ArticleCell2021
A modular master regulator landscape controls cancer transcriptional identity.
Article in Cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT06842030 (Feasibility Trial of Darwin OncoTreat and OncoTarget Precision Medicine Testing to Improve Outcomes for Patients With Limited Metastatic Disease That Failed First-Line Systemic Therapy), which is not on this map. Cited by 84 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.
Feasibility Trial of Darwin OncoTreat and OncoTarget Precision Medicine Testing to Improve Outcomes for Patients With Limited Metastatic Disease That Failed First-Line Systemic Therapy
Who cites it
84 citing papers in PubMed.
- Complex assembly and activity states as multifaceted protein attributes explaining phenotypic variability.Molecular systems biology · 2026Article
- Developmental and MAPK-responsive transcription factors regulate distinct malignant cell states and associated genetic dependencies in pancreatic cancer.Nature genetics · 2026Article
- Article
- GRNContext: an interactive web platform for contextualized gene regulatory networks visualization across human cancers.Bioinformatics (Oxford, England) · 2026Article
- Transcription factor targeting strategies in cancer: mechanisms, challenges and cutting-edge progress.Acta pharmacologica Sinica · 2026Review
- A forward genetic screen identifies Sirtuin1 as a driver of neuroendocrine prostate cancer.The Journal of experimental medicine · 2026Article
- pyVIPER: a fast and scalable Python package for protein activity estimation and master regulator analysis of single-cell RNA sequencing data.BMC bioinformatics · 2026Article
- Statistical knockoffs improve biomarker discovery from transcriptomic data.Briefings in bioinformatics · 2026Article
- Systematic design of combination therapy by targeting master regulators of coexisting diffuse midline glioma cell states.Nature genetics · 2026Article
- Beyond silencing: integrative multi-omics and spatial profiling unravel the systems-level role of piRNAs in HBV-driven Hepatocarcinogenesis.Molecular biology reports · 2026Review
- GREmLN: A Cellular Graph Structure Aware Transcriptomics Foundation Model.bioRxiv : the preprint server for biology · 2026Article
- Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies inScience advances · 2026Article
- Pan-cancer inference and validation of hypermorphic, hypomorphic and neomorphic mutations.Nature genetics · 2026Article
- From correlation to causation: cell-type-specific gene regulatory networks in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Article
- Differentiation Treatment Applied to Lung Cancer Model Reduces Pathogenic Traits in Vitro.Advanced biology · 2026Article
- MPAC: a computational framework for inferring pathway activities from multi-omic data.Bioinformatics (Oxford, England) · 2025Article
- SOX10, MITF, and microRNAs: Decoding their interplay in regulating melanoma plasticity.International journal of cancer · 2025Review
- Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability.bioRxiv : the preprint server for biology · 2025Article
- From Correlation to Causation: Cell-Type-Specific Gene Regulatory Networks in Alzheimer's Disease.bioRxiv : the preprint server for biology · 2025Article
24 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
14 authors.
Funding
Abstract
Despite considerable efforts, the mechanisms linking genomic alterations to the transcriptional identity of cancer cells remain elusive. Integrative genomic analysis, using a network-based approach, identified 407 master regulator (MR) proteins responsible for canalizing the genetics of individual samples from 20 cohorts in The Cancer Genome Atlas (TCGA) into 112 transcriptionally distinct tumor subtypes. MR proteins could be further organized into 24 pan-cancer, master regulator block modules (MRBs), each regulating key cancer hallmarks and predictive of patient outcome in multiple cohorts. Of all somatic alterations detected in each individual sample, >50% were predicted to induce aberrant MR activity, yielding insight into mechanisms linking tumor genetics and transcriptional identity and establishing non-oncogene dependencies. Genetic and pharmacological validation assays confirmed the predicted effect of upstream mutations and MR activity on downstream cellular identity and phenotype. Thus, co-analysis of mutational and gene expression profiles identified elusive subtypes and provided testable hypothesis for mechanisms mediating the effect of genetic alterations.
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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.