ArticleScientific data2018
Unifying cancer and normal RNA sequencing data from different sources.
Article in Scientific data, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers.
What it found
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Who cites it
128 citing papers in PubMed.
- ITPRIPL1: A tumor immune-associated biomarker with prognostic and therapeutic implications in gastrointestinal cancer.Scientific reports · 2026Article
- Integrated Evolutionary and Multi-Omic Analysis of STAT Family Activation Across Solid Tumors.Genes · 2026Article
- Tumor-infiltrating T Lymphocytes Recognize Thyroid-specific Proteins and Neo-antigens in Follicular Cell-derived Thyroid Cancers.The Journal of clinical endocrinology and metabolism · 2026Article
- NELF prevents transcriptional readthrough into DNA replication zones in cancer cells.EMBO reports · 2026Article
- Integrative In Silico mRNA-miRNA Profiling of mTOR Pathway Dysregulation in High-Grade Serous Ovarian Carcinoma.Cancers · 2026Article
- LightGBM-guided discovery of mechanistic biomarkers in thyroid cancer: GALNT7 and SKP1P1 emerge as therapeutic targets.Discover oncology · 2026Article
- DIP2B as a Prognostic Biomarker and Immunotherapy Target: Insights from Pan-Cancer Analysis.Applied biochemistry and biotechnology · 2026Article
- Sample size requirements for machine learning classification of binary outcomes in bulk RNA-Seq data.BMC bioinformatics · 2026Article
- Pan-cancer landscape of protein kinase D3: An integrative TCGA multi-omics analysis of clinical, molecular, and immunological roles.PloS one · 2026Article
- MiR-124-3p inhibits stomach adenocarcinoma progression by targeting AHR to induce autophagy.Cell division · 2025Article
- Unveiling CCR9 and CCL13 as immune biomarkers and therapeutic targets in thymoma.Scientific reports · 2025Article
- Article
- Subgroup Analysis of Differential Networks with Latent Variables.Statistics and computing · 2025Article
- Next-Generation Sequencing: A Review of Its Transformative Impact on Cancer Diagnosis, Treatment, and Resistance Management.Diagnostics (Basel, Switzerland) · 2025Review
- A Protocol for Weighted Gene Co-expression Network Analysis With Module Preservation and Functional Enrichment Analysis for Tumor and Normal Transcriptomic Data.Bio-protocol · 2025Article
- Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression.PLoS genetics · 2025Article
- Proteogenomic approach to immunopeptidomics of ovarian tumors identifies shared peptide vaccine candidates.NPJ vaccines · 2025Article
- HERV-derived epitopes represent new targets for T-cell-based immunotherapies in ovarian cancer.Journal for immunotherapy of cancer · 2025Article
- Hormonally upregulated neu tumor-associated kinase (HUNK) modulates gastric cancer progression through the regulation of cell homeostasis.Cell communication and signaling : CCS · 2025Article
- Article
68 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Driven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude of large-scale studies were conducted recently that have resulted in an unprecedented volume of whole transcriptome sequencing (RNA-seq) data, such as the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA). While these data offer new opportunities to identify the mechanisms underlying disease, the comparison of data from different sources remains challenging, due to differences in sample and data processing. Here, we developed a pipeline that processes and unifies RNA-seq data from different studies, which includes uniform realignment, gene expression quantification, and batch effect removal. We find that uniform alignment and quantification is not sufficient when combining RNA-seq data from different sources and that the removal of other batch effects is essential to facilitate data comparison. We have processed data from GTEx and TCGA and successfully corrected for study-specific biases, enabling comparative analysis between TCGA and GTEx. The normalized datasets are available for download on figshare.
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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.