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Bioinformatics Methodologies to Identify Interactions Between Type 2 Diabetes and Neurological Comorbidities

文献类型：期刊论文

作者Rahman, Md Habibur1,6,7; Peng, Silong1,6; Hu, Xiyuan1,6; Chen, Chen1,6; Uddin, Shahadat2,3; Quinn, Julian M. W.5; Moni, Mohammad Ali4,5
刊名IEEE ACCESS
出版日期2019
卷号7页码:183948-183970
关键词Bioinformatics comorbidities gene set enrichment analysis gene ontology neurological disease pathway semantic similarity Type 2 diabetes
ISSN号2169-3536
DOI10.1109/ACCESS.2019.2960037
通讯作者Moni, Mohammad Ali(mohammad.moni@sydney.edu.au)
英文摘要Type 2 diabetes (T2D) is a chronic metabolic disorder characterised by high blood sugar and insulin insensitivity which greatly increases the risk of developing neurological diseases (NDs). The co-existence of T2D and comorbidities such as NDs can complicate or even cause the failure of standard treatments for those diseases. Comorbidities can be both causally linked and influence each other's development through genetic, molecular, environmental or lifestyle-based risk factors that they share. For T2D and NDs, such underlying common molecular mechanisms remain elusive but large amounts of molecular data accumulated on these diseases enable analytical approaches to identify their interconnected pathways. Here, we propose a framework to explore possible comorbidity interactions between a pair of diseases using a bioinformatic examination of the cellular pathways involved and explore this framework for T2D and NDs with analyses of a large number of publicly available gene expression datasets from tissues affected by these diseases. We designed a bioinformatics pipeline to analyse, utilize and combine gene expression, Gene Ontology (GO) and molecular pathway data by incorporating Gene Set Enrichment Analysis and Semantic Similarity. Our bioinformatics methodology was implemented in R, available at https://github.com/HabibUCAS/T2D_Comorbidity. We identified genes with altered expression shared by T2D and NDs as well as GOs and molecular pathways these diseases share. We also computed the proximity between T2D and neurological pathologies using these genes and GO term semantic similarity. Thus, our method has generated new insights into disease mechanisms important for both T2D and NDs that may mediate their interaction. Our bioinformatics pipeline could be applied to other co-morbidities to identify possible interactions and causal relationships between them.
WOS关键词ENDOPLASMIC-RETICULUM STRESS ; ACTIVATED SIGNALING PATHWAYS ; MONOUNSATURATED FATTY-ACIDS ; SET ENRICHMENT ANALYSIS ; BETA-CELL TURNOVER ; SEMANTIC SIMILARITY ; ALZHEIMERS-DISEASE ; OXIDATIVE STRESS ; GENE-EXPRESSION ; R PACKAGE
资助项目National Natural Science Foundation of China[61571438] ; Chinese Academy of Sciences (CAS)-The World Academy of Sciences (TWAS)[2016CTF014]
WOS研究方向Computer Science ; Engineering ; Telecommunications
语种英语
WOS记录号WOS:000509587800011
出版者IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
资助机构National Natural Science Foundation of China ; Chinese Academy of Sciences (CAS)-The World Academy of Sciences (TWAS)
源URL[http://ir.ia.ac.cn/handle/173211/29507]  
专题自动化研究所_智能制造技术与系统研究中心_多维数据分析团队
通讯作者Moni, Mohammad Ali
作者单位1.Univ Chinese Acad Sci, Beijing 100190, Peoples R China
2.Univ Sydney, Fac Engn, Complex Syst Res Grp, Sydney, NSW 2008, Australia
3.Univ Sydney, Fac Engn, Project Management Program, Sydney, NSW 2008, Australia
4.Univ Sydney, Fac Med & Hlth, Sch Med Sci, Sydney, NSW 2008, Australia
5.Garvan Inst Med Res, Bone Biol Div, Darlinghurst, NSW 2010, Australia
6.Chinese Acad Sci, Inst Automat, Beijing 100190, Peoples R China
7.Islamic Univ, Dept Comp Sci & Engn, Kushtia 7003, Bangladesh
推荐引用方式
GB/T 7714		 Rahman, Md Habibur,Peng, Silong,Hu, Xiyuan,et al. Bioinformatics Methodologies to Identify Interactions Between Type 2 Diabetes and Neurological Comorbidities[J]. IEEE ACCESS,2019,7:183948-183970.
APA Rahman, Md Habibur.,Peng, Silong.,Hu, Xiyuan.,Chen, Chen.,Uddin, Shahadat.,...&Moni, Mohammad Ali.(2019).Bioinformatics Methodologies to Identify Interactions Between Type 2 Diabetes and Neurological Comorbidities.IEEE ACCESS,7,183948-183970.
MLA Rahman, Md Habibur,et al."Bioinformatics Methodologies to Identify Interactions Between Type 2 Diabetes and Neurological Comorbidities".IEEE ACCESS 7(2019):183948-183970.

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来源：自动化研究所

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