ArticleNucleic acids research2015
By the company they keep: interaction networks define the binding ability of transcription factors.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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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.
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Who cites it
4 citing papers in PubMed, 13 citations in OpenAlex.
- Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins.Nucleic acids research · 2021Article
- WSMD: weakly-supervised motif discovery in transcription factor ChIP-seq data.Scientific reports · 2017Article
- Advances in the characterization of RNA-binding proteins.Wiley interdisciplinary reviews. RNA · 2016Review
- An integrative imputation method based on multi-omics datasets.BMC bioinformatics · 2016Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Access to genome-wide data provides the opportunity to address questions concerning the ability of transcription factors (TFs) to assemble in distinct macromolecular complexes. Here, we introduce the PAnDA (Protein And DNA Associations) approach to characterize DNA associations with human TFs using expression profiles, protein-protein interactions and recognition motifs. Our method predicts TF binding events with >0.80 accuracy revealing cell-specific regulatory patterns that can be exploited for future investigations. Even when the precise DNA-binding motifs of a specific TF are not available, the information derived from protein-protein networks is sufficient to perform high-confidence predictions (area under the ROC curve of 0.89). PAnDA is freely available at http://service.tartaglialab.com/new_submission/panda.
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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.