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Unifying cancer and normal RNA sequencing data from different sources

https://doi.org/10.1038/sdata.2018.61

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The Molecular Taxonomy of Primary Prostate Cancer

inferredcites →https://doi.org/10.1038/nbt.3772openalex-snapshot

Toil enables reproducible, open source, big biomedical data analyses

inferredcites →https://doi.org/10.1038/ncomms8816openalex-snapshot

mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data

inferredcites →https://doi.org/10.1038/ng.2653openalex-snapshot

The Genotype-Tissue Expression (GTEx) project

inferredcites →https://doi.org/10.1038/nmeth.3692openalex-snapshot

OASIS: web-based platform for exploring cancer multi-omics data

inferredcites →https://doi.org/10.1093/bib/bbv017openalex-snapshot

Assessing the consistency of public human tissue RNA-seq data sets

inferredcites →https://doi.org/10.1093/bib/bbv117openalex-snapshot

MTD: a mammalian transcriptomic database to explore gene expression and regulation

inferredcites →https://doi.org/10.1093/bioinformatics/bts084openalex-snapshot

RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/bts356openalex-snapshot

RSeQC: quality control of RNA-seq experiments

inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot

STAR: ultrafast universal RNA-seq aligner

inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

inferredcites →https://doi.org/10.1093/biostatistics/kxj037openalex-snapshot

Adjusting batch effects in microarray expression data using empirical Bayes methods

inferredcites →https://doi.org/10.1093/database/bav019openalex-snapshot

BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis

inferredcites →https://doi.org/10.1093/nar/gkt1264openalex-snapshot

CellFinder: a cell data repository

inferredcites →https://doi.org/10.1093/nar/gkt1270openalex-snapshot

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

inferredcites →https://doi.org/10.1093/nar/gkt1406openalex-snapshot

Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

inferredcites →https://doi.org/10.1093/nar/gku864openalex-snapshot

svaseq: removing batch effects and other unwanted noise from sequencing data

inferredcites →https://doi.org/10.1093/nar/gkv1282openalex-snapshot

Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells

inferredcites →https://doi.org/10.1126/science.1262110openalex-snapshot

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

inferredcites →https://doi.org/10.1186/1471-2105-12-323openalex-snapshot

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

inferredcites →https://doi.org/10.6084/m9.figshare.5330539openalex-snapshot

Data record 1

inferredcites →https://doi.org/10.6084/m9.figshare.5330575openalex-snapshot

Data record 2

inferredcites →https://doi.org/10.6084/m9.figshare.5330593openalex-snapshot

Data record 3

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inferred← citeshttps://doi.org/10.1186/s13008-025-00175-9openalex-snapshot

MiR-124-3p inhibits stomach adenocarcinoma progression by targeting AHR to induce autophagy

inferred← citeshttps://doi.org/10.1186/s13059-021-02504-xopenalex-snapshot

Network propagation-based prioritization of long tail genes in 17 cancer types

inferred← citeshttps://doi.org/10.1186/s13073-018-0608-4openalex-snapshot

An integrative approach for building personalized gene regulatory networks for precision medicine

inferred← citeshttps://doi.org/10.1186/s13287-024-03875-1openalex-snapshot

Orai1 and Orai3 act through distinct signalling axes to promote stemness and tumorigenicity of breast cancer stem cells

inferred← citeshttps://doi.org/10.1210/clinem/dgaf639openalex-snapshot

Tumor-infiltrating T Lymphocytes Recognize Thyroid-specific Proteins and Neo-antigens in Follicular Cell-derived Thyroid Cancers

inferred← citeshttps://doi.org/10.1214/23-aoas1771openalex-snapshot

Compressed spectral screening for large-scale differential correlation analysis with application in selecting Glioblastoma gene modules

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006701openalex-snapshot

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009939openalex-snapshot

Transcriptome diversity is a systematic source of variation in RNA-sequencing data

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009954openalex-snapshot

Addressing the mean-correlation relationship in co-expression analysis

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1010342openalex-snapshot

Detection of genes with differential expression dispersion unravels the role of autophagy in cancer progression

