ArticleProceedings of the National Academy of Sciences of the United States of America2016
Big data visualization identifies the multidimensional molecular landscape of human gliomas.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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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
27 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Visualizing genomic characteristics across an RNA-Seq based reference landscape of normal and neoplastic brain.Scientific reports · 2023Pooled it
- Learning Patient Similarity from Genomics for Precision Oncology.medRxiv : the preprint server for health sciences · 2025Article
- An RNA seq-based reference landscape of human normal and neoplastic brain.Research square · 2023Article
- An RNA seq-based reference landscape of human normal and neoplastic brain.bioRxiv : the preprint server for biology · 2023Article
- Machine learning modeling of genome-wide copy number alteration signatures reliably predicts IDH mutational status in adult diffuse glioma.Acta neuropathologica communications · 2021Article
- Clustering Analysis Supports the Detection of Biological Processes Related to Autism Spectrum Disorder.Genes · 2020Article
- Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling.Drug discovery today · 2020Review
- Identification of relevant genetic alterations in cancer using topological data analysis.Nature communications · 2020Article
- Coding of Glioblastoma Progression and Therapy Resistance through Long Noncoding RNAs.Cancers · 2020Review
- Cellular Plasticity and Tumor Microenvironment in Gliomas: The Struggle to Hit a Moving Target.Cancers · 2020Review
- A kinase-deficient NTRK2 splice variant predominates in glioma and amplifies several oncogenic signaling pathways.Nature communications · 2020Article
- Translating Basic Science Discoveries into Improved Outcomes for Glioblastoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2020Article
- Tumor Cell Invasion in Glioblastoma.International journal of molecular sciences · 2020Review
- A Panel of Synapse-Related Genes as a Biomarker for Gliomas.Frontiers in neuroscience · 2020Article
- Next Generation Sequencing and Machine Learning Technologies Are Painting the Epigenetic Portrait of Glioblastoma.Frontiers in oncology · 2020Review
- A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes.BMC medical genomics · 2018Article
- Copy number profiling across glioblastoma populations has implications for clinical trial design.Neuro-oncology · 2018Article
- Inclusion bias of patients with genetically different glioblastoma subgroups in clinical trials.Neuro-oncology · 2018Article
- Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape.Nature genetics · 2018Article
- Next-GenerationFrontiers in oncology · 2018Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We show that visualizing large molecular and clinical datasets enables discovery of molecularly defined categories of highly similar patients. We generated a series of linked 2D sample similarity plots using genome-wide single nucleotide alterations (SNAs), copy number alterations (CNAs), DNA methylation, and RNA expression data. Applying this approach to the combined glioblastoma (GBM) and lower grade glioma (LGG) The Cancer Genome Atlas datasets, we find that combined CNA/SNA data divide gliomas into three highly distinct molecular groups. The mutations commonly used in clinical evaluation of these tumors are regionally distributed in these plots. One of the three groups is a mixture of GBM and LGG that shows similar methylation and survival characteristics to GBM. Altogether, our approach identifies eight molecularly defined glioma groups with distinct sequence/expression/methylation profiles. Importantly, we show that regionally clustered samples are enriched for specific drug targets.
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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.