Identification of novel gene and pathway targets for human epilepsy treatment

BACKGROUND: The aim of this study was to explore epilepsy-related mechanism so as to figure out the possible targets for epilepsy treatment. METHODS: The gene expression profile dataset GES32534 was downloaded from Gene Expression Omnibus database. We identified the differentially expressed genes (D...

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Autores principales:	Jin,Ying, Zhao,Chunzhe, Chen,Lihui, Liu,Xiangyu, Pan,Shuxiao, Ju,Dongsheng, Ma,Jing, Li,Jinying, Wei,Bo
Lenguaje:	English
Publicado:	Sociedad de Biología de Chile 2016
Materias:	Epilepsy Differentially expressed genes Functional annotation Protein-protein interaction network Co-expression module
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602016000100003
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spelling	oai:scielo:S0716-976020160001000032016-12-01Identification of novel gene and pathway targets for human epilepsy treatmentJin,YingZhao,ChunzheChen,LihuiLiu,XiangyuPan,ShuxiaoJu,DongshengMa,JingLi,JinyingWei,Bo Epilepsy Differentially expressed genes Functional annotation Protein-protein interaction network Co-expression module BACKGROUND: The aim of this study was to explore epilepsy-related mechanism so as to figure out the possible targets for epilepsy treatment. METHODS: The gene expression profile dataset GES32534 was downloaded from Gene Expression Omnibus database. We identified the differentially expressed genes (DEGs) by Affy package. Then the DEGs were used to perform gene ontology (GO) and pathway enrichment analyses. Furthermore, a protein-protein interaction (PPI) network was constructed with the DEGs followed by co-expression modules construction and analysis. RESULTS: Total 420 DEGs were screened out, including 214 up-regulated and 206 down-regulated genes. Functional enrichment analysis revealed that down-regulated genes were mainly involved in the process of immunity regulation and biological repairing process while up-regulated genes were closely related to transporter activity. PPI network analysis showed the top ten genes with high degrees were all down-regulated, among which FN1 had the highest degree. The up-regulated and down-regulated DEGs in the PPI network generated two obvious sub-co-expression modules, respectively. In up-co-expression module, SCN3B (sodium channel, voltage gated, type III beta subunit) was enriched in GO:0006814 ~ sodium ion transport. In down-co-expression module, C1QB (complement C1s), CIS (complement component 1, S subcomponent) and CFI (complement factor I) were enriched in GO:0006955 ~ immune response. CONCLUSION: The immune response and complement system play a major role in the pathogenesis of epilepsy. Additionally, C1QB, C1S, CFI, SCN3B and FN1 may be potential therapeutic targets for epilepsy.info:eu-repo/semantics/openAccessSociedad de Biología de ChileBiological Research v.49 20162016-01-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602016000100003en10.1186/s40659-015-0060-5
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Epilepsy Differentially expressed genes Functional annotation Protein-protein interaction network Co-expression module
spellingShingle	Epilepsy Differentially expressed genes Functional annotation Protein-protein interaction network Co-expression module Jin,Ying Zhao,Chunzhe Chen,Lihui Liu,Xiangyu Pan,Shuxiao Ju,Dongsheng Ma,Jing Li,Jinying Wei,Bo Identification of novel gene and pathway targets for human epilepsy treatment
description	BACKGROUND: The aim of this study was to explore epilepsy-related mechanism so as to figure out the possible targets for epilepsy treatment. METHODS: The gene expression profile dataset GES32534 was downloaded from Gene Expression Omnibus database. We identified the differentially expressed genes (DEGs) by Affy package. Then the DEGs were used to perform gene ontology (GO) and pathway enrichment analyses. Furthermore, a protein-protein interaction (PPI) network was constructed with the DEGs followed by co-expression modules construction and analysis. RESULTS: Total 420 DEGs were screened out, including 214 up-regulated and 206 down-regulated genes. Functional enrichment analysis revealed that down-regulated genes were mainly involved in the process of immunity regulation and biological repairing process while up-regulated genes were closely related to transporter activity. PPI network analysis showed the top ten genes with high degrees were all down-regulated, among which FN1 had the highest degree. The up-regulated and down-regulated DEGs in the PPI network generated two obvious sub-co-expression modules, respectively. In up-co-expression module, SCN3B (sodium channel, voltage gated, type III beta subunit) was enriched in GO:0006814 ~ sodium ion transport. In down-co-expression module, C1QB (complement C1s), CIS (complement component 1, S subcomponent) and CFI (complement factor I) were enriched in GO:0006955 ~ immune response. CONCLUSION: The immune response and complement system play a major role in the pathogenesis of epilepsy. Additionally, C1QB, C1S, CFI, SCN3B and FN1 may be potential therapeutic targets for epilepsy.
author	Jin,Ying Zhao,Chunzhe Chen,Lihui Liu,Xiangyu Pan,Shuxiao Ju,Dongsheng Ma,Jing Li,Jinying Wei,Bo
author_facet	Jin,Ying Zhao,Chunzhe Chen,Lihui Liu,Xiangyu Pan,Shuxiao Ju,Dongsheng Ma,Jing Li,Jinying Wei,Bo
author_sort	Jin,Ying
title	Identification of novel gene and pathway targets for human epilepsy treatment
title_short	Identification of novel gene and pathway targets for human epilepsy treatment
title_full	Identification of novel gene and pathway targets for human epilepsy treatment
title_fullStr	Identification of novel gene and pathway targets for human epilepsy treatment
title_full_unstemmed	Identification of novel gene and pathway targets for human epilepsy treatment
title_sort	identification of novel gene and pathway targets for human epilepsy treatment
publisher	Sociedad de Biología de Chile
publishDate	2016
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602016000100003
work_keys_str_mv	AT jinying identificationofnovelgeneandpathwaytargetsforhumanepilepsytreatment AT zhaochunzhe identificationofnovelgeneandpathwaytargetsforhumanepilepsytreatment AT chenlihui identificationofnovelgeneandpathwaytargetsforhumanepilepsytreatment AT liuxiangyu identificationofnovelgeneandpathwaytargetsforhumanepilepsytreatment AT panshuxiao identificationofnovelgeneandpathwaytargetsforhumanepilepsytreatment AT judongsheng identificationofnovelgeneandpathwaytargetsforhumanepilepsytreatment AT majing identificationofnovelgeneandpathwaytargetsforhumanepilepsytreatment AT lijinying identificationofnovelgeneandpathwaytargetsforhumanepilepsytreatment AT weibo identificationofnovelgeneandpathwaytargetsforhumanepilepsytreatment
_version_	1718441546865442816

Identification of novel gene and pathway targets for human epilepsy treatment

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