ArticleNucleic acids research2006
CRSD: a comprehensive web server for composite regulatory signature discovery.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells.Nucleic acids research · 2016Article
- Gene Perturbation Atlas (GPA): a single-gene perturbation repository for characterizing functional mechanisms of coding and non-coding genes.Scientific reports · 2015Article
- Gene network exploration of crosstalk between apoptosis and autophagy in chronic myelogenous leukemia.BioMed research international · 2015Article
- Article
- Inferring microRNA and transcription factor regulatory networks in heterogeneous data.BMC bioinformatics · 2013Article
- Gene expression of human lung cancer cell line CL1-5 in response to a direct current electric field.PloS one · 2011Article
- Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data.Nucleic acids research · 2010Article
- Bioinformatic identification and characterization of human endothelial cell-restricted genes.BMC genomics · 2010Article
- Functional annotation of novel lineage-specific genes using co-expression and promoter analysis.BMC genomics · 2010Article
- Computational discovery of miR-TF regulatory modules in human genome.Bioinformation · 2010Article
- Transcription factor site dependencies in human, mouse and rat genomes.BMC bioinformatics · 2009Article
- GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments.BMC bioinformatics · 2008Article
- A comparison of four clustering methods for brain expression microarray data.BMC bioinformatics · 2008Article
- The LLA23 protein translocates into nuclei shortly before desiccation in developing pollen grains and regulates gene expression in Arabidopsis.Protoplasma · 2008Article
- Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis.BMC genomics · 2008Article
- A functional and regulatory map of asthma.American journal of respiratory cell and molecular biology · 2008Article
- Murine models of chronic lymphocytic leukaemia: role of microRNA-16 in the New Zealand Black mouse model.British journal of haematology · 2007Review
- Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis.BMC bioinformatics · 2007Article
- GeneTrail--advanced gene set enrichment analysis.Nucleic acids research · 2007Article
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7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors (TFs) and microRNAs play important roles in the regulation of human gene expression, and the study of their combinatory regulations of gene expression is a new research field. We constructed a comprehensive web server, the composite regulatory signature database (CRSD), that can be applied in investigating complex regulatory behaviors involving gene expression signatures (GESs), microRNA regulatory signatures (MRSs) and TF regulatory signatures (TRSs). Six well-known and large-scale databases, including the human UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway and Gene Ontology (GO) databases, were integrated to provide the comprehensive analysis in CRSD. Two new genome-wide databases, of MRSs and TRSs, were also constructed and further integrated into CRSD. To accomplish the microarray data analysis at one go, several methods, including microarray data pretreatment, statistical and clustering analysis, iterative enrichment analysis and motif discovery, were closely integrated in the web server, which has not been the case in previous studies. Our implementation showed that the published literature could demonstrate the results of genome-wide enrichment analysis. We conclude that CRSD is a powerful and useful bioinformatic web server and may provide new insights into gene regulation networks. CRSD and the online tutorial are publicly available at http://biochip.nchu.edu.tw/crsd1/.
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