Topologically inferring active miRNA-mediated subpathways toward precise cancer classification by directed random walk

© 2019 The Authors. Published by FEBS Press and John Wiley & Sons Ltd..

Accurate predictions of classification biomarkers and disease status are indispensable for clinical cancer diagnosis and research. However, the robustness of conventional gene biomarkers is limited by issues with reproducibility across different measurement platforms and cohorts of patients. In this study, we collected 4775 samples from 12 different cancer datasets, which contained 4636 TCGA samples and 139 GEO samples. A new method was developed to detect miRNA-mediated subpathway activities by using directed random walk (miDRW). To calculate the activity of each miRNA-mediated subpathway, we constructed a global directed pathway network (GDPN) with genes as nodes. We then identified miRNAs with expression levels which were strongly inversely correlated with differentially expressed target genes in the GDPN. Finally, each miRNA-mediated subpathway activity was integrated with the topological information, differential levels of miRNAs and genes, expression levels of genes, and target relationships between miRNAs and genes. The results showed that the proposed method yielded a more robust and accurate overall performance compared with other existing pathway-based, miRNA-based, and gene-based classification methods. The high-frequency miRNA-mediated subpathways are more reliable in classifying samples and for selecting therapeutic strategies.

Errataetall:

ErratumIn: Mol Oncol. 2019 Nov;13(11):2512. - PMID 31670488

Medienart:

E-Artikel

Erscheinungsjahr:

2019

Erschienen:

2019

Enthalten in:

Zur Gesamtaufnahme - volume:13

Enthalten in:

Molecular oncology - 13(2019), 10 vom: 03. Okt., Seite 2211-2226

Sprache:

Englisch

Beteiligte Personen:

Ning, Ziyu [VerfasserIn]
Feng, Chenchen [VerfasserIn]
Song, Chao [VerfasserIn]
Liu, Wei [VerfasserIn]
Shang, Desi [VerfasserIn]
Li, Meng [VerfasserIn]
Wang, Qiuyu [VerfasserIn]
Zhao, Jianmei [VerfasserIn]
Liu, Yuejuan [VerfasserIn]
Chen, Jiaxin [VerfasserIn]
Yu, Xiaoyang [VerfasserIn]
Zhang, Jian [VerfasserIn]
Li, Chunquan [VerfasserIn]

Links:

Volltext

Themen:

Cancer biomarker
Classification
Journal Article
MiRNA-mediated subpathway
MicroRNAs
Research Support, Non-U.S. Gov't
Topological information

Anmerkungen:

Date Completed 29.06.2020

Date Revised 29.06.2020

published: Print-Electronic

ErratumIn: Mol Oncol. 2019 Nov;13(11):2512. - PMID 31670488

Citation Status MEDLINE

doi:

10.1002/1878-0261.12563

funding:

Förderinstitution / Projekttitel:

PPN (Katalog-ID):

NLM300190190