ArticleBioinformatics (Oxford, England)2013
Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Omics-Based Identification of Shared and Gender Disparity Routes inFrontiers in genetics · 2021Article
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- Uromodulin p.Cys147Trp mutation drives kidney disease by activating ER stress and apoptosis.The Journal of clinical investigation · 2017Article
- Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer.BMC bioinformatics · 2017Article
- Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data.Nature genetics · 2017Article
- NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data.BMC genomics · 2017Article
- Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection.PLoS genetics · 2015Article
- Emerging role of transcription factor-microRNA-target gene feed-forward loops in cancer.Biomedical reports · 2015Article
- HIF1α Represses Cell Stress Pathways to Allow Proliferation of Hypoxic Fetal Cardiomyocytes.Developmental cell · 2015Article
- Mitochondrial reprogramming induced by CaMKIIδ mediates hypertrophy decompensation.Circulation research · 2015Article
- Cyclic stretch of embryonic cardiomyocytes increases proliferation, growth, and expression while repressing Tgf-β signaling.Journal of molecular and cellular cardiology · 2015Article
- Comprehensive analysis of gene-expression profile in chronic obstructive pulmonary disease.International journal of chronic obstructive pulmonary disease · 2015Article
- Transcriptional control of stem cell fate by E2Fs and pocket proteins.Frontiers in genetics · 2015Review
- From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach.PloS one · 2015Article
- The let-7/LIN-41 pathway regulates reprogramming to human induced pluripotent stem cells by controlling expression of prodifferentiation genes.Cell stem cell · 2014Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
summaryWe have developed a web-based query tool, Whole-Genome rVISTA (WGRV), that determines enrichment of transcription factors (TFs) and associated target genes in sets of co-regulated genes. WGRV enables users to query databases containing pre-computed genome coordinates of evolutionarily conserved transcription factor binding sites in the proximal promoters (from 100 bp to 5 kb upstream) of human, mouse and Drosophila genomes. TF binding sites are based on position-weight matrices from the TRANSFAC Professional database. For a given set of co-regulated genes, WGRV returns statistically enriched and evolutionarily conserved binding sites, mapped by the regulatory VISTA (rVISTA) algorithm. Users can then retrieve a list of genes from the query set containing the enriched TF binding sites and their location in the query set promoters. Results are exported in a BED format for rapid visualization in the UCSC genome browser. Flat files of mapped conserved sites and their genomic coordinates are also available for analysis with stand-alone software. AVAILABILITY: http://genome.lbl.gov/cgi-bin/WGRVistaInputCommon.pl.
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