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1011472openalex-snapshot

Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression

inferred← citeshttps://doi.org/10.1371/journal.pgen.1011835openalex-snapshot

Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression

inferred← citeshttps://doi.org/10.1371/journal.pone.0237657openalex-snapshot

Partitioning gene-based variance of complex traits by gene score regression

inferred← citeshttps://doi.org/10.1371/journal.pone.0284820openalex-snapshot

Genomics data analysis via spectral shape and topology

inferred← citeshttps://doi.org/10.1371/journal.pone.0346173openalex-snapshot

Pan-cancer landscape of protein kinase D3: An integrative TCGA multi-omics analysis of clinical, molecular, and immunological roles

inferred← citeshttps://doi.org/10.14309/ctg.0000000000000210openalex-snapshot

Oncogenic Features in Histologically Normal Mucosa: Novel Insights Into Field Effect From a Mega-Analysis of Colorectal Transcriptomes

inferred← citeshttps://doi.org/10.1590/1678-4685-gmb-2019-0373openalex-snapshot

Gene expression evaluation of antioxidant enzymes in patients with hepatocellular carcinoma: RT-qPCR and bioinformatic analyses

inferred← citeshttps://doi.org/10.2174/1386207325666220301110517openalex-snapshot

FIGNL1 Expression and its Prognostic Significance in Pan-cancer Analysis

inferred← citeshttps://doi.org/10.21769/bioprotoc.5447openalex-snapshot

A Protocol for Weighted Gene Co-expression Network Analysis With Module Preservation and Functional Enrichment Analysis for Tumor and Normal Transcriptomic Data

inferred← citeshttps://doi.org/10.23919/ccc55666.2022.9901899openalex-snapshot

Machine learning-based construction of a miRNAs prognostic risk assessment model of cervical cancer

inferred← citeshttps://doi.org/10.26437/hsea1s73openalex-snapshot

Machine Learning Approach for the Prediction of Bladder Cancer Stages Based on Next-Generation Sequencing Data

inferred← citeshttps://doi.org/10.31274/td-20240329-279openalex-snapshot

Enhancing MetaOmGraph software, and using interpretable machine learning to study novel genes in human breast cancer

inferred← citeshttps://doi.org/10.33612/diss.255266474openalex-snapshot

Context matters

inferred← citeshttps://doi.org/10.3384/9789180750097openalex-snapshot

Novel methods and software for disease module inference

inferred← citeshttps://doi.org/10.3389/fbinf.2025.1575790openalex-snapshot

Integrative multi-omics study identifies sex-specific molecular signatures and immune modulation in bladder cancer

inferred← citeshttps://doi.org/10.3389/fgene.2019.00599openalex-snapshot

Cancer as a Tissue Anomaly: Classifying Tumor Transcriptomes Based Only on Healthy Data

inferred← citeshttps://doi.org/10.3389/fgene.2020.00363openalex-snapshot

Novel Immune-Related Gene Signature for Risk Stratification and Prognosis of Survival in Lower-Grade Glioma

inferred← citeshttps://doi.org/10.3389/fgene.2020.595324openalex-snapshot

A Multi-Source Data Fusion Framework for Revealing the Regulatory Mechanism of Breast Cancer Immune Evasion

inferred← citeshttps://doi.org/10.3389/fgene.2021.697043openalex-snapshot

A Ferroptosis-Related Gene Model Predicts Prognosis and Immune Microenvironment for Cutaneous Melanoma

inferred← citeshttps://doi.org/10.3389/fgene.2021.773373openalex-snapshot

Identification and Validation of a Novel Pyroptosis-Related Gene Signature for Prognosis Prediction in Soft Tissue Sarcoma

inferred← citeshttps://doi.org/10.3389/fgene.2023.1117145openalex-snapshot

Comprehensive analysis reveals signal and molecular mechanism of mitochondrial energy metabolism pathway in pancreatic cancer

