Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma.
Our goal of this study was to reconstruct a "genome-scale co-expression network" and find important modules in lung adenocarcinoma so that we could identify the genes involved in lung adenocarcinoma. We integrated gene mutation, GWAS, CGH, array-CGH and SNP array data in order to identify...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3708931?pdf=render |
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| author | Gholamreza Bidkhori Zahra Narimani Saman Hosseini Ashtiani Ali Moeini Abbas Nowzari-Dalini Ali Masoudi-Nejad |
| author_facet | Gholamreza Bidkhori Zahra Narimani Saman Hosseini Ashtiani Ali Moeini Abbas Nowzari-Dalini Ali Masoudi-Nejad |
| author_sort | Gholamreza Bidkhori |
| collection | DOAJ |
| description | Our goal of this study was to reconstruct a "genome-scale co-expression network" and find important modules in lung adenocarcinoma so that we could identify the genes involved in lung adenocarcinoma. We integrated gene mutation, GWAS, CGH, array-CGH and SNP array data in order to identify important genes and loci in genome-scale. Afterwards, on the basis of the identified genes a co-expression network was reconstructed from the co-expression data. The reconstructed network was named "genome-scale co-expression network". As the next step, 23 key modules were disclosed through clustering. In this study a number of genes have been identified for the first time to be implicated in lung adenocarcinoma by analyzing the modules. The genes EGFR, PIK3CA, TAF15, XIAP, VAPB, Appl1, Rab5a, ARF4, CLPTM1L, SP4, ZNF124, LPP, FOXP1, SOX18, MSX2, NFE2L2, SMARCC1, TRA2B, CBX3, PRPF6, ATP6V1C1, MYBBP1A, MACF1, GRM2, TBXA2R, PRKAR2A, PTK2, PGF and MYO10 are among the genes that belong to modules 1 and 22. All these genes, being implicated in at least one of the phenomena, namely cell survival, proliferation and metastasis, have an over-expression pattern similar to that of EGFR. In few modules, the genes such as CCNA2 (Cyclin A2), CCNB2 (Cyclin B2), CDK1, CDK5, CDC27, CDCA5, CDCA8, ASPM, BUB1, KIF15, KIF2C, NEK2, NUSAP1, PRC1, SMC4, SYCE2, TFDP1, CDC42 and ARHGEF9 are present that play a crucial role in cell cycle progression. In addition to the mentioned genes, there are some other genes (i.e. DLGAP5, BIRC5, PSMD2, Src, TTK, SENP2, PSMD2, DOK2, FUS and etc.) in the modules. |
| first_indexed | 2024-12-10T04:54:31Z |
| format | Article |
| id | doaj.art-2d7e027b3d5448e4bf665796877f8f9b |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T04:54:31Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-2d7e027b3d5448e4bf665796877f8f9b2022-12-22T02:01:32ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0187e6755210.1371/journal.pone.0067552Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma.Gholamreza BidkhoriZahra NarimaniSaman Hosseini AshtianiAli MoeiniAbbas Nowzari-DaliniAli Masoudi-NejadOur goal of this study was to reconstruct a "genome-scale co-expression network" and find important modules in lung adenocarcinoma so that we could identify the genes involved in lung adenocarcinoma. We integrated gene mutation, GWAS, CGH, array-CGH and SNP array data in order to identify important genes and loci in genome-scale. Afterwards, on the basis of the identified genes a co-expression network was reconstructed from the co-expression data. The reconstructed network was named "genome-scale co-expression network". As the next step, 23 key modules were disclosed through clustering. In this study a number of genes have been identified for the first time to be implicated in lung adenocarcinoma by analyzing the modules. The genes EGFR, PIK3CA, TAF15, XIAP, VAPB, Appl1, Rab5a, ARF4, CLPTM1L, SP4, ZNF124, LPP, FOXP1, SOX18, MSX2, NFE2L2, SMARCC1, TRA2B, CBX3, PRPF6, ATP6V1C1, MYBBP1A, MACF1, GRM2, TBXA2R, PRKAR2A, PTK2, PGF and MYO10 are among the genes that belong to modules 1 and 22. All these genes, being implicated in at least one of the phenomena, namely cell survival, proliferation and metastasis, have an over-expression pattern similar to that of EGFR. In few modules, the genes such as CCNA2 (Cyclin A2), CCNB2 (Cyclin B2), CDK1, CDK5, CDC27, CDCA5, CDCA8, ASPM, BUB1, KIF15, KIF2C, NEK2, NUSAP1, PRC1, SMC4, SYCE2, TFDP1, CDC42 and ARHGEF9 are present that play a crucial role in cell cycle progression. In addition to the mentioned genes, there are some other genes (i.e. DLGAP5, BIRC5, PSMD2, Src, TTK, SENP2, PSMD2, DOK2, FUS and etc.) in the modules.http://europepmc.org/articles/PMC3708931?pdf=render |
| spellingShingle | Gholamreza Bidkhori Zahra Narimani Saman Hosseini Ashtiani Ali Moeini Abbas Nowzari-Dalini Ali Masoudi-Nejad Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma. PLoS ONE |
| title | Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma. |
| title_full | Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma. |
| title_fullStr | Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma. |
| title_full_unstemmed | Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma. |
| title_short | Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma. |
| title_sort | reconstruction of an integrated genome scale co expression network reveals key modules involved in lung adenocarcinoma |
| url | http://europepmc.org/articles/PMC3708931?pdf=render |
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