ArticleThe pharmacogenomics journal2016
Computational discovery of transcription factors associated with drug response.
Article in The pharmacogenomics journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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
12 citing papers in PubMed, 1 synthesis or guideline pooled it, 21 citations in OpenAlex.
- Pooled it
- VarSAn: associating pathways with a set of genomic variants using network analysis.Nucleic acids research · 2021Article
- Identification of early liver toxicity gene biomarkers using comparative supervised machine learning.Scientific reports · 2020Article
- Estimation and inference for the indirect effect in high-dimensional linear mediation models.Biometrika · 2020Article
- Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response.BMC biology · 2019Article
- Identification of pathways associated with chemosensitivity through network embedding.PLoS computational biology · 2019Article
- Principled multi-omic analysis reveals gene regulatory mechanisms of phenotype variation.Genome research · 2018Article
- The global spectrum of protein-coding pharmacogenomic diversity.The pharmacogenomics journal · 2018Article
- Genetic variation in human drug-related genes.Genome medicine · 2017Article
- Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance.Genome biology · 2017Article
- Model-based unsupervised learning informs metformin-induced cell-migration inhibition through an AMPK-independent mechanism in breast cancer.Oncotarget · 2017Article
- Vascular homeostasis at high-altitude: role of genetic variants and transcription factors.Pulmonary circulationReview
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 at 2 institutions in 1 country.
Funding
Abstract
This study integrates gene expression, genotype and drug response data in lymphoblastoid cell lines with transcription factor (TF)-binding sites from ENCODE (Encyclopedia of Genomic Elements) in a novel methodology that elucidates regulatory contexts associated with cytotoxicity. The method, GENMi (Gene Expression iN the Middle), postulates that single-nucleotide polymorphisms within TF-binding sites putatively modulate its regulatory activity, and the resulting variation in gene expression leads to variation in drug response. Analysis of 161 TFs and 24 treatments revealed 334 significantly associated TF-treatment pairs. Investigation of 20 selected pairs yielded literature support for 13 of these associations, often from studies where perturbation of the TF expression changes drug response. Experimental validation of significant GENMi associations in taxanes and anthracyclines across two triple-negative breast cancer cell lines corroborates our findings. The method is shown to be more sensitive than an alternative, genome-wide association study-based approach that does not use gene expression. These results demonstrate the utility of GENMi in identifying TFs that influence drug response and provide a number of candidates for further testing.
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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.