Tissue-Specific Molecular Biomarker Signatures of Type 2 Diabetes: An Integrative Analysis of Transcriptomics and Protein-Protein Interaction Data

Omics : a Journal of Integrative Biology
Beste CalimliogluKazim Yalcin Arga

Abstract

Type 2 diabetes mellitus is a major global public health burden. A complex metabolic disease, type 2 diabetes affects multiple different tissues, demanding a "systems medicine" approach to biomarker and novel diagnostic discovery, not to mention data integration across omics-es. In the present study, transcriptomics data from different tissues including beta-cells, pancreatic islets, arterial tissue, peripheral blood mononuclear cells, liver, and skeletal muscle of 228 samples were integrated with protein-protein interaction data and genome scale metabolic models to unravel the molecular and tissue-specific biomarker signatures of type 2 diabetes mellitus. Classifying differentially expressed genes, reconstruction and topological analysis of active protein-protein interaction subnetworks indicated that genomic reprogramming depends on the type of tissue, whereas there are common signatures at different levels. Among all tissue and cell types, Mannosidase Alpha Class 1A Member 2 was the common signature at genome level, and activation-ppara reaction, which stimulates a nuclear receptor protein, was found out as the mutual reporter at metabolic level. Moreover, miR-335 and miR-16-5p came into prominence in regulation of transcrip...Continue Reading

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Citations

Dec 10, 2015·Journal of Neural Transmission·Vural ÖzdemirSanjeeva Srivastava
May 20, 2016·Journal of Theoretical Biology·Kubra KaragozKazim Yalcin Arga
Jun 25, 2016·Systems Biology in Reproductive Medicine·Medi KoriKazim Yalcin Arga
Jun 3, 2017·Systems Biology in Reproductive Medicine·Esra GovKazim Yalcin Arga
Jun 18, 2017·The Journal of Obstetrics and Gynaecology Research·Ya-Lei CaoXiu-Juan Dong
Jun 22, 2018·Omics : a Journal of Integrative Biology·Tania IslamNurul Haque Mollah
Jul 14, 2018·Omics : a Journal of Integrative Biology·Siqi GeWei Wang
Apr 5, 2017·Omics : a Journal of Integrative Biology·Dilara AyyildizKazim Yalcin Arga
Oct 20, 2017·Omics : a Journal of Integrative Biology·Beste TuranliKazim Yalcin Arga
Aug 31, 2018·PloS One·Aoife M CurranLorraine Brennan
Apr 16, 2019·Omics : a Journal of Integrative Biology·Elif Dereli EkeBarbara Di Camillo
Jun 1, 2018·International Journal of Endocrinology·Elisa GuarinoFrancesco Dotta
Jul 10, 2019·Expert Review of Precision Medicine and Drug Development·Tongqi QianYujin Hoshida
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Jul 12, 2017·Omics : a Journal of Integrative Biology·Dilara Ayyildiz, Kazim Yalcin Arga
Oct 1, 2019·Seminars in Cancer Biology·Beste TuranliAdil Mardinoglu
Jan 2, 2021·Journal of Clinical Medicine·Enrique Almanza-AguileraOlga Castañer
Apr 30, 2021·Progress in Neuro-psychopharmacology & Biological Psychiatry·Dan LiuBing Cao

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Datasets Mentioned

BETA
GSE9006
GSE25724

Methods Mentioned

BETA
amputations

Software Mentioned

MBRole
BIOMET Toolbox
bioDBnet
Cytoscape
GENOMATIX
DAVID

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