inferred← citeshttps://doi.org/10.3389/fimmu.2022.921223openalex-snapshot

Cross-Talk of Multiple Types of RNA Modification Regulators Uncovers the Tumor Microenvironment and Immune Infiltrates in Soft Tissue Sarcoma

inferred← citeshttps://doi.org/10.3389/fimmu.2022.999551openalex-snapshot

A combined analysis of bulk and single-cell sequencing data reveals that depleted extracellular matrix and enhanced immune processes co-contribute to fluorouracil beneficial responses in gastric cancer

inferred← citeshttps://doi.org/10.3389/fmolb.2021.726902openalex-snapshot

Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies

inferred← citeshttps://doi.org/10.3389/fonc.2020.00208openalex-snapshot

Malignant Evaluation and Clinical Prognostic Values of m6A RNA Methylation Regulators in Glioblastoma

inferred← citeshttps://doi.org/10.3389/fonc.2020.586414openalex-snapshot

A Comprehensive Prognostic and Immune Analysis of SLC41A3 in Pan-Cancer

inferred← citeshttps://doi.org/10.3389/fonc.2022.801411openalex-snapshot

Solid Tumor Opioid Receptor Expression and Oncologic Outcomes: Analysis of the Cancer Genome Atlas and Genotype Tissue Expression Project

inferred← citeshttps://doi.org/10.3389/fonc.2022.801714openalex-snapshot

Opioid Receptor Expression in Colorectal Cancer: A Nested Matched Case-Control Study

inferred← citeshttps://doi.org/10.3389/fonc.2023.1146976openalex-snapshot

Ion channel gene GJB2 influences the intercellular communication by Up-regulating the SPP1 signaling pathway identified by the single-cell RNA sequencing in lung adenocarcinoma

inferred← citeshttps://doi.org/10.3389/fonc.2025.1594540openalex-snapshot

Comprehensive analysis of MGLL as a novel diagnostic and prognostic biomarker for clear cell renal cell carcinoma

inferred← citeshttps://doi.org/10.3389/fphar.2022.904909openalex-snapshot

CPDR: An R Package of Recommending Personalized Drugs for Cancer Patients by Reversing the Individual’s Disease-Related Signature

inferred← citeshttps://doi.org/10.3389/fphar.2023.1217488openalex-snapshot

Deciphering the role of NETosis-related signatures in the prognosis and immunotherapy of soft-tissue sarcoma using machine learning

inferred← citeshttps://doi.org/10.3389/fphar.2023.1229233openalex-snapshot

Integration analysis of senescence-related genes to predict prognosis and immunotherapy response in soft-tissue sarcoma: evidence based on machine learning and experiments

inferred← citeshttps://doi.org/10.3390/biology14070742openalex-snapshot

A TRIM Family-Based Strategy for TRIMCIV Target Prediction in a Pan-Cancer Context with Multi-Omics Data and Protein Docking Integration

inferred← citeshttps://doi.org/10.3390/cancers10090307openalex-snapshot

A Comprehensive Survey of Immune Cytolytic Activity-Associated Gene Co-Expression Networks across 17 Tumor and Normal Tissue Types

inferred← citeshttps://doi.org/10.3390/cancers11091248openalex-snapshot

Gastric Normal Adjacent Mucosa Versus Healthy and Cancer Tissues: Distinctive Transcriptomic Profiles and Biological Features

inferred← citeshttps://doi.org/10.3390/cancers12082077openalex-snapshot

Comprehensive Analysis of LincRNAs in Classical and Basal-Like Subtypes of Pancreatic Cancer

inferred← citeshttps://doi.org/10.3390/cancers12123799openalex-snapshot

A Topic Modeling Analysis of TCGA Breast and Lung Cancer Transcriptomic Data

inferred← citeshttps://doi.org/10.3390/cancers14071749openalex-snapshot

Elevated MACC1 Expression in Colorectal Cancer Is Driven by Chromosomal Instability and Is Associated with Molecular Subtype and Worse Patient Survival

