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Genome wide screening and analysis of Homo sapiens genes and proteins associated with schizophrenia

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Author Affiliations

  • 1Department of Life Sciences, Ravenshaw University, Cuttack, India and Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, India
  • 2Department of Life Sciences, Ravenshaw University, Cuttack, India
  • 3Department of Life Sciences, Ravenshaw University, Cuttack, India

Res. J. Recent Sci., Volume 6, Issue (7), Pages 63-70, June,2 (2017)

Abstract

Implementing traditional methods of browsing scientific information in literature databases like PUBMED to browse the molecular basis of a complex brain disorder like schizophrenia revealed the involvement of hundreds of gene with the disorder. It urged for the necessity to adopt some specialized experimental design including more relevant and reliable data mining technologies and methodologies to screen out the key player genes and proteins involved with our targeted disorder. After searching for all possible available molecular data for schizophrenia in case of Homo sapiens not less than 400 genes were found to be reported in about 900 different studies through GWAS. Various types of further analysis were then carried out on this gene set to filter the exact genes and proteins involved in the disorder based on their physicochemical properties, chromosomal localization, pathway analysis, involvement in biological processes, cellular localization, drug association studies and disease association studies. After all tedious observations and analysis interestingly it is revealed that the human chromosome No. 22 is highly enriched with schizophrenia associated genes, most of the genes are linked with more than one disorder along with schizophrenia, most of the proteins are membrane proteins and very less proteins are available with drugs approved for the disorder.

