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• W2734960082 abstract "Abstract Deciphering gene regulatory networks requires identification of gene expression modules. We describe a novel bottom-up approach to identify gene modules regulated by cis -regulatory motifs from a human gene co-expression network. Target genes of a cis -regulatory motif were identified from the network via the motif’s enrichment or biased distribution towards transcription start sites in the promoters of co-expressed genes. A gene sub-network containing the target genes was extracted and used to derive gene modules. The analysis revealed known and novel gene modules regulated by the NF-Y motif. The binding of NF-Y proteins to these modules’ gene promoters were verified using ENCODE ChIP-Seq data. The analyses also identified 8,048 Sp1 motif target genes, interestingly many of which were not detected by ENCODE ChIP-Seq. These target genes assemble into house-keeping, tissues-specific developmental, and immune response modules. Integration of Sp1 modules with genomic and epigenomic data indicates epigenetic control of Sp1 targets’ expression in a cell/tissue specific manner. Finally, known and novel target genes and modules regulated by the YY1, RFX1, IRF1, and 34 other motifs were also identified. The study described here provides a valuable resource to understand transcriptional regulation of various human developmental, disease, or immunity pathways." @default.
• W2734960082 created "2017-07-21" @default.
• W2734960082 creator A5024120181 @default.
• W2734960082 creator A5049939280 @default.
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• W2734960082 date "2017-07-17" @default.
• W2734960082 modified "2023-09-25" @default.
• W2734960082 title "Discovery of Novel Human Gene Regulatory Modules from Gene Co-expression and Promoter Motif Analysis" @default.
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• W2734960082 doi "https://doi.org/10.1038/s41598-017-05705-2" @default.
• W2734960082 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/5514134" @default.
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• W2734960082 hasPublicationYear "2017" @default.
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