ArticleJCO clinical cancer informatics2020
Multiomic Integration of Public Oncology Databases in Bioconductor.
Article in JCO clinical cancer informatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
58 citing papers in PubMed, 98 citations in OpenAlex.
- Integrating Tumor-Intrinsic and Immunologic Factors to Identify Immunogenic Breast Cancers from a Low-Risk Cohort: Results from the Randomized SweBCG91RT Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Trial
- Biomarker discovery and patient stratification in pancreatic cancer using incomplete multi-omics data.PLoS computational biology · 2026Article
- Semi-supervised Omics Factor Analysis (SOFA) disentangles known and latent sources of variation in multi-omic data.Nature communications · 2026Article
- Insulin receptor substrate 2 (IRS2) confers resistance to PI3K pathway inhibition in PIK3CA mutant breast cancer.The Journal of biological chemistry · 2026Article
- Model Context Protocol: The unexpected catalyst of a bioinformatics interoperability revolution.PLoS computational biology · 2026Article
- Tumor-infiltrating lymphocytes display prognostic signatures associated with chemotherapy response in TNBC patients.iScience · 2026Article
- Praxis-BGM: clustering of omics data using semi-supervised transfer learning for Gaussian mixture models via natural-gradient variational inference.Bioinformatics (Oxford, England) · 2026Article
- CancerOmicsStudio (CoS): a web server for integrative and interpretable analysis of multi-omics cancer data.Bioinformatics (Oxford, England) · 2026Article
- Tumour cell-intrinsic complement C1r and C1s regulate cancer cell fitness and shape the immune microenvironment in triple-negative breast cancer.Cellular and molecular life sciences : CMLS · 2026Article
- Metabolic-Epigenetic Crosstalk in Takayasu Arteritis: The ANK2-MAVS-IL-8 Axis as a Novel Therapeutic Paradigm.International journal of molecular sciences · 2026Review
- Subtype-Stratified Consensus Gene Signatures: Bridging Tumor Cell Biology, Immune Microenvironment, and Clinical Prognosis in Breast Cancer.International journal of molecular sciences · 2026Article
- Intracellular complement Factor H promotes tumor progression through modulation of cell cycle and actin cytoskeleton.Communications biology · 2026Article
- The CXCL10/CXCR3 axis is essential for sustaining immunological dormancy in triple-negative breast cancer.NPJ breast cancer · 2026Article
- Large-scale manual curation and harmonization of metadata from metagenomic and cancer genomic repositories: challenges and solutions.Database : the journal of biological databases and curation · 2026Article
- A narrative review of spatial multi-omics and organ-on-a-chip technologies for cardio-cerebral-renal crosstalk.Frontiers in bioengineering and biotechnology · 2026Review
- Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions.bioRxiv : the preprint server for biology · 2025Article
- Multi-omics and functional characterization of the tumor-killing capacity of Imiquimod-activated plasmacytoid dendritic cells.iScience · 2025Article
- Genomics and integrative clinical data machine learning scoring model to ascertain likely Lynch syndrome patients.BJC reports · 2025Article
- Identification and validation of platinum resistance signature in gastric cancer.Cancer cell international · 2025Article
- Epigenetic mechanisms underlying endometrial cancer outcomes: race-specific patterns of DNA methylation associated with molecular subtypes and survival.Carcinogenesis · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 5 institutions in 1 country.
Funding
Abstract
purposeInvestigations of the molecular basis for the development, progression, and treatment of cancer increasingly use complementary genomic assays to gather multiomic data, but management and analysis of such data remain complex. The cBioPortal for cancer genomics currently provides multiomic data from > 260 public studies, including The Cancer Genome Atlas (TCGA) data sets, but integration of different data types remains challenging and error prone for computational methods and tools using these resources. Recent advances in data infrastructure within the Bioconductor project enable a novel and powerful approach to creating fully integrated representations of these multiomic, pan-cancer databases.
methodsWe provide a set of R/Bioconductor packages for working with TCGA legacy data and cBioPortal data, with special considerations for loading time; efficient representations in and out of memory; analysis platform; and an integrative framework, such as MultiAssayExperiment. Large methylation data sets are provided through out-of-memory data representation to provide responsive loading times and analysis capabilities on machines with limited memory.
resultsWe developed the curatedTCGAData and cBioPortalData R/Bioconductor packages to provide integrated multiomic data sets from the TCGA legacy database and the cBioPortal web application programming interface using the MultiAssayExperiment data structure. This suite of tools provides coordination of diverse experimental assays with clinicopathological data with minimal data management burden, as demonstrated through several greatly simplified multiomic and pan-cancer analyses.
conclusionThese integrated representations enable analysts and tool developers to apply general statistical and plotting methods to extensive multiomic data through user-friendly commands and documented examples.
Indexed as
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What OpenQuestion holds
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.