ArticleDatabase : the journal of biological databases and curation2013
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.
Article in Database : the journal of biological databases and curation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 61 citations in OpenAlex.
- A longitudinal analysis of function annotations of the human proteome reveals consistently high biases.Database : the journal of biological databases and curation · 2025Article
- TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat.Nucleic acids research · 2024Article
- Host Transcriptome Analysis of Ferret Tissues Following Henipavirus Infection.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Accurate detection of benign and malignant renal tumor subtypes with MethylBoostER: An epigenetic marker-driven learning framework.Science advances · 2022Article
- Novel Variance-Component TWAS method for studying complex human diseases with applications to Alzheimer's dementia.PLoS genetics · 2021Article
- Combinatorial analyses reveal cellular composition changes have different impacts on transcriptomic changes of cell type specific genes in Alzheimer's Disease.Scientific reports · 2021Article
- Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution.Frontiers in genetics · 2021Article
- Reconstruction of a directed acyclic graph with intervention.Electronic journal of statistics · 2020Article
- Genetic Variation in Human Gene Regulatory Factors Uncovers Regulatory Roles in Local Adaptation and Disease.Genome biology and evolution · 2019Article
- The Gene Ontology Resource: 20 years and still GOing strong.Nucleic acids research · 2019Article
- ApicoTFdb: the comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors.Database : the journal of biological databases and curation · 2019Article
- Master Regulators of Signaling Pathways: An Application to the Analysis of Gene Regulation in Breast Cancer.Frontiers in genetics · 2019Article
- Identification of active signaling pathways by integrating gene expression and protein interaction data.BMC systems biology · 2018Article
- wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool.BMC bioinformatics · 2018Article
- In silico design of context-responsive mammalian promoters with user-defined functionality.Nucleic acids research · 2017Article
- Using the Gene Ontology to Annotate Key Players in Parkinson's Disease.Neuroinformatics · 2016Article
- Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.Database : the journal of biological databases and curation · 2016Article
- A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe.Frontiers in genetics · 2016Article
- Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.Nature communications · 2015Article
- Gene Ontology Consortium: going forward.Nucleic acids research · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 4 institutions in 3 countries.
Funding
Abstract
Transcription factors control which information in a genome becomes transcribed to produce RNAs that function in the biological systems of cells and organisms. Reliable and comprehensive information about transcription factors is invaluable for large-scale network-based studies. However, existing transcription factor knowledge bases are still lacking in well-documented functional information. Here, we provide guidelines for a curation strategy, which constitutes a robust framework for using the controlled vocabularies defined by the Gene Ontology Consortium to annotate specific DNA binding transcription factors (DbTFs) based on experimental evidence reported in literature. Our standardized protocol and workflow for annotating specific DNA binding RNA polymerase II transcription factors is designed to document high-quality and decisive evidence from valid experimental methods. Within a collaborative biocuration effort involving the user community, we are now in the process of exhaustively annotating the full repertoire of human, mouse and rat proteins that qualify as DbTFs in as much as they are experimentally documented in the biomedical literature today. The completion of this task will significantly enrich Gene Ontology-based information resources for the research community. Database URL: www.tfcheckpoint.org.
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.