over-represented in a set of co-expressed genes. The algorithm successfully identified mediating TFs in control sets of tissue-specific genes and in sets of co-expressed genes from three transcript profiling studies. Simulation studies indicate that oPOSSUM produces few false positives using empirically defined thresholds and can tolerate up to 50% noise in a set of co-expressed genes.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/7fce30e693714bbc3a6c83bcd049ccb8b97e660a
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- N. Wakabayashi
- T. Kensler
- David J. Arenillas
- Shyam Biswal
- Wyeth W. Wasserman
- Aldons J. Lusis
- Jacques van Helden
- Graziano Pesole
Citations in the corpus
- RSAT: regulatory sequence analysis tools (2008, methodology): “For example, oPOSSUM supports human, worm and yeast (25,26).”
- oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets (2012, methodology): “The successful predecessors to oPOSSUM-3, oPOSSUM (Ho Sui et al. 2005) and oPOSSUM-2 (Ho Sui et al. 2007), were developed to identify statistically over-represented, predicted TFBS in co-regulated gene sets.”
- Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes (2009, methodology): “Several other methods currently available [see among others oPOSSUM (10), PAP (11), TFM_EXPLORER”
- Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis (2010, methodology): “Recent publications have emphasized the role of Nrf2 in promoting cell proliferation and cell-cycle progression (17,41), but this report is the first to broadly characterize the direct role of Nrf2 in executing the regulatory program governing proliferation.”
- Transcriptome Analysis of Human Diabetic Kidney Disease (2011, methodology): “binding sites (TFBSs) was determined using oPOSSUM software (20) for the”
- Tissue-specific expression and regulation of sexually dimorphic genes in mice. (2006, methodology): “Analysis of enrichment for TFBS Each sexually dimorphic gene set was analyzed for enrichment of TFBS using the oPOSSUM program ( Ho Sui et al. 2005; http:// www.cisreg.ca/cgi-bin/oPOSSUM/opossum).”