Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Diagnostic comparisons of PTSD and complex PTSD in clinical adolescents: Detection rates and ACEs as risk factors.

European journal of psychotraumatology·2026

Same author

Plumbagin Induces Ferroptosis in Nonfunctioning Pituitary Adenomas via Nrf2/FTH1-Dependent Ferritinophagy.

Drug design, development and therapy·2026

Same author

ReadChop: a high-performance demultiplexer for long-read sequencing data.

Bioinformatics (Oxford, England)·2026

Same author

Non-classical NMDAR subunit GluN3A in a specialized hippocampal region regulates stress-coping strategies in male mice.

Communications biology·2026

Same author

Study on Influencing Factors for Short-Term Symptom Resolution After Reinforced Radiculoplasty for Sacral Cysts: Focus on Bladder-Bowel Dysfunction.

Journal of clinical medicine·2026

Same author

Multi-Responsive SEBS/MXene Janus Membranes Enabling Piezoelectric Energy Harvesting, Humidity Sensing, and Infrared Stealth.

Nano-micro letters·2026

Search research articles

Related Experiment Video

Updated: Oct 9, 2025

Cancer-Associated Fibroblasts from Mouse Mammary Tumors as Tools for Molecular and Computational Studies

Cancer-Associated Fibroblasts from Mouse Mammary Tumors as Tools for Molecular and Computational Studies

Published on: July 3, 2025

Comprehensive Analysis of Large-Scale Transcriptomes from Multiple Cancer Types.

Baoting Nong¹, Mengbiao Guo¹, Weiwen Wang²

¹Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.

|December 24, 2021

Summary

PipeOne integrates multi-modal RNA sequencing data for cancer research. This workflow identifies key cancer features and subtypes, revealing shared and specific disease mechanisms across multiple cancer types.

Keywords:

RNA-seq workflow TCGA alternative splicing cancer subtyping feature prioritization mitochondria ribosome somatic mutation

More Related Videos

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases

Published on: May 17, 2019

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Published on: April 5, 2018

Related Experiment Videos

Last Updated: Oct 9, 2025

Cancer-Associated Fibroblasts from Mouse Mammary Tumors as Tools for Molecular and Computational Studies

Cancer-Associated Fibroblasts from Mouse Mammary Tumors as Tools for Molecular and Computational Studies

Published on: July 3, 2025

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases

Published on: May 17, 2019

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Published on: April 5, 2018

Area of Science:

Genomics
Bioinformatics
Cancer Research

Background:

Transcriptional regulation abnormalities are common in cancers.
Integrating multi-modal RNA sequencing (RNA-seq) data remains a challenge for uncovering cancer mechanisms.

Purpose of the Study:

To present PipeOne, a comprehensive workflow for large-scale transcriptome data analysis.
To integrate multi-modal RNA-seq data for improved disease mechanism discovery and patient stratification.

Main Methods:

Developed PipeOne, a cross-platform workflow using Nextflow for reproducible analysis.
Integrated eight tools for RNA-seq data processing and feature extraction.
Employed a random forest algorithm for patient stratification based on multi-modal information.

Main Results:

Applied PipeOne to five cancer types (colon, liver, kidney, stomach, thyroid; n=2024), identifying key dysregulated features (e.g., PVT1 expression, ABI3BP splicing) and pathways (e.g., liver/kidney dysfunction).
Discovered clinically relevant patient subtypes in four cancers, often linked to specific driver mutations (TP53, BRAF, etc.) and biological processes (ribosome biogenesis, mitochondrial function).

Conclusions:

PipeOne efficiently analyzes diverse cancer types, revealing both shared and cancer-specific contributing factors.
The workflow is adaptable for other diseases and available for public use.