Pathway analysis for genome-wide association study of basal cell carcinoma of the skin.

Recently, a pathway-based approach has been developed to evaluate the cumulative contribution of the functionally related genes for genome-wide association studies (GWASs), which may help utilize GWAS data to a greater extent.In this study, we applied this approach for the GWAS of basal cell carcino...
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Autor*in:	Mingfeng Zhang [verfasserIn] Liming Liang [verfasserIn] Mousheng Xu [verfasserIn] Abrar A Qureshi [verfasserIn] Jiali Han [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2011

Übergeordnetes Werk:	In: PLoS ONE - Public Library of Science (PLoS), 2007, 6(2011), 7, p e22760
Übergeordnetes Werk:	volume:6 ; year:2011 ; number:7, p e22760

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1371/journal.pone.0022760

Katalog-ID:	DOAJ04414458X

Internformat


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520			\|a Recently, a pathway-based approach has been developed to evaluate the cumulative contribution of the functionally related genes for genome-wide association studies (GWASs), which may help utilize GWAS data to a greater extent.In this study, we applied this approach for the GWAS of basal cell carcinoma (BCC) of the skin. We first conducted the BCC GWAS among 1,797 BCC cases and 5,197 controls in Caucasians with 740,760 genotyped SNPs. 115,688 SNPs were grouped into gene transcripts within 20 kb in distance and then into 174 Kyoto Encyclopedia of Genes and Genomes pathways, 205 BioCarta pathways, as well as two positive control gene sets (pigmentation gene set and BCC risk gene set). The association of each pathway with BCC risk was evaluated using the weighted Kolmogorov-Smirnov test. One thousand permutations were conducted to assess the significance.Both of the positive control gene sets reached pathway p-values<0.05. Four other pathways were also significantly associated with BCC risk: the heparan sulfate biosynthesis pathway (p = 0.007, false discovery rate, FDR = 0.35), the mCalpain pathway (p = 0.002, FDR = 0.12), the Rho cell motility signaling pathway (p = 0.011, FDR = 0.30), and the nitric oxide pathway (p = 0.022, FDR = 0.42).We identified four pathways associated with BCC risk, which may offer new insights into the etiology of BCC upon further validation, and this approach may help identify potential biological pathways that might be missed by the standard GWAS approach.
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allfields	10.1371/journal.pone.0022760 doi (DE-627)DOAJ04414458X (DE-599)DOAJ8c1b4d62b29f47a782ccc2b18d33fb9e DE-627 ger DE-627 rakwb eng Mingfeng Zhang verfasserin aut Pathway analysis for genome-wide association study of basal cell carcinoma of the skin. 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Recently, a pathway-based approach has been developed to evaluate the cumulative contribution of the functionally related genes for genome-wide association studies (GWASs), which may help utilize GWAS data to a greater extent.In this study, we applied this approach for the GWAS of basal cell carcinoma (BCC) of the skin. We first conducted the BCC GWAS among 1,797 BCC cases and 5,197 controls in Caucasians with 740,760 genotyped SNPs. 115,688 SNPs were grouped into gene transcripts within 20 kb in distance and then into 174 Kyoto Encyclopedia of Genes and Genomes pathways, 205 BioCarta pathways, as well as two positive control gene sets (pigmentation gene set and BCC risk gene set). The association of each pathway with BCC risk was evaluated using the weighted Kolmogorov-Smirnov test. One thousand permutations were conducted to assess the significance.Both of the positive control gene sets reached pathway p-values<0.05. Four other pathways were also significantly associated with BCC risk: the heparan sulfate biosynthesis pathway (p = 0.007, false discovery rate, FDR = 0.35), the mCalpain pathway (p = 0.002, FDR = 0.12), the Rho cell motility signaling pathway (p = 0.011, FDR = 0.30), and the nitric oxide pathway (p = 0.022, FDR = 0.42).We identified four pathways associated with BCC risk, which may offer new insights into the etiology of BCC upon further validation, and this approach may help identify potential biological pathways that might be missed by the standard GWAS approach. Medicine R Science Q Liming Liang verfasserin aut Mousheng Xu verfasserin aut Abrar A Qureshi verfasserin aut Jiali Han verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 6(2011), 7, p e22760 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:6 year:2011 number:7, p e22760 https://doi.org/10.1371/journal.pone.0022760 kostenfrei https://doaj.org/article/8c1b4d62b29f47a782ccc2b18d33fb9e kostenfrei http://europepmc.org/articles/PMC3145747?pdf=render kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2011 7, p e22760
