Next Article in Journal
Hydrogen-Bonding Interactions in Luminescent Quinoline-Triazoles with Dominant 1D Crystals
Next Article in Special Issue
Identification of DNA-Binding Proteins Using Mixed Feature Representation Methods
Previous Article in Journal
Polyyne-Enriched Extract from Oplopanax elatus Significantly Ameliorates the Progression of Colon Carcinogenesis in ApcMin/+ Mice
Previous Article in Special Issue
EPuL: An Enhanced Positive-Unlabeled Learning Algorithm for the Prediction of Pupylation Sites
Article Menu
Issue 10 (October) cover image

Export Article

Open AccessArticle
Molecules 2017, 22(10), 1599;

Integrative Pathway Analysis of Genes and Metabolites Reveals Metabolism Abnormal Subpathway Regions and Modules in Esophageal Squamous Cell Carcinoma

1,2,†,* , 1,†,* , 3,†
Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Department of Computer Science and Technology, Heilongjiang University, Harbin 150080, China
These authors contributed equally to this work.
Authors to whom correspondence should be addressed.
Received: 22 August 2017 / Revised: 20 September 2017 / Accepted: 20 September 2017 / Published: 22 September 2017
(This article belongs to the Special Issue Computational Analysis for Protein Structure and Interaction)
Full-Text   |   PDF [2928 KB, uploaded 22 September 2017]   |  


Aberrant metabolism is one of the main driving forces in the initiation and development of ESCC. Both genes and metabolites play important roles in metabolic pathways. Integrative pathway analysis of both genes and metabolites will thus help to interpret the underlying biological phenomena. Here, we performed integrative pathway analysis of gene and metabolite profiles by analyzing six gene expression profiles and seven metabolite profiles of ESCC. Multiple known and novel subpathways associated with ESCC, such as ‘beta-Alanine metabolism’, were identified via the cooperative use of differential genes, differential metabolites, and their positional importance information in pathways. Furthermore, a global ESCC-Related Metabolic (ERM) network was constructed and 31 modules were identified on the basis of clustering analysis in the ERM network. We found that the three modules located just to the center regions of the ERM network—especially the core region of Module_1—primarily consisted of aldehyde dehydrogenase (ALDH) superfamily members, which contributes to the development of ESCC. For Module_4, pyruvate and the genes and metabolites in its adjacent region were clustered together, and formed a core region within the module. Several prognostic genes, including GPT, ALDH1B1, ABAT, WBSCR22 and MDH1, appeared in the three center modules of the network, suggesting that they can become potentially prognostic markers in ESCC. View Full-Text
Keywords: metabolic pathway; network; ESCC metabolic pathway; network; ESCC

Graphical abstract

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


Share & Cite This Article

MDPI and ACS Style

Li, C.; Wang, Q.; Ma, J.; Shi, S.; Chen, X.; Yang, H.; Han, J. Integrative Pathway Analysis of Genes and Metabolites Reveals Metabolism Abnormal Subpathway Regions and Modules in Esophageal Squamous Cell Carcinoma. Molecules 2017, 22, 1599.

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



[Return to top]
Molecules EISSN 1420-3049 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top