• TRANSFAC

  • Referenced in 74 articles [sw17201]
  • regulation. TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding ... data on plant sites and factors. Moreover, TRANSFAC has been extended by two new modules ... relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features...
  • JASPAR

  • Referenced in 42 articles [sw18502]
  • open‐access database for eukaryotic transcription factor binding profiles. The analysis of regulatory regions ... based on the detection of potential transcription factor binding sites. The preferred models for representation ... transcription factor binding specificity have been termed position‐specific scoring matrices. JASPAR is an open ... annotated, high‐quality, matrix‐based transcription factor binding site profiles for multicellular eukaryotes. The profiles...
  • RegulonDB

  • Referenced in 51 articles [sw25948]
  • classified as strong or weak. Transcription factors are classified by origin of their effectors ... mapping efforts. RegulonDB v.6.0 now expands beyond transcription initiation, including RNA regulatory elements, specifically riboswitches...
  • RSIR

  • Referenced in 15 articles [sw26716]
  • motif discovery. MOTIVATION: Identification of transcription factor binding motifs (TFBMs) is a crucial first step...
  • TileMap

  • Referenced in 14 articles [sw35530]
  • survey genomic transcriptional activities and transcription factor binding sites at high resolution. The goal ... tools to identify genomic loci that show transcriptional or protein binding patterns of interest. Results...
  • MEME

  • Referenced in 13 articles [sw15711]
  • Applications include the discovery of new transcription factor binding sites and protein domains. MEME works...
  • PhyME

  • Referenced in 9 articles [sw35645]
  • paper addresses the problem of discovering transcription factor binding sites in heterogeneous sequence data, which...
  • Babelomics

  • Referenced in 6 articles [sw36144]
  • Swiss-Prot keywords, analysis of predicted transcription factor binding sites, chromosomal positions and presence ... assignment and transference of information), FatiWise, transcription factor association test, GenomeGO and tissues mining tool...
  • MATCH

  • Referenced in 5 articles [sw23010]
  • MATCH: A tool for searching transcription factor binding sites in DNA sequences. Match ... matrix-based tool for searching putative transcription factor binding sites in DNA sequences. Match ... great variety of different transcription factor binding sites. Several sets of optimised matrix...
  • iNR-PhysChem

  • Referenced in 8 articles [sw26878]
  • form a family of ligand-activated transcription factors that regulate a wide variety of biological...
  • BayesPeak

  • Referenced in 8 articles [sw18843]
  • aims to find the locations of transcription factor binding sites, modified histones or nucleosomes...
  • WordSpy

  • Referenced in 5 articles [sw19955]
  • WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar. Transcription ... factor (TF) binding sites or motifs (TFBMs) are functional cis-regulatory DNA sequences that play ... essential role in gene transcriptional regulation. Although many experimental and computational methods have been developed...
  • REDfly

  • Referenced in 5 articles [sw29315]
  • database of cis-regulatory modules and transcription factor binding sites in Drosophila. The identification ... long history of experimental studies of transcriptional regulation, represents the ideal system for regulatory bioinformatics ... modules and the FlyReg database of transcription factor binding sites (TFBSs), into a single integrated ... both computational and experimental studies of transcriptional regulation. REDfly is freely accessible at http://redfly.ccr.buffalo.edu...
  • SIRENE

  • Referenced in 7 articles [sw17419]
  • genes from non-targets for each transcription factor. SIRENE is thus conceptually simple and computationally...
  • FindPeaks

  • Referenced in 7 articles [sw29575]
  • identifying areas of gene enrichment and transcription factor binding site locations, as well...
  • DWE

  • Referenced in 3 articles [sw29590]
  • Discriminating Word Enumerator. Motivation: Tissue-specific transcription factor binding sites give insight into tissue-specific ... tool for de novo tissue-specific transcription factor binding site discovery using expression information ... direct statistical approach to find overrepresented transcription factor binding sites in a foreground promoter sequence ... approach naturally extends to synergistic transcription factor binding site search. We find putative transcription factor...
  • BioOptimizer

  • Referenced in 6 articles [sw17421]
  • function approach to motif discovery. Motivation: Transcription factors (TFs) bind directly to short segments ... thousands of base pairs upstream of gene transcription start sites, to regulate gene expression...
  • rVISTA

  • Referenced in 4 articles [sw18501]
  • rVISTA 2.0: evolutionary analysis of transcription factor binding sites. dentifying and characterizing the transcription factor ... regulatory language the genome uses to dictate transcriptional dynamics. Several studies have demonstrated that regulatory...
  • PlantTFDB

  • Referenced in 4 articles [sw17023]
  • PlantTFDB. Plant Transcription Factor Database. Based on the family assignment rules, we identified ... transcription factors from 165 species and classified them into 58 families. Species included in PlantTFDB ... architecture and evolutionary features of plant transcriptional regulatory networks at ATRM (Brief Guide in English...
  • CONFAC

  • Referenced in 4 articles [sw35535]
  • analysis. Here we describe the conserved transcription factor binding site (CONFAC) software that enables ... high-throughput identification of conserved transcription factor binding sites (TFBSs) in the regulatory regions...