spelling	10.1371/journal.pone.0022760 doi (DE-627)DOAJ04414458X (DE-599)DOAJ8c1b4d62b29f47a782ccc2b18d33fb9e DE-627 ger DE-627 rakwb eng Mingfeng Zhang verfasserin aut Pathway analysis for genome-wide association study of basal cell carcinoma of the skin. 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Recently, a pathway-based approach has been developed to evaluate the cumulative contribution of the functionally related genes for genome-wide association studies (GWASs), which may help utilize GWAS data to a greater extent.In this study, we applied this approach for the GWAS of basal cell carcinoma (BCC) of the skin. We first conducted the BCC GWAS among 1,797 BCC cases and 5,197 controls in Caucasians with 740,760 genotyped SNPs. 115,688 SNPs were grouped into gene transcripts within 20 kb in distance and then into 174 Kyoto Encyclopedia of Genes and Genomes pathways, 205 BioCarta pathways, as well as two positive control gene sets (pigmentation gene set and BCC risk gene set). The association of each pathway with BCC risk was evaluated using the weighted Kolmogorov-Smirnov test. One thousand permutations were conducted to assess the significance.Both of the positive control gene sets reached pathway p-values<0.05. Four other pathways were also significantly associated with BCC risk: the heparan sulfate biosynthesis pathway (p = 0.007, false discovery rate, FDR = 0.35), the mCalpain pathway (p = 0.002, FDR = 0.12), the Rho cell motility signaling pathway (p = 0.011, FDR = 0.30), and the nitric oxide pathway (p = 0.022, FDR = 0.42).We identified four pathways associated with BCC risk, which may offer new insights into the etiology of BCC upon further validation, and this approach may help identify potential biological pathways that might be missed by the standard GWAS approach. Medicine R Science Q Liming Liang verfasserin aut Mousheng Xu verfasserin aut Abrar A Qureshi verfasserin aut Jiali Han verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 6(2011), 7, p e22760 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:6 year:2011 number:7, p e22760 https://doi.org/10.1371/journal.pone.0022760 kostenfrei https://doaj.org/article/8c1b4d62b29f47a782ccc2b18d33fb9e kostenfrei http://europepmc.org/articles/PMC3145747?pdf=render kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2011 7, p e22760
allfields_unstemmed	10.1371/journal.pone.0022760 doi (DE-627)DOAJ04414458X (DE-599)DOAJ8c1b4d62b29f47a782ccc2b18d33fb9e DE-627 ger DE-627 rakwb eng Mingfeng Zhang verfasserin aut Pathway analysis for genome-wide association study of basal cell carcinoma of the skin. 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Recently, a pathway-based approach has been developed to evaluate the cumulative contribution of the functionally related genes for genome-wide association studies (GWASs), which may help utilize GWAS data to a greater extent.In this study, we applied this approach for the GWAS of basal cell carcinoma (BCC) of the skin. We first conducted the BCC GWAS among 1,797 BCC cases and 5,197 controls in Caucasians with 740,760 genotyped SNPs. 115,688 SNPs were grouped into gene transcripts within 20 kb in distance and then into 174 Kyoto Encyclopedia of Genes and Genomes pathways, 205 BioCarta pathways, as well as two positive control gene sets (pigmentation gene set and BCC risk gene set). The association of each pathway with BCC risk was evaluated using the weighted Kolmogorov-Smirnov test. One thousand permutations were conducted to assess the significance.Both of the positive control gene sets reached pathway p-values<0.05. Four other pathways were also significantly associated with BCC risk: the heparan sulfate biosynthesis pathway (p = 0.007, false discovery rate, FDR = 0.35), the mCalpain pathway (p = 0.002, FDR = 0.12), the Rho cell motility signaling pathway (p = 0.011, FDR = 0.30), and the nitric oxide pathway (p = 0.022, FDR = 0.42).We identified four pathways associated with BCC risk, which may offer new insights into the etiology of BCC upon further validation, and this approach may help identify potential biological pathways that might be missed by the standard GWAS approach. Medicine R Science Q Liming Liang verfasserin aut Mousheng Xu verfasserin aut Abrar A Qureshi verfasserin aut Jiali Han verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 6(2011), 7, p e22760 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:6 year:2011 number:7, p e22760 https://doi.org/10.1371/journal.pone.0022760 kostenfrei https://doaj.org/article/8c1b4d62b29f47a782ccc2b18d33fb9e kostenfrei http://europepmc.org/articles/PMC3145747?pdf=render kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2011 7, p e22760
