Additional file 1: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Juan Fernรกndez-Tajes (6517679)
Kyle Gaulton (497560)
Martijn Bunt (6517658)
Jason Torres (6517661)
Matthias Thurner (6517664)
Anubha Mahajan (206768)
Anna Gloyn (3810184)
Kasper Lage (42180)
Mark McCarthy (157523)

Publication date

March 2019

DOI

10.6084/m9.figshare.7900988.v1

Abstract

Table S1. 101 loci and candidate genes by loci used to calculate the positional candidacy score (PCS). Table S2. DisGeNet results. Table S3. Gene set enrichment analysis by community. Table S4. Gene set enrichment analysis in beta cell islet-specific network. Table S5. List of genes from the seven T2D GWAS locus subset networks. (ZIP 360 kb

Extracted data

We use cookies to provide a better user experience.

Data Protection

Additional file 1: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Juan Fernรกndez-Tajes (6517679)
Kyle Gaulton (497560)
Martijn Bunt (6517658)
Jason Torres (6517661)
Matthias Thurner (6517664)
Anubha Mahajan (206768)
Anna Gloyn (3810184)
Kasper Lage (42180)
Mark McCarthy (157523)

Open link

Publication date

March 2019

DOI

10.6084/m9.figshare.7900988.v1

Abstract

Extracted data

Lőrinc Pongor (3574811)
Máté Kormos (3574814)
Christos Hatzis (565382)
Lajos Pusztai (78763)
András Szabó (3034779)
Balázs Győrffy (110652)

October 2015

The complete set of all genes included in the metagenes for each of the putative driver genes listed...

Additional file 2: of Genome-wide association studies for diabetic macular edema and proliferative diabetic retinopathy

Patricia Graham (3207738)
Georgia Kaidonis (5185217)
Sotoodeh Abhary (252379)
Mark Gillies (700017)
Mark Daniell (506570)
Rohan Essex (5185220)
John Chang (364595)
Stewart Lake (5185223)
Bishwanath Pal (5185214)
Alicia Jenkins (804281)
Alex Hewitt (3457262)
Ecosse Lamoureux (827837)
Philip Hykin (450726)
Nikolai Petrovsky (252418)
Matthew Brown (307585)
Jamie Craig (3410213)
Kathryn Burdon (3410231)

May 2018

Association results for Proliferative Diabetic Retinopathy GWAS. Only SNPs with pâ<âÂ 0.05 are i...

Additional file 1: of Pancreatic cancer as a sentinel for hereditary cancer predisposition

Erin Young (5454515)
Bryony Thompson (5454527)
Deborah Neklason (5454509)
Matthew Firpo (5454512)
Theresa Werner (5454542)
Russell Bell (4539349)
Justin Berger (272454)
Alison Fraser (5454530)
Amanda Gammon (5454539)
Cathryn Koptiuch (5454518)
Wendy Kohlmann (5454536)
Leigh Neumayer (5454533)
David Goldgar (29053)
Sean Mulvihill (5454524)
Lisa Cannon-Albright (523061)
Sean Tavtigian (5454521)

June 2018

Table S1. contains the list of the genes used in the study, as well as indicators for which pathway ...

Additional file 9: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Juan Fernรกndez-Tajes (6517679)
Kyle Gaulton (497560)
Martijn Bunt (6517658)
Jason Torres (6517661)
Matthias Thurner (6517664)
Anubha Mahajan (206768)
Anna Gloyn (3810184)
Kasper Lage (42180)
Mark McCarthy (157523)

March 2019

Figure S8. Sub-networks for seven T2D GWAS locus subset categories in the islet-specific network. (P...

Additional file 8: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Juan Fernรกndez-Tajes (6517679)
Kyle Gaulton (497560)
Martijn Bunt (6517658)
Jason Torres (6517661)
Matthias Thurner (6517664)
Anubha Mahajan (206768)
Anna Gloyn (3810184)
Kasper Lage (42180)
Mark McCarthy (157523)

March 2019

Figure S7. GWAS signal enrichment in the PPI-generic network derived from T2D GWAs subsets. (TIFF 30...

Additional file 10: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Juan Fernรกndez-Tajes (6517679)
Kyle Gaulton (497560)
Martijn Bunt (6517658)
Jason Torres (6517661)
Matthias Thurner (6517664)
Anubha Mahajan (206768)
Anna Gloyn (3810184)
Kasper Lage (42180)
Mark McCarthy (157523)

March 2019

Figure S9. Sub-networks for seven T2D GWAS locus subset categories in the PPI generic network. (PDF ...

