ArticleBioinformatics (Oxford, England)2010
Identification of context-dependent motifs by contrasting ChIP binding data.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 42 citations in OpenAlex.
- Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery.Heliyon · 2024Article
- ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery.Bioinformatics (Oxford, England) · 2019Article
- RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.Nucleic acids research · 2017Article
- Direct AUC optimization of regulatory motifs.Bioinformatics (Oxford, England) · 2017Article
- WSMD: weakly-supervised motif discovery in transcription factor ChIP-seq data.Scientific reports · 2017Article
- Composing a Tumor Specific Bacterial Promoter.PloS one · 2016Article
- A Fast Cluster Motif Finding Algorithm for ChIP-Seq Data Sets.BioMed research international · 2015Article
- De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.BMC genomics · 2014Article
- Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models.Nucleic acids research · 2014Article
- Genome-wide view of TGFβ/Foxh1 regulation of the early mesendoderm program.Development (Cambridge, England) · 2014Article
- Article
- Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast.BMC genomics · 2014Article
- Discriminative motif optimization based on perceptron training.Bioinformatics (Oxford, England) · 2014Article
- Gene regulatory networks mediating canonical Wnt signal-directed control of pluripotency and differentiation in embryo stem cells.Stem cells (Dayton, Ohio) · 2013Article
- The pluripotency factor-bound intron 1 of Xist is dispensable for X chromosome inactivation and reactivation in vitro and in vivo.Cell reports · 2013Article
- A novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal/noise distributions.Nucleic acids research · 2012Article
- An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters.BMC bioinformatics · 2012Article
- RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets.Nucleic acids research · 2012Article
- coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq data.Bioinformatics (Oxford, England) · 2011Article
- DECOD: fast and accurate discriminative DNA motif finding.Bioinformatics (Oxford, England) · 2011Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
motivationDNA binding proteins play crucial roles in the regulation of gene expression. Transcription factors (TFs) activate or repress genes directly while other proteins influence chromatin structure for transcription. Binding sites of a TF exhibit a similar sequence pattern called a motif. However, a one-to-one map does not exist between each TF and motif. Many TFs in a protein family may recognize the same motif with subtle nucleotide differences leading to different binding affinities. Additionally, a particular TF may bind different motifs under certain conditions, for example in the presence of different co-regulators. The availability of genome-wide binding data of multiple collaborative TFs makes it possible to detect such context-dependent motifs.
resultsWe developed a contrast motif finder (CMF) for the de novo identification of motifs that are differentially enriched in two sets of sequences. Applying this method to a number of TF binding datasets from mouse embryonic stem cells, we demonstrate that CMF achieves substantially higher accuracy than several well-known motif finding methods. By contrasting sequences bound by distinct sets of TFs, CMF identified two different motifs that may be recognized by Oct4 dependent on the presence of another co-regulator and detected subtle motif signals that may be associated with potential competitive binding between Sox2 and Tcf3. AVAILABILITY: The software CMF is freely available for academic use at www.stat.ucla.edu/∼zhou/CMF.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.