allfieldsGer	10.1371/journal.pone.0022760 doi (DE-627)DOAJ04414458X (DE-599)DOAJ8c1b4d62b29f47a782ccc2b18d33fb9e DE-627 ger DE-627 rakwb eng Mingfeng Zhang verfasserin aut Pathway analysis for genome-wide association study of basal cell carcinoma of the skin. 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Recently, a pathway-based approach has been developed to evaluate the cumulative contribution of the functionally related genes for genome-wide association studies (GWASs), which may help utilize GWAS data to a greater extent.In this study, we applied this approach for the GWAS of basal cell carcinoma (BCC) of the skin. We first conducted the BCC GWAS among 1,797 BCC cases and 5,197 controls in Caucasians with 740,760 genotyped SNPs. 115,688 SNPs were grouped into gene transcripts within 20 kb in distance and then into 174 Kyoto Encyclopedia of Genes and Genomes pathways, 205 BioCarta pathways, as well as two positive control gene sets (pigmentation gene set and BCC risk gene set). The association of each pathway with BCC risk was evaluated using the weighted Kolmogorov-Smirnov test. One thousand permutations were conducted to assess the significance.Both of the positive control gene sets reached pathway p-values<0.05. Four other pathways were also significantly associated with BCC risk: the heparan sulfate biosynthesis pathway (p = 0.007, false discovery rate, FDR = 0.35), the mCalpain pathway (p = 0.002, FDR = 0.12), the Rho cell motility signaling pathway (p = 0.011, FDR = 0.30), and the nitric oxide pathway (p = 0.022, FDR = 0.42).We identified four pathways associated with BCC risk, which may offer new insights into the etiology of BCC upon further validation, and this approach may help identify potential biological pathways that might be missed by the standard GWAS approach. Medicine R Science Q Liming Liang verfasserin aut Mousheng Xu verfasserin aut Abrar A Qureshi verfasserin aut Jiali Han verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 6(2011), 7, p e22760 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:6 year:2011 number:7, p e22760 https://doi.org/10.1371/journal.pone.0022760 kostenfrei https://doaj.org/article/8c1b4d62b29f47a782ccc2b18d33fb9e kostenfrei http://europepmc.org/articles/PMC3145747?pdf=render kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2011 7, p e22760
allfieldsSound	10.1371/journal.pone.0022760 doi (DE-627)DOAJ04414458X (DE-599)DOAJ8c1b4d62b29f47a782ccc2b18d33fb9e DE-627 ger DE-627 rakwb eng Mingfeng Zhang verfasserin aut Pathway analysis for genome-wide association study of basal cell carcinoma of the skin. 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Recently, a pathway-based approach has been developed to evaluate the cumulative contribution of the functionally related genes for genome-wide association studies (GWASs), which may help utilize GWAS data to a greater extent.In this study, we applied this approach for the GWAS of basal cell carcinoma (BCC) of the skin. We first conducted the BCC GWAS among 1,797 BCC cases and 5,197 controls in Caucasians with 740,760 genotyped SNPs. 115,688 SNPs were grouped into gene transcripts within 20 kb in distance and then into 174 Kyoto Encyclopedia of Genes and Genomes pathways, 205 BioCarta pathways, as well as two positive control gene sets (pigmentation gene set and BCC risk gene set). The association of each pathway with BCC risk was evaluated using the weighted Kolmogorov-Smirnov test. One thousand permutations were conducted to assess the significance.Both of the positive control gene sets reached pathway p-values<0.05. Four other pathways were also significantly associated with BCC risk: the heparan sulfate biosynthesis pathway (p = 0.007, false discovery rate, FDR = 0.35), the mCalpain pathway (p = 0.002, FDR = 0.12), the Rho cell motility signaling pathway (p = 0.011, FDR = 0.30), and the nitric oxide pathway (p = 0.022, FDR = 0.42).We identified four pathways associated with BCC risk, which may offer new insights into the etiology of BCC upon further validation, and this approach may help identify potential biological pathways that might be missed by the standard GWAS approach. Medicine R Science Q Liming Liang verfasserin aut Mousheng Xu verfasserin aut Abrar A Qureshi verfasserin aut Jiali Han verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 6(2011), 7, p e22760 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:6 year:2011 number:7, p e22760 https://doi.org/10.1371/journal.pone.0022760 kostenfrei https://doaj.org/article/8c1b4d62b29f47a782ccc2b18d33fb9e kostenfrei http://europepmc.org/articles/PMC3145747?pdf=render kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2011 7, p e22760
language	English
source	In PLoS ONE 6(2011), 7, p e22760 volume:6 year:2011 number:7, p e22760
sourceStr	In PLoS ONE 6(2011), 7, p e22760 volume:6 year:2011 number:7, p e22760
format_phy_str_mv	Article
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container_title	PLoS ONE
authorswithroles_txt_mv	Mingfeng Zhang @@aut@@ Liming Liang @@aut@@ Mousheng Xu @@aut@@ Abrar A Qureshi @@aut@@ Jiali Han @@aut@@
publishDateDaySort_date	2011-01-01T00:00:00Z
hierarchy_top_id	523574592
id	DOAJ04414458X
language_de	englisch
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author	Mingfeng Zhang
spellingShingle	Mingfeng Zhang misc Medicine misc R misc Science misc Q Pathway analysis for genome-wide association study of basal cell carcinoma of the skin.
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topic_title	Pathway analysis for genome-wide association study of basal cell carcinoma of the skin
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title	Pathway analysis for genome-wide association study of basal cell carcinoma of the skin.
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title_full	Pathway analysis for genome-wide association study of basal cell carcinoma of the skin