inferred← citeshttps://doi.org/10.3390/cancers14194961openalex-snapshot

Gene Regulatory Network Characterization of Gastric Cancer’s Histological Subtypes: Distinctive Biological and Clinically Relevant Master Regulators

inferred← citeshttps://doi.org/10.3390/cancers17213454openalex-snapshot

TILDA-X: Transcriptome-Informed Lung Cancer Disparities via Explainable AI

inferred← citeshttps://doi.org/10.3390/diagnostics14192178openalex-snapshot

Enhancing Non-Small Cell Lung Cancer Survival Prediction through Multi-Omics Integration Using Graph Attention Network

inferred← citeshttps://doi.org/10.3390/diagnostics15192425openalex-snapshot

Next-Generation Sequencing: A Review of Its Transformative Impact on Cancer Diagnosis, Treatment, and Resistance Management

inferred← citeshttps://doi.org/10.3390/genes16010056openalex-snapshot

Pan-Cancer Upregulation of the FOXM1 Transcription Factor

inferred← citeshttps://doi.org/10.3390/genes17050547openalex-snapshot

Integrated Evolutionary and Multi-Omic Analysis of STAT Family Activation Across Solid Tumors

inferred← citeshttps://doi.org/10.3390/ijms20020296openalex-snapshot

High-Throughput Omics and Statistical Learning Integration for the Discovery and Validation of Novel Diagnostic Signatures in Colorectal Cancer

inferred← citeshttps://doi.org/10.3390/ijms22094563openalex-snapshot

Artificial Intelligence in Bulk and Single-Cell RNA-Sequencing Data to Foster Precision Oncology

inferred← citeshttps://doi.org/10.3390/jpm11100948openalex-snapshot

Integrated Molecular Characterization to Reveal the Association between Kynurenine 3-Monooxygenase Expression and Tumorigenesis in Human Breast Cancers

inferred← citeshttps://doi.org/10.3390/medicina62101971openalex-snapshot

Integrative Molecular Profiling and Single-Cell Characterization of LHFPL5 Reveal Cancer-Specific Regulatory Features in Clear Cell Renal Cell Carcinoma and Lung Adenocarcinoma

inferred← citeshttps://doi.org/10.48550/arxiv.1904.06366openalex-snapshot

Visualization of Labeled Mixed-featured Datasets

inferred← citeshttps://doi.org/10.6084/m9.figshare.16767520openalex-snapshot

Additional file 5 of Network propagation-based prioritization of long tail genes in 17 cancer types

inferred← citeshttps://doi.org/10.6084/m9.figshare.16767532openalex-snapshot

Additional file 9 of Network propagation-based prioritization of long tail genes in 17 cancer types

inferred← citeshttps://doi.org/10.6084/m9.figshare.22600045openalex-snapshot

Additional file 1 of Identifying cancer driver genes based on multi-view heterogeneous graph convolutional network and self-attention mechanism

inferred← citeshttps://doi.org/10.6084/m9.figshare.26602012openalex-snapshot

Additional file 1 of DeeP4med: deep learning for P4 medicine to predict normal and cancer transcriptome in multiple human tissues

inferred← citeshttps://doi.org/10.6084/m9.figshare.26602015openalex-snapshot

Additional file 2 of DeeP4med: deep learning for P4 medicine to predict normal and cancer transcriptome in multiple human tissues

inferred← citeshttps://doi.org/10.64898/2025.12.12.693322openalex-snapshot

Connecting spatial regions to clinical phenotypes by transferring knowledge from bulk patient data

inferred← citeshttps://doi.org/10.70675/b8144805z57bfz47c2zbf7ezb00ae1597604openalex-snapshot

Advancements in Graph Representation Learning and Applications in Computational Biology

inferred← citeshttps://doi.org/10.7150/ijbs.85126openalex-snapshot

Protection of c-Fos from autophagic degradation by PRMT1-mediated methylation fosters gastric tumorigenesis

inferred← citeshttps://doi.org/10.7555/jbr.34.20200027openalex-snapshot

From human genome epidemiology to systems epidemiology: current progress and future perspective

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