Pathways and Genes under positive selection in metabolic ... · Gene Set Enrichment Analysis (GSEA)...
Transcript of Pathways and Genes under positive selection in metabolic ... · Gene Set Enrichment Analysis (GSEA)...
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Pathways and Genes under positive selection inmetabolic diseases
Alexandra Vatsiou
3rd International Conference on Epidemiology and Public Health
August 2015
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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Positive Selection
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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Why do we study positive selection?
Ingram et al. 2009
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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Gene Set Enrichment Analysis (GSEA)
Data
1 SNP data: Hapmap phase II (3 populations (CEU, YRI,CHB+JTP)
2 Gene data: Entrez NCBI database on the 5/2014 (Number ofgenes: 27081)
3 Gene Sets: Biosystems database on the 5/2014. (Number ofpathways: 2362)
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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Gene Set Enrichment Analysis (GSEA)
Data
1 SNP data: Hapmap phase II (3 populations (CEU, YRI,CHB+JTP)
2 Gene data: Entrez NCBI database on the 5/2014 (Number ofgenes: 27081)
3 Gene Sets: Biosystems database on the 5/2014. (Number ofpathways: 2362)
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
![Page 6: Pathways and Genes under positive selection in metabolic ... · Gene Set Enrichment Analysis (GSEA) Data 1 SNP data: Hapmap phase II (3 populations (CEU, YRI, CHB+JTP) 2 Gene data:](https://reader030.fdocuments.in/reader030/viewer/2022041106/5f092b0a7e708231d4258cc1/html5/thumbnails/6.jpg)
How to detect positive selection on pathways?
Detect selection on SNPs (Selection Scores)
Assign SNPs to genes (Gene score)
SEL-GSEA (Daub et al. 2013)
Gowinda (Kofler&Schlotterer ,2012)
Gene Set Enrichment Analysis in Pathways
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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SEL-GSEA
1 Python tool for Gene and Gene Set Enrichment Analysisfollowing Daub et al. (2013) methodology
2 Using SNP data and a gene-set list
3 User-friendly and flexible
4 Freely available:https://github.com/INTERCROSSING/SEL_GSEA
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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Which method to use to detect selection on SNPs?
Detect selection on SNPs (Selection Scores)???
Assign SNPs to genes (Gene score)
SEL-GSEA (Daub et al. 2013)
Gowinda (Kofler&Schlotterer ,2012)
Gene Set Enrichment Analysis in Pathways
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
![Page 9: Pathways and Genes under positive selection in metabolic ... · Gene Set Enrichment Analysis (GSEA) Data 1 SNP data: Hapmap phase II (3 populations (CEU, YRI, CHB+JTP) 2 Gene data:](https://reader030.fdocuments.in/reader030/viewer/2022041106/5f092b0a7e708231d4258cc1/html5/thumbnails/9.jpg)
Which method to use to detect selection?
Detect selection on SNPs using XPCLR and iHS
Assign SNPs to genes (Gene score)
SEL-GSEA (Daub et al. 2013)
Gowinda (Kofler&Schlotterer ,2012)
Gene Set Enrichment Analysis in Pathways
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
![Page 10: Pathways and Genes under positive selection in metabolic ... · Gene Set Enrichment Analysis (GSEA) Data 1 SNP data: Hapmap phase II (3 populations (CEU, YRI, CHB+JTP) 2 Gene data:](https://reader030.fdocuments.in/reader030/viewer/2022041106/5f092b0a7e708231d4258cc1/html5/thumbnails/10.jpg)
Results of GSEA
XPCLR + SEL-GSEA
iHS + Gowinda
XPCLR + Gowinda
iHS + SEL-GSEA
7
12
5
152 4
1
1
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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What about metabolic diseases?
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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From hunting ... to ... burgers
1 Glycolysis and gluconeogenesis (4.2e-05)
2 Signal attenuation (0.0003)
3 Glucose transport (0.003)
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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From hunting ... to ... burgers
1 Glycolysis and gluconeogenesis (4.2e-05)
2 Signal attenuation (0.0003)
3 Glucose transport (0.003)
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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Gene Analysis
683 genes directly or indirectly associated with:
1 obesity or
2 metabolic syndrome or
3 diabetes
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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Positively selected genes in metabolic diseases
1 25 candidate genes for positive selection
2 12 of them play a risk role
3 7 of them play a protective role
4 10 of them were detected to be under positive selection before
5 15 new candidates for metabolic diseases
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Take Home Message
1 multifactorial diseases
2 study the whole system
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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Acknowledgements
Eric Bazin (LECA, Grenoble), Oscar Gaggiotti (LECA, Grenoble/St Andrews, UK)
Thank you for your attention.
Any Questions?
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases
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Acknowledgements
Eric Bazin (LECA, Grenoble), Oscar Gaggiotti (LECA, Grenoble/St Andrews, UK)
Thank you for your attention.
Any Questions?
Alexandra Vatsiou Pathways and Genes under positive selection in metabolic diseases