Semantic Modeling for SNPs Associated with Ethnic Disparities in HapMap Samples
Single-nucleotide polymorphisms (SNPs) have been emerging out of the efforts to research human diseases and ethnic disparities. A semantic network is needed for in-depth understanding of the impacts of SNPs, because phenotypes are modulated by complex networks, including biochemical and physiologica...
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BioMed Central
2014-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-12-35.pdf |
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| author | HyoYoung Kim Won Gi Yoo Junhyung Park Heebal Kim Byeong-Chul Kang |
| author_facet | HyoYoung Kim Won Gi Yoo Junhyung Park Heebal Kim Byeong-Chul Kang |
| author_sort | HyoYoung Kim |
| collection | DOAJ |
| description | Single-nucleotide polymorphisms (SNPs) have been emerging out of the efforts to research human diseases and ethnic disparities. A semantic network is needed for in-depth understanding of the impacts of SNPs, because phenotypes are modulated by complex networks, including biochemical and physiological pathways. We identified ethnicity-specific SNPs by eliminating overlapped SNPs from HapMap samples, and the ethnicity-specific SNPs were mapped to the UCSC RefGene lists. Ethnicity-specific genes were identified as follows: 22 genes in the USA (CEU) individuals, 25 genes in the Japanese (JPT) individuals, and 332 genes in the African (YRI) individuals. To analyze the biologically functional implications for ethnicity-specific SNPs, we focused on constructing a semantic network model. Entities for the network represented by "Gene," "Pathway," "Disease," "Chemical," "Drug," "ClinicalTrials," "SNP," and relationships between entity-entity were obtained through curation. Our semantic modeling for ethnicity-specific SNPs showed interesting results in the three categories, including three diseases ("AIDS-associated nephropathy," "Hypertension," and "Pelvic infection"), one drug ("Methylphenidate"), and five pathways ("Hemostasis," "Systemic lupus erythematosus," "Prostate cancer," "Hepatitis C virus," and "Rheumatoid arthritis"). We found ethnicity-specific genes using the semantic modeling, and the majority of our findings was consistent with the previous studies - that an understanding of genetic variability explained ethnicity-specific disparities. |
| format | Article |
| id | doaj-art-11ad2c0717004cdd9ab517c10c6a6db9 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2014-03-01 |
| publisher | BioMed Central |
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| series | Genomics & Informatics |
| spelling | doaj-art-11ad2c0717004cdd9ab517c10c6a6db92025-02-03T02:38:40ZengBioMed CentralGenomics & Informatics1598-866X2234-07422014-03-01121354110.5808/GI.2014.12.1.35123Semantic Modeling for SNPs Associated with Ethnic Disparities in HapMap SamplesHyoYoung Kim0Won Gi Yoo1Junhyung Park2Heebal Kim3Byeong-Chul Kang4Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea.Codes Division, Insilicogen, Inc., Suwon 441-813, Korea.Codes Division, Insilicogen, Inc., Suwon 441-813, Korea.Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea.Codes Division, Insilicogen, Inc., Suwon 441-813, Korea.Single-nucleotide polymorphisms (SNPs) have been emerging out of the efforts to research human diseases and ethnic disparities. A semantic network is needed for in-depth understanding of the impacts of SNPs, because phenotypes are modulated by complex networks, including biochemical and physiological pathways. We identified ethnicity-specific SNPs by eliminating overlapped SNPs from HapMap samples, and the ethnicity-specific SNPs were mapped to the UCSC RefGene lists. Ethnicity-specific genes were identified as follows: 22 genes in the USA (CEU) individuals, 25 genes in the Japanese (JPT) individuals, and 332 genes in the African (YRI) individuals. To analyze the biologically functional implications for ethnicity-specific SNPs, we focused on constructing a semantic network model. Entities for the network represented by "Gene," "Pathway," "Disease," "Chemical," "Drug," "ClinicalTrials," "SNP," and relationships between entity-entity were obtained through curation. Our semantic modeling for ethnicity-specific SNPs showed interesting results in the three categories, including three diseases ("AIDS-associated nephropathy," "Hypertension," and "Pelvic infection"), one drug ("Methylphenidate"), and five pathways ("Hemostasis," "Systemic lupus erythematosus," "Prostate cancer," "Hepatitis C virus," and "Rheumatoid arthritis"). We found ethnicity-specific genes using the semantic modeling, and the majority of our findings was consistent with the previous studies - that an understanding of genetic variability explained ethnicity-specific disparities.http://genominfo.org/upload/pdf/gni-12-35.pdfethnic groupsHapMap Projectmodelingsemanticsingle nucleotide polymorphism |
| spellingShingle | HyoYoung Kim Won Gi Yoo Junhyung Park Heebal Kim Byeong-Chul Kang Semantic Modeling for SNPs Associated with Ethnic Disparities in HapMap Samples Genomics & Informatics ethnic groups HapMap Project modeling semantic single nucleotide polymorphism |
| title | Semantic Modeling for SNPs Associated with Ethnic Disparities in HapMap Samples |
| title_full | Semantic Modeling for SNPs Associated with Ethnic Disparities in HapMap Samples |
| title_fullStr | Semantic Modeling for SNPs Associated with Ethnic Disparities in HapMap Samples |
| title_full_unstemmed | Semantic Modeling for SNPs Associated with Ethnic Disparities in HapMap Samples |
| title_short | Semantic Modeling for SNPs Associated with Ethnic Disparities in HapMap Samples |
| title_sort | semantic modeling for snps associated with ethnic disparities in hapmap samples |
| topic | ethnic groups HapMap Project modeling semantic single nucleotide polymorphism |
| url | http://genominfo.org/upload/pdf/gni-12-35.pdf |
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