ArticleNucleic acids research2016
TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2,657 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
2,657 citing papers in PubMed.
- miR‑324‑5p in oncology: Molecular mechanisms and clinical outlook (Review).Oncology reports · 2026Review
- Diverse patterns of transcriptional regulation and epigenetic reprogramming within PMDs contribute to ESCC progression by regulating EMT and immunosuppression.Epigenetics · 2026Article
- Integrative in silico and clinical validation of urinary lncRNAs (SNHG7 & LINC00675) and β-catenin mRNA as molecular markers for early bladder cancer detection.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Article
- Article
- Metastasis-associated DNA methylation of the lncRNAs LINC01354 and LINC01510 in clear cell renal cell carcinoma.Clinical epigenetics · 2026Article
- A renal cyst-clear cell renal cell carcinoma comorbidity analysis identifies a FOXM1-positive epithelial COL6A1-CD44 axis that remodels fibroblasts.Translational oncology · 2026Article
- Integrative multi-omics profiling of insomnia-related molecular features reveals microbiome, immune, and therapy-relevant heterogeneity in colorectal cancer.Microbiology spectrum · 2026Article
- Switches in alternatively spliced isoforms impact protein and drug interactions in melanoma, ovarian cancer, and acute myeloid leukemia.British journal of cancer · 2026Article
- SSX1 and TRIM58 expression stratifies lung squamous cell carcinoma by tumor immune microenvironment characteristics and informs potential immunotherapy responsiveness.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Article
- Overview on Epstein-Barr Virus-Host Interactions With a Focus on Host Cell Transcriptome Alterations.Cell biochemistry and function · 2026Review
- Investigating the role of CpG islands and DNA methylation at 3'UTRs in cancer.Life science alliance · 2026Article
- LncRNA MIR22HG and miR-10a-5p: Pioneering serum biomarkers for pancreatic cancer diagnosis and progression assessment.Non-coding RNA research · 2026Article
- A transcriptional signature of resting mast cells is associated with improved disease outcome in HRGenes and immunity · 2026Article
- Adipose triglyceride lipase driven lipolysis as a targetable metabolic vulnerability in prostate cancer with intrinsic metabolic inflexibility.British journal of cancer · 2026Article
- Asynchronous Evolution of Epithelium and Stroma Differentiates Precursor Lesions from Pancreatic Cancer.Cancer discovery · 2026Article
- Deoxythymidylate Kinase (DTYMK)-Driven Pyrimidine Hypermetabolism Is Associated with a Folate-Dependent Macrophage Programme in Triple-Negative Breast Cancer.International journal of molecular sciences · 2026Article
- An integrated spatially defined roadmap of normal and cancer-associated colon fibroblasts.Molecular systems biology · 2026Article
- Multi-Omics Integration Identifies Epithelial-Stromal-Immune Co-Regulators Bridging Ulcerative Colitis and Colorectal Cancer.Biomedicines · 2026Article
- Exploratory Transcriptomic, Genomic, Pharmacogenomic, and Cellular Evaluation of FKBP4 in Lung Adenocarcinoma.Biology · 2026Article
- HopRatio: Profiling single-sample transcriptomic dysregulation using stable gene-ordering relationships.iScience · 2026Article
2,597 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
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers. However, mining the TCGA data presents several bioinformatics challenges, such as data retrieval and integration with clinical data and other molecular data types (e.g. RNA and DNA methylation). We developed an R/Bioconductor package called TCGAbiolinks to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies and in our own group. Using four different TCGA tumor types (Kidney, Brain, Breast and Colon) as examples, we provide case studies to illustrate examples of reproducibility, integrative analysis and utilization of different Bioconductor packages to advance and accelerate novel discoveries.
Indexed as
Identifiers
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.