ArticleNature communications2017
Pancancer modelling predicts the context-specific impact of somatic mutations on transcriptional programs.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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
19 citing papers in PubMed.
- Integrative Computational Framework,bioRxiv : the preprint server for biology · 2024Article
- Mapping drug biology to disease genetics to discover drug impacts on the human phenome.Bioinformatics advances · 2024Article
- COVID-19db linkage maps of cell surface proteins and transcription factors in immune cells.Journal of medical virology · 2023Article
- Linking Expression of Cell-Surface Receptors with Transcription Factors by Computational Analysis of Paired Single-Cell Proteomes and Transcriptomes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers.Nucleic acids research · 2022Article
- The Oncogenic PI3K-Induced Transcriptomic Landscape Reveals Key Functions in Splicing and Gene Expression Regulation.Cancer research · 2022Article
- Fibroblast mechanotransduction network predicts targets for mechano-adaptive infarct therapies.eLife · 2022Article
- SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators.Nucleic acids research · 2021Article
- Efficient representations of tumor diversity with paired DNA-RNA aberrations.PLoS computational biology · 2021Article
- ProbeRating: a recommender system to infer binding profiles for nucleic acid-binding proteins.Bioinformatics (Oxford, England) · 2020Article
- Benchmark and integration of resources for the estimation of human transcription factor activities.Genome research · 2019Article
- Footprint-based functional analysis of multiomic data.Current opinion in systems biology · 2019Review
- Insights into breast cancer phenotying through molecular omics approaches and therapy response.Cancer drug resistance (Alhambra, Calif.) · 2019Review
- Pan-Cancer and Single-Cell Modeling of Genomic Alterations Through Gene Expression.Frontiers in genetics · 2019Article
- Integrative Molecular Characterization of Malignant Pleural Mesothelioma.Cancer discovery · 2018Article
- Typing tumors using pathways selected by somatic evolution.Nature communications · 2018Article
- CEP55 is a determinant of cell fate during perturbed mitosis in breast cancer.EMBO molecular medicine · 2018Article
- Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.Cancer research · 2018Article
- Overexpression of the E2F target geneOncotarget · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Pancancer studies have identified many genes that are frequently somatically altered across multiple tumour types, suggesting that pathway-targeted therapies can be deployed across diverse cancers. However, the same 'actionable mutation' impacts distinct context-specific gene regulatory programs and signalling networks-and interacts with different genetic backgrounds of co-occurring alterations-in different cancers. Here we apply a computational strategy for integrating parallel (phospho)proteomic and mRNA sequencing data across 12 TCGA tumour data sets to interpret the context-specific impact of somatic alterations in terms of functional signatures such as (phospho)protein and transcription factor (TF) activities. Our analysis predicts distinct dysregulated transcriptional regulators downstream of somatic alterations in different cancers, and we validate the context-specific differential activity of TFs associated to mutant PIK3CA in isogenic cancer cell line models. These results have implications for the pancancer use of targeted drugs and potentially for the design of combination therapies.
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