ArticleBioinformatics (Oxford, England)2010
Assigning roles to DNA regulatory motifs using comparative genomics.
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 138 papers, 4 of them syntheses 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
138 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Comparative meta-analysis of barely transcriptome: Pathogen type determines host preference.PloS one · 2025Pooled it
- A comprehensive meta-analysis of transcriptome data to identify signature genes associated with pancreatic ductal adenocarcinoma.PloS one · 2024Pooled it
- Identification of biomarker genes from multiple studies for abiotic stress in maize through machine learning.Journal of biosciences · 2024Pooled it
- Integrative systems biology analysis of barley transcriptome ─ hormonal signaling against biotic stress.PloS one · 2023Pooled it
- Replication-origin inversions accompany compositional skew and phylogenetic artifacts in fan worm mitochondrial genomes.iScience · 2026Article
- FUS controls muscle differentiation through phase separation-mediated recruitment of the transcription factors MEF2 and ETV5.The EMBO journal · 2026Article
- GapR stiffens AT-rich and overtwisted DNA leading to differential effects on transcription based on gene context.Nucleic acids research · 2026Article
- Functional divergence of MADS-box genes and the dual regulatory role of a long noncoding RNA underlie sex determination in Ginkgo biloba.BMC plant biology · 2026Article
- NAT10 maintains stem cell homeostasis by mitigating mRNA decay through an acNature cell biology · 2026Article
- Genome-Wide Identification of GRAS Gene Family and Drought Response Analysis of DELLA Proteins inCurrent issues in molecular biology · 2026Article
- Integrative cross-study analysis of maize microarray datasets identifies key abiotic stress-responsive genes, highlighting ZmOSM34 and ZmANAH.Scientific reports · 2026Article
- DeepECC: a deep learning framework for genome-wide identification and analysis of human cancer eccDNAs.Nucleic acids research · 2026Article
- Article
- Modular RNA interactions shape FXR1 condensates involved in mRNA localization and translation.Nature communications · 2025Article
- Key regulatory genes in sugar beet's defense against curly top virus identified by network analysis and qRT-PCR.Biochemistry and biophysics reports · 2025Article
- Network-based analysis of candidate oncogenes and pathways in hepatocellular carcinoma.Biochemistry and biophysics reports · 2025Article
- Article
- DNMT1-mediated regulation of somatostatin-positive interneuron migration impacts cortical architecture and function.Nature communications · 2025Article
- Function of cytochrome P450 CYP72A1182 in metabolic herbicide resistance evolution in Amaranthus palmeri populations.Journal of experimental botany · 2025Article
- Identification of single nucleotide polymorphisms (SNPs) associated with heat stress and milk production traits in Chinese holstein cows.BMC genomics · 2025Article
78 more citing papers are in PubMed but not listed here.
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.
Funding
Abstract
motivationTranscription factors (TFs) are crucial during the lifetime of the cell. Their functional roles are defined by the genes they regulate. Uncovering these roles not only sheds light on the TF at hand but puts it into the context of the complete regulatory network.
resultsHere, we present an alignment- and threshold-free comparative genomics approach for assigning functional roles to DNA regulatory motifs. We incorporate our approach into the Gomo algorithm, a computational tool for detecting associations between a user-specified DNA regulatory motif [expressed as a position weight matrix (PWM)] and Gene Ontology (GO) terms. Incorporating multiple species into the analysis significantly improves Gomo's ability to identify GO terms associated with the regulatory targets of TFs. Including three comparative species in the process of predicting TF roles in Saccharomyces cerevisiae and Homo sapiens increases the number of significant predictions by 75 and 200%, respectively. The predicted GO terms are also more specific, yielding deeper biological insight into the role of the TF. Adjusting motif (binding) affinity scores for individual sequence composition proves to be essential for avoiding false positive associations. We describe a novel DNA sequence-scoring algorithm that compensates a thermodynamic measure of DNA-binding affinity for individual sequence base composition. GOMO's prediction accuracy proves to be relatively insensitive to how promoters are defined. Because GOMO uses a threshold-free form of gene set analysis, there are no free parameters to tune. Biologists can investigate the potential roles of DNA regulatory motifs of interest using GOMO via the web (http://meme.nbcr.net).
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.