• Expression Profiler

  • Referenced in 6 articles [sw08351]
  • analysis of promoter sequences for predicting transcription factor binding sites. Several clustering analysis method implementations...
  • STAMP

  • Referenced in 6 articles [sw17264]
  • expected to facilitate the identification of transcription factors that potentially interact with newly discovered motifs...
  • MatInspector

  • Referenced in 5 articles [sw21812]
  • large library of matrix descriptions for transcription factor binding sites to locate matches...
  • F-Seq

  • Referenced in 5 articles [sw17297]
  • identify specific sequence features, such as transcription factor binding sites (ChIP-seq) or regions...
  • CisModule

  • Referenced in 5 articles [sw35646]
  • sites for a set of interacting transcription factors have the tendency to colocalize...
  • DREME

  • Referenced in 3 articles [sw17299]
  • DREME: motif discovery in transcription factor ChIP-seq data. Motivation: Transcription factor (TF) ChIP...
  • cosmo

  • Referenced in 3 articles [sw06106]
  • example, represent a common transcription factor binding site. The algorithm is similar to MEME ... knowledge about the structure of the transcription factor in question. The unknown motif width...
  • COMODE

  • Referenced in 3 articles [sw36145]
  • motifs in DNA sequences. Identification of transcription factor binding sites (regulatory motifs) is a major ... data. Some of the transcription factor binding data of Lee et al. (2002) were also...
  • gNCA

  • Referenced in 4 articles [sw08821]
  • gNCA: A framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation ... makes use of the connectivity structure from transcriptional regulatory networks to restrict the decomposition...
  • plsgenomics

  • Referenced in 4 articles [sw07949]
  • with microarray data and prediction of transcription factor activities from combined ChIP-chip analysis...
  • WebMOTIFS

  • Referenced in 4 articles [sw35522]
  • used to determine the class of transcription factors that is most likely to regulate...
  • KIRMES

  • Referenced in 4 articles [sw35269]
  • important problem is the identification of transcription factor (TF) binding sites in promoter regions...
  • HPeak

  • Referenced in 4 articles [sw29576]
  • higher prevalence of the expected transcription factor binding motifs in ChIP-enriched sequences relative...
  • GAME

  • Referenced in 4 articles [sw17420]
  • genetic algorithm. Motivation: Identification of a transcription factor binding sites is an important aspect...
  • PICS

  • Referenced in 3 articles [sw37329]
  • profile genome-wide in vivo transcription factor-DNA association with higher sensitivity, specificity, and spatial ... identifying regions bound by transcription factors from aligned reads. PICS identifies binding event locations...
  • HPAM

  • Referenced in 3 articles [sw10931]
  • motifs that characterize the regulatory factors operating in the transcription of a gene, becomes crucial ... targets and its connectivity with other transcription factors, which sometimes require multiple functional binding sites...
  • TFBSTools

  • Referenced in 2 articles [sw18912]
  • TFBSTools: an R/bioconductor package for transcription factor binding site analysis. TFBSTools is a package ... analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency...
  • fREDUCE

  • Referenced in 2 articles [sw35521]
  • make novel motif predictions for transcription factors with poorly characterized binding sites. Conclusion: We demonstrate ... tool for the prediction of degenerate transcription factor binding sites, especially from array datasets with...
  • ORegAnno

  • Referenced in 2 articles [sw18500]
  • experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. The current release ... over 3853 genes and 465 transcription factors from 19 species. A new feature called...
  • CONREAL

  • Referenced in 2 articles [sw18497]
  • server: identification and visualization of conserved transcription factor binding sites. The use of orthologous sequences ... developed for the identification of conserved transcription factor binding sites (TFBSs), which are characterized...