ArticleMolecular cell2009
Revealing global regulatory perturbations across human cancers.
Article in Molecular cell, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
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Who cites it
146 citing papers in PubMed.
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- Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer.Science advances · 2026Article
- The GENEVA platform models tumor mosaicism to reveal variations of responses to KRAS inhibitors and identify improved drug combinations.Nature cancer · 2026Article
- Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.Cell reports. Medicine · 2026Article
- Single-nucleus transcriptome atlas of orbitofrontal cortex in ALS with a deep learning-based decoding of alternative polyadenylation mechanisms.Cell genomics · 2025Article
- LsrL modulates Lsr2-induced chromatin structure to tune biosynthetic gene cluster regulation inbioRxiv : the preprint server for biology · 2025Article
- Conserved Heterochromatin-like Structures with Local Regulators Mediate the Iron Stress Response in Mycobacteria.bioRxiv : the preprint server for biology · 2025Article
- DNA methylation affects gene expression but not global chromatin structure inJournal of bacteriology · 2025Article
- A generative framework for enhanced cell-type specificity in rationally designed mRNAs.bioRxiv : the preprint server for biology · 2024Article
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- A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation.Scientific reports · 2024Article
- Developmental-status-aware transcriptional decomposition establishes a cell state panorama of human cancers.Genome medicine · 2024Article
- Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.Cell reports · 2024Article
- Systematic identification of post-transcriptional regulatory modules.Nature communications · 2024Article
- pyPAGE: A framework for Addressing biases in gene-set enrichment analysis-A case study on Alzheimer's disease.PLoS computational biology · 2024Article
- Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate ofmSphere · 2024Article
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- Regulation of theRNA (New York, N.Y.) · 2024Article
- Loss of CREBBP and KMT2D cooperate to accelerate lymphomagenesis and shape the lymphoma immune microenvironment.Nature communications · 2024Article
86 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
The discovery of pathways and regulatory networks whose perturbation contributes to neoplastic transformation remains a fundamental challenge for cancer biology. We show that such pathway perturbations, and the cis-regulatory elements through which they operate, can be efficiently extracted from global gene expression profiles. Our approach utilizes information-theoretic analysis of expression levels, pathways, and genomic sequences. Analysis across a diverse set of human cancers reveals the majority of previously known cancer pathways. Through de novo motif discovery we associate these pathways with transcription-factor binding sites and miRNA targets, including those of E2F, NF-Y, p53, and let-7. Follow-up experiments confirmed that these predictions correspond to functional in vivo regulatory interactions. Strikingly, the majority of the perturbations, associated with putative cis-regulatory elements, fall outside of known cancer pathways. Our study provides a systems-level dissection of regulatory perturbations in cancer-an essential component of a rational strategy for therapeutic intervention and drug-target discovery.
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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.