ArticleBioinformatics (Oxford, England)2011
coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq data.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
5 citing papers in PubMed, 8 citations in OpenAlex.
- MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs.Bioinformatics (Oxford, England) · 2020Article
- Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets.Nucleic acids research · 2018Article
- Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Article
- MatrixCatch--a novel tool for the recognition of composite regulatory elements in promoters.BMC bioinformatics · 2013Article
- YY1TargetDB: an integral information resource for Yin Yang 1 target loci.Database : the journal of biological databases and curation · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
motivationChIP-seq data are enriched in binding sites for the protein immunoprecipitated. Some sequences may also contain binding sites for a coregulator. Biologists are interested in knowing which coregulatory factor motifs may be present in the sequences bound by the protein ChIP'ed.
resultsWe present a finite mixture framework with an expectation-maximization algorithm that considers two motifs jointly and simultaneously determines which sequences contain both motifs, either one or neither of them. Tested on 10 simulated ChIP-seq datasets, our method performed better than repeated application of MEME in predicting sequences containing both motifs. When applied to a mouse liver Foxa2 ChIP-seq dataset involving ~ 12 000 400-bp sequences, coMOTIF identified co-occurrence of Foxa2 with Hnf4a, Cebpa, E-box, Ap1/Maf or Sp1 motifs in ~6-33% of these sequences. These motifs are either known as liver-specific transcription factors or have an important role in liver function. AVAILABILITY: Freely available at http://www.niehs.nih.gov/research/resources/software/comotif/. CONTACT: li3@niehs.nih.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.