ArticleNucleic acids research2013
Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed, 22 citations in OpenAlex.
- BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function.International journal of molecular sciences · 2024Article
- Vitamin D in Neurological Diseases.International journal of molecular sciences · 2022Review
- Article
- Enhancer grammar in development, evolution, and disease: dependencies and interplay.Developmental cell · 2021Review
- Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues.PloS one · 2019Article
- PTE, a novel module to target Polycomb Repressive Complex 1 to the human cyclin D2 (The Journal of biological chemistry · 2018Article
- Investigating transcription factor synergism in humans.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization.PloS one · 2018Article
- Removing Background Co-occurrences of Transcription Factor Binding Sites Greatly Improves the Prediction of Specific Transcription Factor Cooperations.Frontiers in genetics · 2018Article
- Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq.Nucleic acids research · 2017Article
- Combinatorial Cis-regulation in Saccharomyces Species.G3 (Bethesda, Md.) · 2016Article
- PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information.BMC bioinformatics · 2015Article
- Article
- CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining.PloS one · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In higher organisms, gene regulation is controlled by the interplay of non-random combinations of multiple transcription factors (TFs). Although numerous attempts have been made to identify these combinations, important details, such as mutual positioning of the factors that have an important role in the TF interplay, are still missing. The goal of the present work is in silico mapping of some of such associating factors based on their mutual positioning, using computational screening. We have selected the process of myogenesis as a study case, and we focused on TF combinations involving master myogenic TF Myogenic differentiation (MyoD) with other factors situated at specific distances from it. The results of our work show that some muscle-specific factors occur together with MyoD within the range of ±100 bp in a large number of promoters. We confirm co-occurrence of the MyoD with muscle-specific factors as described in earlier studies. However, we have also found novel relationships of MyoD with other factors not specific for muscle. Additionally, we have observed that MyoD tends to associate with different factors in proximal and distal promoter areas. The major outcome of our study is establishing the genome-wide connection between biological interactions of TFs and close co-occurrence of their binding sites.
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.