ArticleMolecular systems biology2012
Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma.
Article in Molecular systems biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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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.
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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
65 citing papers in PubMed.
- Temporal Expression Analysis to Unravel Gene Regulatory Dynamics by microRNAs.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML.NPJ systems biology and applications · 2024Article
- Methods for multi-omic data integration in cancer research.Frontiers in genetics · 2024Review
- SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data.Nature biotechnology · 2023Article
- Inferring the Cancer Cellular Epigenome Heterogeneity via DNA Methylation Patterns.Cancer treatment and research · 2023Article
- miRSCAPE - inferring miRNA expression from scRNA-seq data.iScience · 2022Article
- Computing microRNA-gene interaction networks in pan-cancer using miRDriver.Scientific reports · 2022Article
- MicroRNA‑218 inhibits the malignant phenotypes of glioma by modulating the TNC/AKT/AP‑1/TGFβ1 feedback signaling loop.International journal of molecular medicine · 2021Article
- Article
- Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma.Molecular systems biology · 2020Article
- Circulating microRNA trafficking and regulation: computational principles and practice.Briefings in bioinformatics · 2020Review
- Multi-Omic Regulation of the PAM50 Gene Signature in Breast Cancer Molecular Subtypes.Frontiers in oncology · 2020Article
- Review
- Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.An international journal on information fusion · 2019Article
- Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers.Nature communications · 2019Article
- Integrative Analysis Reveals Subtype-Specific Regulatory Determinants in Triple Negative Breast Cancer.Cancers · 2019Article
- LINC00261 functions as a competing endogenous RNA to regulate BCL2L11 expression by sponging miR-132-3p in endometriosis.American journal of translational research · 2019Article
- MicroRNA-365 suppressed cell proliferation and migration via targeting PAX6 in glioblastoma.American journal of translational research · 2019Article
- regQTLs: Single nucleotide polymorphisms that modulate microRNA regulation of gene expression in tumors.PLoS genetics · 2018Article
5 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
10 authors.
Funding
Abstract
Large-scale cancer genomics projects are profiling hundreds of tumors at multiple molecular layers, including copy number, mRNA and miRNA expression, but the mechanistic relationships between these layers are often excluded from computational models. We developed a supervised learning framework for integrating molecular profiles with regulatory sequence information to reveal regulatory programs in cancer, including miRNA-mediated regulation. We applied our approach to 320 glioblastoma profiles and identified key miRNAs and transcription factors as common or subtype-specific drivers of expression changes. We confirmed that predicted gene expression signatures for proneural subtype regulators were consistent with in vivo expression changes in a PDGF-driven mouse model. We tested two predicted proneural drivers, miR-124 and miR-132, both underexpressed in proneural tumors, by overexpression in neurospheres and observed a partial reversal of corresponding tumor expression changes. Computationally dissecting the role of miRNAs in cancer may ultimately lead to small RNA therapeutics tailored to subtype or individual.
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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.