Next Article in Journal
Could Vitamin D Analogues Be Used to Target Leukemia Stem Cells?
Next Article in Special Issue
Gene Set−Based Integrative Analysis Revealing Two Distinct Functional Regulation Patterns in Four Common Subtypes of Epithelial Ovarian Cancer
Previous Article in Journal
The Complete Chloroplast Genome Sequences of the Medicinal Plant Pogostemon cablin
Previous Article in Special Issue
The Clinical Significance of the Insulin-Like Growth Factor-1 Receptor Polymorphism in Non-Small-Cell Lung Cancer with Epidermal Growth Factor Receptor Mutation
Article Menu
Issue 6 (June) cover image

Export Article

Open AccessArticle
Int. J. Mol. Sci. 2016, 17(6), 886; doi:10.3390/ijms17060886

Gene Set-Based Functionome Analysis of Pathogenesis in Epithelial Ovarian Serous Carcinoma and the Molecular Features in Different FIGO Stages

1
Institute of Oral Biology, National Yang-Ming University, Taipei 112, Taiwan
2
School of Medicine, National Yang-Ming University, Taipei 112, Taiwan
3
Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 112, Taiwan
4
Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan
5
Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan
6
Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei 112, Taiwan
7
Department & Institute of Pharmacology, National Yang-Ming University, Taipei 112, Taiwan
*
Author to whom correspondence should be addressed.
Academic Editor: William Chi-shing Cho
Received: 13 April 2016 / Revised: 7 May 2016 / Accepted: 16 May 2016 / Published: 6 June 2016
(This article belongs to the Special Issue Big Data for Oncology)
View Full-Text   |   Download PDF [5249 KB, uploaded 6 June 2016]   |  

Abstract

Serous carcinoma (SC) is the most common subtype of epithelial ovarian carcinoma and is divided into four stages by the Federation of Gynecologists and Obstetrics (FIGO) staging system. Currently, the molecular functions and biological processes of SC at different FIGO stages have not been quantified. Here, we conducted a whole-genome integrative analysis to investigate the functions of SC at different stages. The function, as defined by the GO term or canonical pathway gene set, was quantified by measuring the changes in the gene expressional order between cancerous and normal control states. The quantified function, i.e., the gene set regularity (GSR) index, was utilized to investigate the pathogenesis and functional regulation of SC at different FIGO stages. We showed that the informativeness of the GSR indices was sufficient for accurate pattern recognition and classification for machine learning. The function regularity presented by the GSR indices showed stepwise deterioration during SC progression from FIGO stage I to stage IV. The pathogenesis of SC was centered on cell cycle deregulation and accompanied with multiple functional aberrations as well as their interactions. View Full-Text
Keywords: epithelial serous ovarian cancer; function; integrative analysis; gene expression microarray; gene set; machine learning epithelial serous ovarian cancer; function; integrative analysis; gene expression microarray; gene set; machine learning
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Chang, C.-M.; Chuang, C.-M.; Wang, M.-L.; Yang, M.-J.; Chang, C.-C.; Yen, M.-S.; Chiou, S.-H. Gene Set-Based Functionome Analysis of Pathogenesis in Epithelial Ovarian Serous Carcinoma and the Molecular Features in Different FIGO Stages. Int. J. Mol. Sci. 2016, 17, 886.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top