Integrative analysis of multi-omics data for identifying multi-markers for diagnosing pancreatic cancer

BMC Genomics
Min-Seok KwonTaesung Park

Abstract

microRNA (miRNA) expression plays an influential role in cancer classification and malignancy, and miRNAs are feasible as alternative diagnostic markers for pancreatic cancer, a highly aggressive neoplasm with silent early symptoms, high metastatic potential, and resistance to conventional therapies. In this study, we evaluated the benefits of multi-omics data analysis by integrating miRNA and mRNA expression data in pancreatic cancer. Using support vector machine (SVM) modelling and leave-one-out cross validation (LOOCV), we evaluated the diagnostic performance of single- or multi-markers based on miRNA and mRNA expression profiles from 104 PDAC tissues and 17 benign pancreatic tissues. For selecting even more reliable and robust markers, we performed validation by independent datasets from the Gene Expression Omnibus (GEO) data depository. For validation, miRNA activity was estimated by miRNA-target gene interaction and mRNA expression datasets in pancreatic cancer. Using a comprehensive identification approach, we successfully identified 705 multi-markers having powerful diagnostic performance for PDAC. In addition, these marker candidates annotated with cancer pathways using gene ontology analysis. Our prediction models hav...Continue Reading

References

May 15, 2004·Nature Reviews. Genetics·David P Bartel, Chang-Zheng Chen
May 17, 2006·Genes & Development·Aram F HezelRonald A Depinho
Jun 1, 2006·Nature Genetics·Nikolaus Rajewsky
Mar 30, 2007·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Elisa WurmbachJosep M Llovet
Aug 19, 2007·Cancer Research·Charles D JohnsonFrank J Slack
Sep 26, 2007·Nature Genetics·Michael KerteszEran Segal
Dec 11, 2007·Trends in Pharmacological Sciences·Angelika KuehbacherStefanie Dimmeler
Mar 6, 2009·Nature Reviews. Cancer·Milena S NicolosoGeorge A Calin
Mar 7, 2009·Breast Cancer Research and Treatment·Dung-Tsa ChenTimothy Yeatman
May 2, 2009·Pancreatology : Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]·Kwang-Hyuck LeeAnirban Maitra
May 23, 2009·Cell Death and Differentiation·H Hermeking
Jun 25, 2009·International Journal of Cancer. Journal International Du Cancer·Thomas GreitherHelge Taubert
Oct 5, 2010·Nature Reviews. Drug Discovery·Ramiro GarzonCarlo M Croce
Nov 13, 2010·Nucleic Acids Research·Sheng-Da HsuHsien-Da Huang
Sep 29, 2011·International Journal of Cancer. Journal International Du Cancer·Johanna B MundingStephan A Hahn
Jan 21, 2012·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Timothy R DonahueHong Wu
Oct 3, 2012·Journal of Proteomics·Alison ChanIvan M Blasutig
Nov 30, 2012·Nucleic Acids Research·Tanya BarrettAlexandra Soboleva
Jul 23, 2013·Nature Protocols·Huaiyu MiPaul D Thomas
Feb 25, 2014·Cancer Letters·Sanjeev K SrivastavaAjay P Singh

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Citations

Jan 31, 2019·Genes·Bilal MirzaPeipei Ping
Nov 28, 2019·Epigenomes·Rahul R SinghRick J Jansen
Jan 10, 2020·Computational and Mathematical Methods in Medicine·Jayeon LimSungHwan Kim
Apr 23, 2020·Frontiers in Oncology·Guillermo de Anda-Jáuregui, Enrique Hernández-Lemus
Apr 17, 2018·Briefings in Bioinformatics·Lan ZhaoMaarten F Bijlsma
Feb 6, 2017·BioData Mining·SungHwan KimJa-Yong Koo
Apr 25, 2020·Cancers·Ariadna Martín-BlázquezOctavio Caba
May 11, 2018·BMC Bioinformatics·Yongkang KimTaesung Park
Mar 20, 2021·Scientific Reports·Muta Tah HiraMosharraf Sarker
Apr 2, 2021·Biotechnology Advances·Parminder S ReelEmily Jefferson
Aug 28, 2021·Omics : a Journal of Integrative Biology·K J SindhuDevarajan Karunagaran

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Software Mentioned

PITA
TargetScan
miRvestigator
Cytoscape
PANTHER
R
SVM
LOOCV

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