The proposed model has the following advantages: 1) find both positive and negative co-regulated genes in a shot, 2) get away from the restriction of magnitude transformation relationship among co-regulated genes, and 3) guarantee quality of clusters and significance of regulations using a novel ...
Co-regulated genes in 501Mel and Hermes 3A cells.Dana KoludrovicPatrick LauretteThomas StrubCéline KeimeMadeleine Le CozSebastien CoassoloGabrielle MengusLionel LarueIrwin Davidson
1 A Clustering Algorithm Based on Generalized Similarity for Co-regulated Genes 一种基于广义相似性的共调控基因聚类算法
We have developed a novel tool, "CORE_TF" (Conserved and Over-REpresented Transcription Factor binding sites) that identifies common transcription factor binding sites in promoters of co-regulated genes. To improve upon existing binding site predictions, the tool searches for position weight matrices ...
In this paper, we proposed, from systems biology perspective, the concept of co-regulated gene module, which consists of genes that are regulated by the same regulator(s). Given a time series gene expression data, a hidden Markov modelbased Bayesian model was developed to calculate the ...
We found eighteen (17 up-regulated and 1 down-regulated) differentially expressed genes that were co-regulated by transcription factors and miRNAs. KEGG pathway analysis revealed that these genes were part of the extracellular matrix-receptor interaction and focal adhesion signaling pathways. In ...
Using motif detection programs it is fairly straightforward to identify conserved cis-sequences in promoters of co-regulated genes. In contrast, the identification of the transcription factors (TFs) interacting with these cis-sequences is much more elabo
Co-regulated SFs were associated with aggressive breast cancer phenotypes and enhanced metastasis formation, resulting in the classification of Enhancer- (21 genes) and Suppressor-SFs (64 genes). High Enhancer-SF levels were related to distinct splicing patterns and expression of known oncogenic ...
as a stand-alone or Web-based application for the automatic discovery of conserved motifs in a set of related DNA sequences from coregulated genes. The... G Pavesi,G Pesole - 《Current Protocols in Bioinformatics》 被引量: 44发表: 2006年 Promzea: a pipeline for discovery of co-regulatory...
Salmonella Patogenicity Island 1 (SPI-1) is a chromosomal region containing 39 genes that have crucial virulence roles. The AraC-like transcriptional regulator HilD, encoded in SPI-1, positively controls the expression of the SPI-1 genes, as well as of several other virulence genes located out...