ArticleProceedings of the National Academy of Sciences of the United States of America2003
Integrating regulatory motif discovery and genome-wide expression analysis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers.
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Who cites it
135 citing papers in PubMed.
- Trial
- Article
- Predicting regional somatic mutation rates using DNA motifs.PLoS computational biology · 2023Article
- Identifying genetic regulatory variants that affect transcription factor activity.Cell genomics · 2023Article
- Article
- Silver and gold nanoparticles induced differential antimicrobial potential in calli cultures of Prunella vulgaris.BMC chemistry · 2022Article
- Quantifying the tissue-specific regulatory information within enhancer DNA sequences.NAR genomics and bioinformatics · 2021Article
- Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data.Bioinformatics (Oxford, England) · 2021Article
- Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes inPlants (Basel, Switzerland) · 2020Article
- Molecular networks in Network Medicine: Development and applications.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
- Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting.PLoS neglected tropical diseases · 2020Article
- Sex chromosome evolution in parasitic nematodes of humans.Nature communications · 2020Article
- Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.Nature biotechnology · 2020Article
- SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.Bioinformatics (Oxford, England) · 2019Article
- Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features.PLoS computational biology · 2019Article
- Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice.Scientific reports · 2019Article
- Transcriptional orchestration of mitochondrial homeostasis in a cellular model of PGC-1-related coactivator-dependent thyroid tumor.Oncotarget · 2018Article
- Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning.Bioinformatics (Oxford, England) · 2017Article
- Past Roadblocks and New Opportunities in Transcription Factor Network Mapping.Trends in genetics : TIG · 2016Review
- Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells.Cell reports · 2016Article
75 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
We propose motif regressor for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression regression analysis, resulting in high sensitivity and specificity. motif regressor is particularly effective in discovering expression-mediating motifs of medium to long width with multiple degenerate positions. When applied to Saccharomyces cerevisiae, motif regressor identified the ROX1 and YAP1 motifs from Rox1p and Yap1p overexpression experiments, respectively; predicted that Gcn4p may have increased activity in YAP1 deletion mutants; reported a group of motifs (including GCN4, PHO4, MET4, STRE, USR1, RAP1, M3A, and M3B) that may mediate the transcriptional response to amino acid starvation; and found all of the known cell-cycle regulation motifs from 18 expression microarrays over two cell cycles.
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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.