Additional file 4: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Juan Fernรกndez-Tajes (6517679)
Kyle Gaulton (497560)
Martijn Bunt (6517658)
Jason Torres (6517661)
Matthias Thurner (6517664)
Anubha Mahajan (206768)
Anna Gloyn (3810184)
Kasper Lage (42180)
Mark McCarthy (157523)

March 2019

Figure S3. Distribution of PCS and correlation of semantic and risk variant link scores. (TIFF 3072 ...

Additional file 1: Table S1. of Susceptibility to type 2 diabetes may be modulated by haplotypes in G6PC2, a target of positive selection

Nasser Al-Daghri (350024)
Chiara Pontremoli (722520)
Rachele Cagliani (24208)
Diego Forni (335427)
Majed Alokail (771998)
Omar Al-Attas (214555)
Shaun Sabico (772000)
Stefania Riva (543985)
Mario Clerici (34848)
Manuela Sironi (24204)

February 2017

List of metazoan species used for the phylogenetic analysis. Table S2. List of mammalian species use...

Additional file 1: Table S1. of Predicting gene targets from integrative analyses of summary data from GWAS and eQTL studies for 28 human complex traits

Jennifer Pavlides (3449879)
Zhihong Zhu (227325)
Jacob Gratten (3300798)
Allan McRae (3400103)
Naomi Wray (3449882)
Jian Yang (12136)

August 2016

GWAS information. Table S2. SMR results (P SMR <8.4 × 10–6). Table S3. SMR and HEIDI results (P HEID...

Additional file 1: of Dietary and genetic risk scores and incidence of type 2 diabetes

Ulrika Ericson (156578)
George Hindy (512699)
Isabel Drake (115126)
Christina-Alexandra Schulz (727982)
Louise Brunkwall (5145233)
Sophie Hellstrand (727981)
Peter Almgren (11999)
Marju Orho-Melander (12001)

May 2018

Table S1. Single nucleotide polymorphisms included in the GRS as they were reported to associate wit...

Additional file 1: of Complex patterns of direct and indirect association between the transcription Factor-7 like 2 gene, body mass index and type 2 diabetes diagnosis in adulthood in the Hispanic Community Health Study/Study of Latinos

Lindsay Fernández-Rhodes (281326)
Annie Howard (3453077)
Mariaelisa Graff (802540)
Carmen Isasi (4773717)
Heather Highland (5808698)
Kristin Young (3457226)
Esteban Parra (179104)
Jennifer Below (3532292)
Qibin Qi (172143)
Robert Kaplan (419010)
Anne Justice (4511098)
George Papanicolaou (202106)
Cathy Laurie (169902)
Struan Grant (5677610)
Christopher Haiman (120857)
Ruth Loos (3968261)
Kari North (34035)

October 2018

Figure S1. LDlink plot showing the regional r2 patterning between 1000 Genomes AMR and EUR reference...

Additional file 1: Table S1. of Spectrum of mutations in monogenic diabetes genes identified from high-throughput DNA sequencing of 6888 individuals

Vikas Bansal (79044)
Johann Gassenhuber (2893028)
Tierney Phillips (4664332)
Glenn Oliveira (727212)
Rebecca Harbaugh (4664329)
Nikki Villarasa (71214)
Eric Topol (4664335)
Thomas Seufferlein (232037)
Bernhard Boehm (486686)

December 2017

List of 22 genes associated with monogenic forms of diabetes that were analyzed in this paper. Table...

Additional file 1: Table S1a. of Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India

Viswanathan Mohan (239503)
Venkatesan Radha (4624417)
Thong Nguyen (1893943)
Eric Stawiski (256718)
Kanika Pahuja (4234612)
Leonard Goldstein (3455636)
Jennifer Tom (4269544)
Ranjit Anjana (3474065)
Monica Kong-Beltran (4851871)
Tushar Bhangale (269603)
Suresh Jahnavi (4851868)
Radhakrishnan Chandni (4851862)
Vijay Gayathri (4851880)
Paul George (4851874)
Na Zhang (333280)
Sakthivel Murugan (4851856)
Sameer Phalke (4851865)
Subhra Chaudhuri (4851859)
Ravi Gupta (208247)
Jingli Zhang (231460)
Sam Santhosh (4851877)
Jeremy Stinson (279794)
Zora Modrusan (37892)
V. Ramprasad (4851883)
Somasekar Seshagiri (83458)
Andrew Peterson (1987636)

February 2018

Sample information and clinical characteristics. Table S1b. Summary of clinical characteristics of M...

Additional file 2: Table S2. of A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients

Lőrinc Pongor (3574811)
Máté Kormos (3574814)
Christos Hatzis (565382)
Lajos Pusztai (78763)
András Szabó (3034779)
Balázs Győrffy (110652)

October 2015

The complete set of all genes included in the metagenes for each of the putative driver genes listed...

