Copyright
©The Author(s) 2020. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Clin Oncol. Sep 24, 2020; 11(9): 679-704
Published online Sep 24, 2020. doi: 10.5306/wjco.v11.i9.679
Published online Sep 24, 2020. doi: 10.5306/wjco.v11.i9.679
Powerful quantifiers for cancer transcriptomics
Dumitru Andrei Iacobas, Personalized Genomics Laboratory, CRI Center for Computational Systems Biology, Roy G Perry College of Engineering, Prairie View A&M University, Prairie View, TX 77446, United States
Author contributions: Iacobas DA performed the analyses and wrote the paper.
Conflict-of-interest statement: Authors declare no conflict of interests for this article.
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/
Corresponding author: Dumitru Andrei Iacobas, MSc, PhD, Director, Professor, Personalized Genomics Laboratory, CRI Center for Computational Systems Biology, Roy G Perry College of Engineering, Prairie View A&M University, Prairie View, TX 77446, United States. daiacobas@pvamu.edu
Received: March 15, 2020
Peer-review started: March 15, 2020
First decision: April 18, 2020
Revised: June 6, 2020
Accepted: July 1, 2020
Article in press: July 1, 2020
Published online: September 24, 2020
Peer-review started: March 15, 2020
First decision: April 18, 2020
Revised: June 6, 2020
Accepted: July 1, 2020
Article in press: July 1, 2020
Published online: September 24, 2020
Core Tip
Core Tip: The Genomic Fabric Paradigm was developed as a holistic alternative to the biomarker approach of cancer transcriptomics. The genomic fabric of a functional pathway is the transcriptome associated with the most interconnected and stably expressed gene network responsible for that pathway. We present the associated analytical tools to characterize the topology, remodeling during cancer progression and in response to a therapy, and interplay of the genomic fabrics and identify the most legitimate targets in cancer gene therapy. The analyses are illustrated with examples from our transcriptomic studies on human cancer tissues and cell lines.