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title_sort	pathway analysis for genome-wide association study of basal cell carcinoma of the skin
title_auth	Pathway analysis for genome-wide association study of basal cell carcinoma of the skin.
abstract	Recently, a pathway-based approach has been developed to evaluate the cumulative contribution of the functionally related genes for genome-wide association studies (GWASs), which may help utilize GWAS data to a greater extent.In this study, we applied this approach for the GWAS of basal cell carcinoma (BCC) of the skin. We first conducted the BCC GWAS among 1,797 BCC cases and 5,197 controls in Caucasians with 740,760 genotyped SNPs. 115,688 SNPs were grouped into gene transcripts within 20 kb in distance and then into 174 Kyoto Encyclopedia of Genes and Genomes pathways, 205 BioCarta pathways, as well as two positive control gene sets (pigmentation gene set and BCC risk gene set). The association of each pathway with BCC risk was evaluated using the weighted Kolmogorov-Smirnov test. One thousand permutations were conducted to assess the significance.Both of the positive control gene sets reached pathway p-values<0.05. Four other pathways were also significantly associated with BCC risk: the heparan sulfate biosynthesis pathway (p = 0.007, false discovery rate, FDR = 0.35), the mCalpain pathway (p = 0.002, FDR = 0.12), the Rho cell motility signaling pathway (p = 0.011, FDR = 0.30), and the nitric oxide pathway (p = 0.022, FDR = 0.42).We identified four pathways associated with BCC risk, which may offer new insights into the etiology of BCC upon further validation, and this approach may help identify potential biological pathways that might be missed by the standard GWAS approach.
abstractGer	Recently, a pathway-based approach has been developed to evaluate the cumulative contribution of the functionally related genes for genome-wide association studies (GWASs), which may help utilize GWAS data to a greater extent.In this study, we applied this approach for the GWAS of basal cell carcinoma (BCC) of the skin. We first conducted the BCC GWAS among 1,797 BCC cases and 5,197 controls in Caucasians with 740,760 genotyped SNPs. 115,688 SNPs were grouped into gene transcripts within 20 kb in distance and then into 174 Kyoto Encyclopedia of Genes and Genomes pathways, 205 BioCarta pathways, as well as two positive control gene sets (pigmentation gene set and BCC risk gene set). The association of each pathway with BCC risk was evaluated using the weighted Kolmogorov-Smirnov test. One thousand permutations were conducted to assess the significance.Both of the positive control gene sets reached pathway p-values<0.05. Four other pathways were also significantly associated with BCC risk: the heparan sulfate biosynthesis pathway (p = 0.007, false discovery rate, FDR = 0.35), the mCalpain pathway (p = 0.002, FDR = 0.12), the Rho cell motility signaling pathway (p = 0.011, FDR = 0.30), and the nitric oxide pathway (p = 0.022, FDR = 0.42).We identified four pathways associated with BCC risk, which may offer new insights into the etiology of BCC upon further validation, and this approach may help identify potential biological pathways that might be missed by the standard GWAS approach.
abstract_unstemmed	Recently, a pathway-based approach has been developed to evaluate the cumulative contribution of the functionally related genes for genome-wide association studies (GWASs), which may help utilize GWAS data to a greater extent.In this study, we applied this approach for the GWAS of basal cell carcinoma (BCC) of the skin. We first conducted the BCC GWAS among 1,797 BCC cases and 5,197 controls in Caucasians with 740,760 genotyped SNPs. 115,688 SNPs were grouped into gene transcripts within 20 kb in distance and then into 174 Kyoto Encyclopedia of Genes and Genomes pathways, 205 BioCarta pathways, as well as two positive control gene sets (pigmentation gene set and BCC risk gene set). The association of each pathway with BCC risk was evaluated using the weighted Kolmogorov-Smirnov test. One thousand permutations were conducted to assess the significance.Both of the positive control gene sets reached pathway p-values<0.05. Four other pathways were also significantly associated with BCC risk: the heparan sulfate biosynthesis pathway (p = 0.007, false discovery rate, FDR = 0.35), the mCalpain pathway (p = 0.002, FDR = 0.12), the Rho cell motility signaling pathway (p = 0.011, FDR = 0.30), and the nitric oxide pathway (p = 0.022, FDR = 0.42).We identified four pathways associated with BCC risk, which may offer new insights into the etiology of BCC upon further validation, and this approach may help identify potential biological pathways that might be missed by the standard GWAS approach.
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title_short	Pathway analysis for genome-wide association study of basal cell carcinoma of the skin.
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Pathway analysis for genome-wide association study of basal cell carcinoma of the skin.

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