Additional file 2: of Genome-wide association studies for diabetic macular edema and proliferative diabetic retinopathy

Patricia Graham (3207738)
Georgia Kaidonis (5185217)
Sotoodeh Abhary (252379)
Mark Gillies (700017)
Mark Daniell (506570)
Rohan Essex (5185220)
John Chang (364595)
Stewart Lake (5185223)
Bishwanath Pal (5185214)
Alicia Jenkins (804281)
Alex Hewitt (3457262)
Ecosse Lamoureux (827837)
Philip Hykin (450726)
Nikolai Petrovsky (252418)
Matthew Brown (307585)
Jamie Craig (3410213)
Kathryn Burdon (3410231)

May 2018

Association results for Proliferative Diabetic Retinopathy GWAS. Only SNPs with pâ<âÂ 0.05 are i...

Additional file 1: of Pancreatic cancer as a sentinel for hereditary cancer predisposition

Erin Young (5454515)
Bryony Thompson (5454527)
Deborah Neklason (5454509)
Matthew Firpo (5454512)
Theresa Werner (5454542)
Russell Bell (4539349)
Justin Berger (272454)
Alison Fraser (5454530)
Amanda Gammon (5454539)
Cathryn Koptiuch (5454518)
Wendy Kohlmann (5454536)
Leigh Neumayer (5454533)
David Goldgar (29053)
Sean Mulvihill (5454524)
Lisa Cannon-Albright (523061)
Sean Tavtigian (5454521)

June 2018

Table S1. contains the list of the genes used in the study, as well as indicators for which pathway ...

Additional file 9: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Juan Fernรกndez-Tajes (6517679)
Kyle Gaulton (497560)
Martijn Bunt (6517658)
Jason Torres (6517661)
Matthias Thurner (6517664)
Anubha Mahajan (206768)
Anna Gloyn (3810184)
Kasper Lage (42180)
Mark McCarthy (157523)

March 2019

Figure S8. Sub-networks for seven T2D GWAS locus subset categories in the islet-specific network. (P...

Additional file 8: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Juan Fernรกndez-Tajes (6517679)
Kyle Gaulton (497560)
Martijn Bunt (6517658)
Jason Torres (6517661)
Matthias Thurner (6517664)
Anubha Mahajan (206768)
Anna Gloyn (3810184)
Kasper Lage (42180)
Mark McCarthy (157523)

March 2019

Figure S7. GWAS signal enrichment in the PPI-generic network derived from T2D GWAs subsets. (TIFF 30...

Additional file 10: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Juan Fernรกndez-Tajes (6517679)
Kyle Gaulton (497560)
Martijn Bunt (6517658)
Jason Torres (6517661)
Matthias Thurner (6517664)
Anubha Mahajan (206768)
Anna Gloyn (3810184)
Kasper Lage (42180)
Mark McCarthy (157523)

March 2019

Figure S9. Sub-networks for seven T2D GWAS locus subset categories in the PPI generic network. (PDF ...

Additional file 4: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Juan Fernรกndez-Tajes (6517679)
Kyle Gaulton (497560)
Martijn Bunt (6517658)
Jason Torres (6517661)
Matthias Thurner (6517664)
Anubha Mahajan (206768)
Anna Gloyn (3810184)
Kasper Lage (42180)
Mark McCarthy (157523)

March 2019

Figure S3. Distribution of PCS and correlation of semantic and risk variant link scores. (TIFF 3072 ...

Additional file 1: Table S1. of Susceptibility to type 2 diabetes may be modulated by haplotypes in G6PC2, a target of positive selection

Nasser Al-Daghri (350024)
Chiara Pontremoli (722520)
Rachele Cagliani (24208)
Diego Forni (335427)
Majed Alokail (771998)
Omar Al-Attas (214555)
Shaun Sabico (772000)
Stefania Riva (543985)
Mario Clerici (34848)
Manuela Sironi (24204)

February 2017

List of metazoan species used for the phylogenetic analysis. Table S2. List of mammalian species use...

Additional file 1: Table S1. of Predicting gene targets from integrative analyses of summary data from GWAS and eQTL studies for 28 human complex traits

Jennifer Pavlides (3449879)
Zhihong Zhu (227325)
Jacob Gratten (3300798)
Allan McRae (3400103)
Naomi Wray (3449882)
Jian Yang (12136)

August 2016

GWAS information. Table S2. SMR results (P SMR <8.4 × 10–6). Table S3. SMR and HEIDI results (P HEID...

