ArticleNucleic acids research2008
Associating transcription factor-binding site motifs with target GO terms and target genes.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis.Functional & integrative genomics · 2020Pooled it
- Translation efficiency covariation identifies conserved coordination patterns across cell types.Nature biotechnology · 2026Article
- Interrelationship between miRNA and splicing factors in pancreatic ductal adenocarcinoma.Epigenetics · 2022Review
- Transcription factor WRKY22 regulates canker susceptibility in sweet orange (Citrus sinensis Osbeck) by enhancing cell enlargement and CsLOB1 expression.Horticulture research · 2021Article
- hnRNP K Supports High-Amplitude D Site-Binding Protein mRNA (Molecular and cellular biology · 2020Article
- SoyCSN: Soybean context-specific network analysis and prediction based on tissue-specific transcriptome data.Plant direct · 2019Article
- The Poly(C) Motif in the Proximal Promoter Region of the D Site-Binding Protein Gene (Molecular and cellular biology · 2019Article
- Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study.Briefings in bioinformatics · 2018Article
- Assessing computational methods for transcription factor target gene identification based on ChIP-seq data.PLoS computational biology · 2013Article
- Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome.PloS one · 2012Article
- GOmotif: A web server for investigating the biological role of protein sequence motifs.BMC bioinformatics · 2011Article
- Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data.BMC bioinformatics · 2010Article
- Assigning roles to DNA regulatory motifs using comparative genomics.Bioinformatics (Oxford, England) · 2010Article
- TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.BMC genomics · 2010Article
- Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances.PLoS computational biology · 2010Article
- Nutritional control of gene expression in Drosophila larvae via TOR, Myc and a novel cis-regulatory element.BMC cell biology · 2010Article
- Inferring Transcriptional Interactions by the Optimal Integration of ChIP-chip and Knock-out Data.Bioinformatics and biology insights · 2009Article
- MEME SUITE: tools for motif discovery and searching.Nucleic acids research · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The roles and target genes of many transcription factors (TFs) are still unknown. To predict the roles of TFs, we present a computational method for associating Gene Ontology (GO) terms with TF-binding motifs. The method works by ranking all genes as potential targets of the TF, and reporting GO terms that are significantly associated with highly ranked genes. We also present an approach, whereby these predicted GO terms can be used to improve predictions of TF target genes. This uses a novel gene-scoring function that reflects the insight that genes annotated with GO terms predicted to be associated with the TF are more likely to be its targets. We construct validation sets of GO terms highly associated with known targets of various yeast and human TF. On the yeast reference sets, our prediction method identifies at least one correct GO term for 73% of the TF, 49% of the correct GO terms are predicted and almost one-third of the predicted GO terms are correct. Results on human reference sets are similarly encouraging. Validation of our target gene prediction method shows that its accuracy exceeds that of simple motif scanning.
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.