References

  1. Craddock N., O, The genetics of schizophrenia and bipolar disorder: dissecting psychosis., J Med Genet., 42(3), 193-204. doi:10.1136/jmg.2005.030718
  2. Karam C.S., Ballon J.S., Bivens N.M., Freyberg Z., Girgis R.R., Lizardi-Ortiz J.E., Markx S., Lieberman J. A. and Javitch J.A. (2010)., Signaling pathways in schizophrenia: emerging targets and therapeutic strategies., Trends in Pharmacological Sciences, 31(8), 381-390. doi: 10.1016/j.tips.2010.05.004.
  3. MacArthur J., Bowler E., Cerezo M., Gil L., Hall P., Hastings E., Junkins H., McMahon A., Milano A., Morales J., Pendlington Z., Welter D., Burdett T., Hindorff L., Flicek P., Cunningham F. and Parkinson H. (2017)., The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)., Nucleic Acids Research, 45(D1), D896-D901.
  4. Welter D., MacArthur J., Morales J., Burdett T., Hall P., Junkins H., Klemm A., Flicek P., Manolio T., Hindorff L. and Parkinson H. (2014)., The NHGRI GWAS Catalog, a curated resource of SNP-trait associations., Nucleic Acids Research, 42(D1), D1001-D1006.
  5. Hindorff L.A., Sethupathy P., Junkins H.A., Ramos E.M., Mehta J.P., Collins F.S. and Manolio T.A.(2009)., Potential etiologic and functional implications of genome-wide association loci for human diseases and traits., Proc. Natl Acad. Sci. USA, 106(23), 9362-9367.
  6. Jourquin J., Duncan D., Shi Z. and Zhang B. (2012)., GLAD4U: deriving and prioritizing gene lists from PubMed literature., BMC Genomics, 13(Suppl 8), S20. doi: 10.1186/1471-2164-13-S8-S20
  7. McDonagh E.M., Whirl-Carrillo M., Altman R.B. and Klein T.E. (2015)., Enabling the Curation of Your Pharmacogenetic Study., Clinical Pharmacology & Therapeutics, 97(2), 116-119. doi: 10.1002/cpt.15
  8. Kevin H.J., Jeffrey R.B., Katrin S., Daniel J.M., Yuan J., Susan G.L., Steven L.J., Rebecca L.G., Dana L.C., Adrian L.L., Todd C.S., Stuart A.S., Julia C.S., Teri E.K., Kelly E.C. and Andrea G. (2015)., Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2D6 and CYP2C19 Genotypes and Dosing of Selective Serotonin Reuptake Inhibitors., Clin Pharmacol Ther., 98(2), 127-134. doi: 10.1002/cpt.147.
  9. Bauer-Mehren A., Bundschus M., Rautschka M., Mayer M.A., Sanz F. and Furlong L.I. (2011)., Gene-Disease Network Analysis Reveals Functional Modules in Mendelian, Complex and Environmental Diseases., PLoS ONE, 6(6), e20284. https://doi.org/10.1371/ journal.pone.0020284
  10. Bauer-Mehren A., Bundschus M., Rautschka M., Mayer M.A., Sanz F. and Furlong L. I. (2010)., DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene–disease networks., Bioinformatics, 26(22), 2924-2926. doi:10.1093/bioinformatics/btq538
  11. Frezal J. (1998)., Genatlas database, genes and development defects., C. R. Acad Sci III, 321(10), 805-817.
  12. Boutet E., Lieberherr D., Tognolli M., Schneider M., Bansal P., Bridge A.J., Poux S., Bougueleret L. and Xenarios I. (2016)., UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View., Methods Mol Biol., 1374, 23-54. doi: 10.1007/978-1-4939-3167-5_2.
  13. Alpi E., Griss J., Wilter A., Silva S., Bely B., Antunes R., Zellner H., Daniel Ríos, Claire O, Analysis of the tryptic search space in UniProt databases., Proteomics, 15(1), 48-57. doi: 10.1002/pmic.201400227
  14. Knox C., Law V., Jewison T., Liu P., Ly S., Frolkis A., Pon A., Banco K., Mak C., Neveu V., Djoumbou Y., Eisner R., Guo A.C. and Wishart D.S. (2011)., DrugBank 3.0: a comprehensive resource for, Nucleic Acids Res., 39(suppl_1), D1035-D1041. doi: 10.1093/nar/gkq1126.
  15. Law V., Knox C., Djoumbou Y., Jewison T., Guo A.C., Liu Y., Maciejewski A., Arndt D., Wilson M., Neveu V., Tang A., Gabriel G., Ly C., Adamjee S., Dame Z.T., Han B., Zhou Y. and Wishart D.S. ( 2014)., DrugBank 4.0: shedding new light on drug metabolism., Nucleic Acids Res., 42(D1), D1091-D1097. Doi: 10.1093/nar/gkt1068.
  16. Szklarczyk D., Franceschini A., Wyder S., Forslund K., Heller D., Huerta-Cepas J., Simonovic M., Roth A., Santos A., Tsafou K.P., Kuhn M., Bork P., Jensen L.J. and Von Mering C. (2015)., STRING v10: protein-protein interaction networks, integrated over the tree of life., Nucleic Acids Res., 43(D1), D447-D452. doi: 10.1093/nar/gku1003.
  17. Mi H., Dong Q., Muruganujan A., Gaudet P., Lewis S. and Thomas P.D. (2010)., PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium., Nucleic Acids Res., 38(suppl_1), D204-D210. doi: 10.1093/nar/gkp1019.
  18. Rebhan M., Chalifa-Caspi V., Prilusky J. and Lancet D. (1997)., GeneCards: integrating information about genes, proteins and diseases., Trends Genet., 13(4), 163. doi:10.1016/S0168-9525(97)01103-7
  19. Stelzer G., Dalah I., Iny Stein T., Satanower Y., Rosen N., Nativ N., Oz-Levi D., Olender T., Belinky F., Bahir I., Krug H., Perco P., Mayer B., Kolker E., Safran M. and Lancet D. (2011)., In-silico Human Genomics with GeneCards., Human Genomics, 5(6), 709-717. doi:10.1186/1479-7364-5-6-709.
  20. Mi H., Muruganujan A. and Thomas P.D. (2013)., PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees., Nucleic Acids Res., 41(D1), D377-D386. doi: 10.1093/nar/gks1118.
  21. Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D. and Bairoch A. (2005)., Protein Identification and Analysis Tools on the ExPASy Server., The Proteomics Protocols Handbook, Humana Press, 571-607.