Additional file 1: of Dietary and genetic risk scores and incidence of type 2 diabetes

Ulrika Ericson (156578)
George Hindy (512699)
Isabel Drake (115126)
Christina-Alexandra Schulz (727982)
Louise Brunkwall (5145233)
Sophie Hellstrand (727981)
Peter Almgren (11999)
Marju Orho-Melander (12001)

May 2018

Table S1. Single nucleotide polymorphisms included in the GRS as they were reported to associate wit...

Lindsay Fernández-Rhodes (281326)
Annie Howard (3453077)
Mariaelisa Graff (802540)
Carmen Isasi (4773717)
Heather Highland (5808698)
Kristin Young (3457226)
Esteban Parra (179104)
Jennifer Below (3532292)
Qibin Qi (172143)
Robert Kaplan (419010)
Anne Justice (4511098)
George Papanicolaou (202106)
Cathy Laurie (169902)
Struan Grant (5677610)
Christopher Haiman (120857)
Ruth Loos (3968261)
Kari North (34035)

October 2018

Figure S1. LDlink plot showing the regional r2 patterning between 1000 Genomes AMR and EUR reference...

Additional file 1: Table S1. of Spectrum of mutations in monogenic diabetes genes identified from high-throughput DNA sequencing of 6888 individuals

Vikas Bansal (79044)
Johann Gassenhuber (2893028)
Tierney Phillips (4664332)
Glenn Oliveira (727212)
Rebecca Harbaugh (4664329)
Nikki Villarasa (71214)
Eric Topol (4664335)
Thomas Seufferlein (232037)
Bernhard Boehm (486686)

December 2017

List of 22 genes associated with monogenic forms of diabetes that were analyzed in this paper. Table...

Additional file 1: Table S1a. of Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India

Viswanathan Mohan (239503)
Venkatesan Radha (4624417)
Thong Nguyen (1893943)
Eric Stawiski (256718)
Kanika Pahuja (4234612)
Leonard Goldstein (3455636)
Jennifer Tom (4269544)
Ranjit Anjana (3474065)
Monica Kong-Beltran (4851871)
Tushar Bhangale (269603)
Suresh Jahnavi (4851868)
Radhakrishnan Chandni (4851862)
Vijay Gayathri (4851880)
Paul George (4851874)
Na Zhang (333280)
Sakthivel Murugan (4851856)
Sameer Phalke (4851865)
Subhra Chaudhuri (4851859)
Ravi Gupta (208247)
Jingli Zhang (231460)
Sam Santhosh (4851877)
Jeremy Stinson (279794)
Zora Modrusan (37892)
V. Ramprasad (4851883)
Somasekar Seshagiri (83458)
Andrew Peterson (1987636)

February 2018

Sample information and clinical characteristics. Table S1b. Summary of clinical characteristics of M...

Additional file 2: Table S2. of A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients

Lőrinc Pongor (3574811)
Máté Kormos (3574814)
Christos Hatzis (565382)
Lajos Pusztai (78763)
András Szabó (3034779)
Balázs Győrffy (110652)

October 2015

The complete set of all genes included in the metagenes for each of the putative driver genes listed...

Additional file 2: of Genome-wide association studies for diabetic macular edema and proliferative diabetic retinopathy

Patricia Graham (3207738)
Georgia Kaidonis (5185217)
Sotoodeh Abhary (252379)
Mark Gillies (700017)
Mark Daniell (506570)
Rohan Essex (5185220)
John Chang (364595)
Stewart Lake (5185223)
Bishwanath Pal (5185214)
Alicia Jenkins (804281)
Alex Hewitt (3457262)
Ecosse Lamoureux (827837)
Philip Hykin (450726)
Nikolai Petrovsky (252418)
Matthew Brown (307585)
Jamie Craig (3410213)
Kathryn Burdon (3410231)

May 2018

Association results for Proliferative Diabetic Retinopathy GWAS. Only SNPs with pâ<âÂ 0.05 are i...

Additional file 1: of Pancreatic cancer as a sentinel for hereditary cancer predisposition

Erin Young (5454515)
Bryony Thompson (5454527)
Deborah Neklason (5454509)
Matthew Firpo (5454512)
Theresa Werner (5454542)
Russell Bell (4539349)
Justin Berger (272454)
Alison Fraser (5454530)
Amanda Gammon (5454539)
Cathryn Koptiuch (5454518)
Wendy Kohlmann (5454536)
Leigh Neumayer (5454533)
David Goldgar (29053)
Sean Mulvihill (5454524)
Lisa Cannon-Albright (523061)
Sean Tavtigian (5454521)

June 2018

Table S1. contains the list of the genes used in the study, as well as indicators for which pathway ...

Additional file 1: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Abstract

Extracted data

Additional file 1: of Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Abstract

Extracted data

Related items

Related items