scholarly journals Integrative analysis of transcriptome-wide association study and gene expression profiling identifies candidate genes associated with stroke

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7435
Author(s):  
Jian Yang ◽  
Bin Yan ◽  
Yajuan Fan ◽  
Lihong Yang ◽  
Binbin Zhao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Candidate Genes ◽  
Expression Profiling ◽  
Enrichment Analysis ◽  
Integrative Analysis ◽  
Functional Gene ◽  
Gene Sets ◽  
Go Enrichment ◽  
Go Enrichment Analysis

Background Stroke is a major public health burden worldwide. Although genetic variation is known to play a role in the pathogenesis of stroke, the specific pathogenic mechanisms are still unclear. Transcriptome-wide association studies (TWAS) is a powerful approach to prioritize candidate risk genes underlying complex traits. However, this approach has not been applied in stroke. Methods We conducted an integrative analysis of TWAS using data from the MEGASTROKE Consortium and gene expression profiling to identify candidate genes for the pathogenesis of stroke. Gene ontology (GO) enrichment analysis was also conducted to detect functional gene sets. Results The TWAS identified 515 transcriptome-wide significant tissue-specific genes, among which SLC25A44 (P = 5.46E−10) and LRCH1 (P = 1.54E−6) were significant by Bonferroni test for stroke. After validation with gene expression profiling, 19 unique genes were recognized. GO enrichment analysis identified eight significant GO functional gene sets, including regulation of cell shape (P = 0.0059), face morphogenesis (P = 0.0247), and positive regulation of ATPase activity (P = 0.0256). Conclusions Our study identified multiple stroke-associated genes and gene sets, and this analysis provided novel insights into the genetic mechanisms underlying stroke.

scholarly journals Gene expression profiling reveals candidate genes for defining spider silk gland types

2021 ◽  
pp. 103594
Author(s):  
R. Crystal Chaw ◽  
Thomas H. Clarke ◽  
Peter Arensburger ◽  
Nadia A. Ayoub ◽  
Cheryl Y. Hayashi
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Candidate Genes ◽  
Expression Profiling ◽  
Spider Silk ◽  
Silk Gland

The Use of Gene-Expression Profiling to Identify Candidate Genes in Human Sepsis

2007 ◽  
Vol 176 (7) ◽  
pp. 676-684 ◽  
Author(s):  
Benjamin M. P. Tang ◽  
Anthony S. McLean ◽  
Ian W. Dawes ◽  
Stephen J. Huang ◽  
Ruby C. Y. Lin
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Candidate Genes ◽  
Expression Profiling ◽  
Human Sepsis

scholarly journals Transcriptome of Chicken Liver Tissues Reveals the Candidate Genes and Pathways Responsible for Adaptation into Two Different Climatic Conditions

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1076 ◽  
Author(s):  
Himansu Kumar ◽  
Asankadyr U. Iskender ◽  
Krishnamoorthy Srikanth ◽  
Hana Kim ◽  
Asankadyr T. Zhunushov ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Environmental Changes ◽  
Enrichment Analysis ◽  
Climatic Conditions ◽  
False Discovery ◽  
Go Enrichment ◽  
Liver Transcriptome ◽  
Commercial Chicken ◽  
Go Enrichment Analysis ◽  
Catabolic Process

RNA sequencing was used to profile the liver transcriptome of a Korean commercial chicken (Hanhyup) at two different environments (Korea and Kyrgyzstan) to investigate their role during acclimatization into different climatic conditions. Ten samples from each location were analyzed to identify candidate genes that respond to environmental changes such as altitude, humidity, temperature, etc. Sequencing reads were preprocessed, aligned with the reference genome, assembled and expressions were estimated through bioinformatics approaches. At a false discovery rate (FDR) <0.05 and fold change (FC) ≥2, we found 315 genes were DE. Out of 315 DE genes, 174 and 141 were up- and down-regulated respectively in the Kyrgyz environment. Gene ontology (GO) enrichment analysis showed that the differentially expressed genes (DEGs) were associated with energy metabolism such as pyruvate and lactate metabolic processes, and glycerol catabolic process. Similarly, KEGG pathway analysis indicated pyruvate metabolism, glycolysis/gluconeogenesis, biosynthesis, citrate cycles were differentially enriched in the Kyrgyz environment. DEGs like TSKU, VTG1, SGK, CDK2, etc. in such pathways are highly involved in the adaptation of organisms into diverse climatic conditions. Our investigation may serve as a resource for the chicken industry, especially in exporting Hanhyup chicken from Korea to other countries.

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