Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells

@article{citeulike:2836840, abstract = {We introduce the GibbsModule algorithm for de novo detection of cis-regulatory motifs and modules in eukaryote genomes. GibbsModule models the co-expressed genes within one species as sharing a core cis-regulatory motif and each homologous gene group as sharing a homologous cis-regulatory module (CRM), characterized by a similar composition of motifs. Without using a pre-determined alignment result, GibbsModule iteratively updates the core motif shared by co-expressed genes and traces the homologous CRMs that contain the core motif. GibbsModule achieved substantial improvements in both precision and recall as compared to peer algorithms on a number of synthetic and real datasets. Applying GibbsModule to analyze the binding regions of the Kruppel-like factor (Klf) transcription factor in embryonic stem cells (ESCs), we discovered a motif that differs from a previously published Klf motif identified by a SELEX experiment, but the new motif is consistent with mutagenesis analysis. Sox2 motif was found to be a collaborating motif to the Klf motif in ESCs. We used quantitative chromatin immunoprecipitation (ChIP) analysis to test whether GibbsModule could distinguish functional and non-functional binding sites. All 7 tested binding sites in GibbsModule predicted CRMs had higher ChIP signals as compared to the other 7 tested binding sites located outside of predicted CRMs. GibbsModule is available at http://biocomp.bioen.uiuc.edu/GibbsModule. 10.1101/gr.072769.107}, author = {Xie, Dan and Cai, Jun and Chia, Na-Yu and Ng, Huck and Zhong, Sheng }, citeulike-article-id = {2836840}, doi = {10.1101/gr.072769.107}, journal = {Genome Res.}, keywords = {cis-regulation, crm, motif-discovery, tool}, month = {May}, pages = {gr.072769.107+}, posted-at = {2008-05-27 09:53:11}, priority = {3}, title = {Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells}, url = {http://dx.doi.org/10.1101/gr.072769.107}, year = {2008} }

TY - JOUR ID - citeulike:2836840 L3 - citeulike-article-id:2836840 TI - Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells JF - Genome Res. SP - gr.072769.107 N2 - We introduce the GibbsModule algorithm for de novo detection of cis-regulatory motifs and modules in eukaryote genomes. GibbsModule models the co-expressed genes within one species as sharing a core cis-regulatory motif and each homologous gene group as sharing a homologous cis-regulatory module (CRM), characterized by a similar composition of motifs. Without using a pre-determined alignment result, GibbsModule iteratively updates the core motif shared by co-expressed genes and traces the homologous CRMs that contain the core motif. GibbsModule achieved substantial improvements in both precision and recall as compared to peer algorithms on a number of synthetic and real datasets. Applying GibbsModule to analyze the binding regions of the Kruppel-like factor (Klf) transcription factor in embryonic stem cells (ESCs), we discovered a motif that differs from a previously published Klf motif identified by a SELEX experiment, but the new motif is consistent with mutagenesis analysis. Sox2 motif was found to be a collaborating motif to the Klf motif in ESCs. We used quantitative chromatin immunoprecipitation (ChIP) analysis to test whether GibbsModule could distinguish functional and non-functional binding sites. All 7 tested binding sites in GibbsModule predicted CRMs had higher ChIP signals as compared to the other 7 tested binding sites located outside of predicted CRMs. GibbsModule is available at http://biocomp.bioen.uiuc.edu/GibbsModule. 10.1101/gr.072769.107 KW - cis-regulation KW - crm KW - motif-discovery KW - tool AU - Xie, Dan AU - Cai, Jun AU - Chia, Na-Yu AU - Ng, Huck AU - Zhong, Sheng PY - 2008/05/15/ UR - http://dx.doi.org/10.1101/gr.072769.107 ER -