Bioinformatics Methodologies to Identify Interactions Between Type 2 Diabetes and Neurological Comorbidities | |
Rahman, Md Habibur2,3,4; Peng, Silong2,3; Hu, Xiyuan2,3; Chen, Chen2,3; Uddin, Shahadat5,6; Quinn, Julian M. W.1; Moni, Mohammad Ali1,7 | |
刊名 | IEEE ACCESS |
2019 | |
期号 | 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 |
DOI | 10.1109/ACCESS.2019.2960037 |
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. |
资助项目 | National Natural Science Foundation of China[61571438] ; Chinese Academy of Sciences (CAS)-The World Academy of Sciences (TWAS)[2016CTF014] |
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 |
WOS研究方向 | Computer Science ; Engineering ; Telecommunications |
语种 | 英语 |
出版者 | IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC |
WOS记录号 | WOS:000509587800011 |
内容类型 | 期刊论文 |
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.Garvan Inst Med Res, Bone Biol Div, Darlinghurst, NSW 2010, Australia 2.Chinese Acad Sci, Inst Automat, Beijing 100190, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100190, Peoples R China 4.Islamic Univ, Dept Comp Sci & Engn, Kushtia 7003, Bangladesh 5.Univ Sydney, Fac Engn, Complex Syst Res Grp, Sydney, NSW 2008, Australia 6.Univ Sydney, Fac Engn, Project Management Program, Sydney, NSW 2008, Australia 7.Univ Sydney, Fac Med & Hlth, Sch Med Sci, Sydney, NSW 2008, Australia |
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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