1-CMDb

A Curated Database of Genomic Variations of the One-Carbon Metabolism Pathway

Manoj K. Bhat, Veerendra P. Gadekar, Aditya Jain, Bobby Paul, Padmalatha S. Rai, Kapaettu Satyamoorthy

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

The one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded. Hence, we designed the one-carbon metabolism database (1-CMDb) as a platform to interrogate its association with a host of human disorders. Methods: DNA sequence and network information of a total of 48 genes were extracted from a literature survey and KEGG pathway that are involved in the one-carbon folate-mediated pathway. The information generated, collected, and compiled for all these genes from the UCSC genome browser included the single nucleotide polymorphisms (SNPs), CpGs, copy number variations (CNVs), and miRNAs, and a comprehensive database was created. Furthermore, a significant correlation analysis was performed for SNPs in the pathway genes. Results: Detailed data of SNPs, CNVs, CpG islands, and miRNAs for 48 folate pathway genes were compiled. The SNPs in CNVs (9670), CpGs (984), and miRNAs (14) were also compiled for all pathway genes. The SIFT score, the prediction and PolyPhen score, as well as the prediction for each of the SNPs were tabulated and represented for folate pathway genes. Also included in the database for folate pathway genes were the links to 124 various phenotypes and disease associations as reported in the literature and from publicly available information. Conclusion: A comprehensive database was generated consisting of genomic elements within and among SNPs, CNVs, CpGs, and miRNAs of one-carbon metabolism pathways to facilitate (a) single source of information and (b) integration into large-genome scale network analysis to be developed in the future by the scientific community. The database can be accessed at http://slsdb.manipal.edu/ocm/. .

Original languageEnglish
Pages (from-to)136-141
Number of pages6
JournalPublic Health Genomics
Volume20
Issue number2
DOIs
Publication statusPublished - 01-09-2017

Fingerprint

Carbon
Databases
Single Nucleotide Polymorphism
Folic Acid
MicroRNAs
Genes
Genome
CpG Islands
Information Services
Epigenomics
Methionine
Homeostasis
Phenotype
Health

All Science Journal Classification (ASJC) codes

  • Public Health, Environmental and Occupational Health
  • Genetics(clinical)

Cite this

Bhat, Manoj K. ; Gadekar, Veerendra P. ; Jain, Aditya ; Paul, Bobby ; Rai, Padmalatha S. ; Satyamoorthy, Kapaettu. / 1-CMDb : A Curated Database of Genomic Variations of the One-Carbon Metabolism Pathway. In: Public Health Genomics. 2017 ; Vol. 20, No. 2. pp. 136-141.
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abstract = "The one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded. Hence, we designed the one-carbon metabolism database (1-CMDb) as a platform to interrogate its association with a host of human disorders. Methods: DNA sequence and network information of a total of 48 genes were extracted from a literature survey and KEGG pathway that are involved in the one-carbon folate-mediated pathway. The information generated, collected, and compiled for all these genes from the UCSC genome browser included the single nucleotide polymorphisms (SNPs), CpGs, copy number variations (CNVs), and miRNAs, and a comprehensive database was created. Furthermore, a significant correlation analysis was performed for SNPs in the pathway genes. Results: Detailed data of SNPs, CNVs, CpG islands, and miRNAs for 48 folate pathway genes were compiled. The SNPs in CNVs (9670), CpGs (984), and miRNAs (14) were also compiled for all pathway genes. The SIFT score, the prediction and PolyPhen score, as well as the prediction for each of the SNPs were tabulated and represented for folate pathway genes. Also included in the database for folate pathway genes were the links to 124 various phenotypes and disease associations as reported in the literature and from publicly available information. Conclusion: A comprehensive database was generated consisting of genomic elements within and among SNPs, CNVs, CpGs, and miRNAs of one-carbon metabolism pathways to facilitate (a) single source of information and (b) integration into large-genome scale network analysis to be developed in the future by the scientific community. The database can be accessed at http://slsdb.manipal.edu/ocm/. .",
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1-CMDb : A Curated Database of Genomic Variations of the One-Carbon Metabolism Pathway. / Bhat, Manoj K.; Gadekar, Veerendra P.; Jain, Aditya; Paul, Bobby; Rai, Padmalatha S.; Satyamoorthy, Kapaettu.

In: Public Health Genomics, Vol. 20, No. 2, 01.09.2017, p. 136-141.

Research output: Contribution to journalArticle

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