ArticleNucleic acids research2003
An approach to identify over-represented cis-elements in related sequences.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 53 citations in OpenAlex.
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- Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells.Frontiers in genetics · 2016Review
- Bioinformatic detection of E47, E2F1 and SREBP1 transcription factors as potential regulators of genes associated to acquisition of endometrial receptivity.Reproductive biology and endocrinology : RB&E · 2011Article
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- Small interfering RNA against transcription factor STAT6 leads to increased cholesterol synthesis in lung cancer cell lines.PloS one · 2011Article
- TaNF-YC11, one of the light-upregulated NF-YC members in Triticum aestivum, is co-regulated with photosynthesis-related genes.Functional & integrative genomics · 2010Article
- Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data.BMC bioinformatics · 2010Article
- Gene expression profiling and network analysis reveals lipid and steroid metabolism to be the most favored by TNFalpha in HepG2 cells.PloS one · 2010Article
- Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes.Nucleic acids research · 2009Article
- Gene profiling of patients with chronic fatigue syndrome/myalgic encephalomyelitis.Current rheumatology reports · 2008Article
- Identification of regulatory pathways controlling gene expression of stress-responsive mitochondrial proteins in Arabidopsis.Plant physiology · 2008Article
- DiRE: identifying distant regulatory elements of co-expressed genes.Nucleic acids research · 2008Article
- Bioinformatics in China: a personal perspective.PLoS computational biology · 2008Review
- Computational methods to dissect cis-regulatory transcriptional networks.Journal of biosciences · 2007Review
- Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site.PloS one · 2007Article
- Predicting transcription factor binding sites using local over-representation and comparative genomics.BMC bioinformatics · 2006Article
- Regulation of the neuronal proteasome by Zif268 (Egr1).The Journal of neuroscience : the official journal of the Society for Neuroscience · 2006Article
- Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT.Genome biology · 2006Article
- oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes.Nucleic acids research · 2005Article
- Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays.Nucleic acids research · 2005Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computational identification of transcription factor binding sites is an important research area of computational biology. Positional weight matrix (PWM) is a model to describe the sequence pattern of binding sites. Usually, transcription factor binding sites prediction methods based on PWMs require user-defined thresholds. The arbitrary threshold and also the relatively low specificity of the algorithm prevent the result of such an analysis from being properly interpreted. In this study, a method was developed to identify over-represented cis-elements with PWM-based similarity scores. Three sets of closely related promoters were analyzed, and only over- represented motifs with high PWM similarity scores were reported. The thresholds to evaluate the similarity scores to the PWMs of putative transcription factors binding sites can also be automatically determined during the analysis, which can also be used in further research with the same PWMs. The online program is available on the website: http://www.bioinfo.tsinghua.edu.cn/- zhengjsh/OTFBS/.
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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.