ArticlePLoS computational biology2005
Ab initio prediction of transcription factor targets using structural knowledge.
Article in PLoS computational biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 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
61 citing papers in PubMed, 112 citations in OpenAlex.
- Transposable elements drive the evolution of metazoan zinc finger genes.Genome research · 2023Article
- On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF.NAR genomics and bioinformatics · 2020Article
- FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1).Nucleic acids research · 2018Article
- An efficient algorithm for improving structure-based prediction of transcription factor binding sites.BMC bioinformatics · 2017Article
- Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data.Nucleic acids research · 2017Article
- Structural Insights into c-Myc-interacting Zinc Finger Protein-1 (Miz-1) Delineate Domains Required for DNA Scanning and Sequence-specific Binding.The Journal of biological chemistry · 2017Article
- Article
- Determination of specificity influencing residues for key transcription factor families.Quantitative biology (Beijing, China) · 2015Article
- Pervasive variation of transcription factor orthologs contributes to regulatory network evolution.PLoS genetics · 2015Article
- A systematic survey of the Cys2His2 zinc finger DNA-binding landscape.Nucleic acids research · 2015Article
- Absence of a simple code: how transcription factors read the genome.Trends in biochemical sciences · 2014Review
- Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding.Molecular cell · 2014Article
- An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins.Nucleic acids research · 2014Article
- The Brm-HDAC3-Erm repressor complex suppresses dedifferentiation in Drosophila type II neuroblast lineages.eLife · 2014Article
- Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.Nucleic acids research · 2014Article
- De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins.Nucleic acids research · 2014Article
- Modeling the specificity of protein-DNA interactions.Quantitative biology (Beijing, China) · 2013Article
- Screening of potential pseudo att sites of Streptomyces phage ΦC31 integrase in the human genome.Acta pharmacologica Sinica · 2013Article
- Article
- Computational predictions provide insights into the biology of TAL effector target sites.PLoS computational biology · 2013Article
1 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
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structure-based approach applicable to transcription factors with no prior binding data. Our approach combines sequence data and structural information to infer context-specific amino acid-nucleotide recognition preferences. These are used to predict binding sites for novel transcription factors from the same structural family. We demonstrate our approach on the Cys(2)His(2) Zinc Finger protein family, and show that the learned DNA-recognition preferences are compatible with experimental results. We use these preferences to perform a genome-wide scan for direct targets of Drosophila melanogaster Cys(2)His(2) transcription factors. By analyzing the predicted targets along with gene annotation and expression data we infer the function and activity of these proteins.
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.