A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development
Autor(a) principal: | |
---|---|
Data de Publicação: | 2014 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10400.7/375 |
Resumo: | Neurons of the mammalian neocortex are produced by proliferating cells located in the ventricular zone (VZ) lining the lateral ventricles. This is a complex and sequential process, requiring precise control of cell cycle progression, fate commitment and differentiation. We have analyzed publicly available databases from mouse and human to identify candidate genes that are potentially involved in regulating early neocortical development and neurogenesis. We used a mouse in situ hybridization dataset (The Allen Institute for Brain Science) to identify 13 genes (Cdon, Celsr1, Dbi, E2f5, Eomes, Hmgn2, Neurog2, Notch1, Pcnt, Sox3, Ssrp1, Tead2, Tgif2) with high correlation of expression in the proliferating cells of the VZ of the neocortex at early stages of development (E15.5). We generated a similar human brain network using microarray and RNA-seq data (BrainSpan Atlas) and identified 407 genes with high expression in the developing human VZ and subventricular zone (SVZ) at 8-9 post-conception weeks. Seven of the human genes were also present in the mouse VZ network. The human and mouse networks were extended using available genetic and proteomic datasets through GeneMANIA. A gene ontology search of the mouse and human networks indicated that many of the genes are involved in the cell cycle, DNA replication, mitosis and transcriptional regulation. The reported involvement of Cdon, Celsr1, Dbi, Eomes, Neurog2, Notch1, Pcnt, Sox3, Tead2, and Tgif2 in neural development or diseases resulting from the disruption of neurogenesis validates these candidate genes. Taken together, our knowledge-based discovery method has validated the involvement of many genes already known to be involved in neocortical development and extended the potential number of genes by 100's, many of which are involved in functions related to cell proliferation but others of which are potential candidates for involvement in the regulation of neocortical development. |
id |
RCAP_8a575a09c0302b85db77fda81517f829 |
---|---|
oai_identifier_str |
oai:arca.igc.gulbenkian.pt:10400.7/375 |
network_acronym_str |
RCAP |
network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository_id_str |
7160 |
spelling |
A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical developmentthe allen institute for brain scienceneocortex developmentgene expressionventricular zone (VZ)subventricular zone (SVZ)GeneMANIANeurons of the mammalian neocortex are produced by proliferating cells located in the ventricular zone (VZ) lining the lateral ventricles. This is a complex and sequential process, requiring precise control of cell cycle progression, fate commitment and differentiation. We have analyzed publicly available databases from mouse and human to identify candidate genes that are potentially involved in regulating early neocortical development and neurogenesis. We used a mouse in situ hybridization dataset (The Allen Institute for Brain Science) to identify 13 genes (Cdon, Celsr1, Dbi, E2f5, Eomes, Hmgn2, Neurog2, Notch1, Pcnt, Sox3, Ssrp1, Tead2, Tgif2) with high correlation of expression in the proliferating cells of the VZ of the neocortex at early stages of development (E15.5). We generated a similar human brain network using microarray and RNA-seq data (BrainSpan Atlas) and identified 407 genes with high expression in the developing human VZ and subventricular zone (SVZ) at 8-9 post-conception weeks. Seven of the human genes were also present in the mouse VZ network. The human and mouse networks were extended using available genetic and proteomic datasets through GeneMANIA. A gene ontology search of the mouse and human networks indicated that many of the genes are involved in the cell cycle, DNA replication, mitosis and transcriptional regulation. The reported involvement of Cdon, Celsr1, Dbi, Eomes, Neurog2, Notch1, Pcnt, Sox3, Tead2, and Tgif2 in neural development or diseases resulting from the disruption of neurogenesis validates these candidate genes. Taken together, our knowledge-based discovery method has validated the involvement of many genes already known to be involved in neocortical development and extended the potential number of genes by 100's, many of which are involved in functions related to cell proliferation but others of which are potential candidates for involvement in the regulation of neocortical development.Alexander von Humboldt foundation (FlorianFreudenberg), the FSU Department of Biomedical Sciences, FCT grant: (PTDC/NEU-NMC/0315/2012).Frontiers Research FoundationARCAVied, Cynthia M.Freudenberg, FlorianWang, YutingRaposo, Alexandre A. S. F.Feng, DavidNowakowski, Richard S.2015-10-07T10:45:21Z2014-08-212014-08-21T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.7/375engViedCM,FreudenbergF,WangY,RaposoAASF,FengDandNowakowski RS (2014)Amulti-resourcedataintegrationapproach:identificationofcandidate genesregulatingcellproliferationduringneocorticaldevelopment.Front.Neurosci. 8:257. doi:10.3389/fnins.2014.0025710.3389/fnins.2014.00257info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2022-11-29T14:34:46Zoai:arca.igc.gulbenkian.pt:10400.7/375Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T16:11:40.669499Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development |
title |
A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development |
spellingShingle |
A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development Vied, Cynthia M. the allen institute for brain science neocortex development gene expression ventricular zone (VZ) subventricular zone (SVZ) GeneMANIA |
title_short |
A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development |
title_full |
A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development |
title_fullStr |
A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development |
title_full_unstemmed |
A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development |
title_sort |
A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development |
author |
Vied, Cynthia M. |
author_facet |
Vied, Cynthia M. Freudenberg, Florian Wang, Yuting Raposo, Alexandre A. S. F. Feng, David Nowakowski, Richard S. |
author_role |
author |
author2 |
Freudenberg, Florian Wang, Yuting Raposo, Alexandre A. S. F. Feng, David Nowakowski, Richard S. |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
ARCA |
dc.contributor.author.fl_str_mv |
Vied, Cynthia M. Freudenberg, Florian Wang, Yuting Raposo, Alexandre A. S. F. Feng, David Nowakowski, Richard S. |
dc.subject.por.fl_str_mv |
the allen institute for brain science neocortex development gene expression ventricular zone (VZ) subventricular zone (SVZ) GeneMANIA |
topic |
the allen institute for brain science neocortex development gene expression ventricular zone (VZ) subventricular zone (SVZ) GeneMANIA |
description |
Neurons of the mammalian neocortex are produced by proliferating cells located in the ventricular zone (VZ) lining the lateral ventricles. This is a complex and sequential process, requiring precise control of cell cycle progression, fate commitment and differentiation. We have analyzed publicly available databases from mouse and human to identify candidate genes that are potentially involved in regulating early neocortical development and neurogenesis. We used a mouse in situ hybridization dataset (The Allen Institute for Brain Science) to identify 13 genes (Cdon, Celsr1, Dbi, E2f5, Eomes, Hmgn2, Neurog2, Notch1, Pcnt, Sox3, Ssrp1, Tead2, Tgif2) with high correlation of expression in the proliferating cells of the VZ of the neocortex at early stages of development (E15.5). We generated a similar human brain network using microarray and RNA-seq data (BrainSpan Atlas) and identified 407 genes with high expression in the developing human VZ and subventricular zone (SVZ) at 8-9 post-conception weeks. Seven of the human genes were also present in the mouse VZ network. The human and mouse networks were extended using available genetic and proteomic datasets through GeneMANIA. A gene ontology search of the mouse and human networks indicated that many of the genes are involved in the cell cycle, DNA replication, mitosis and transcriptional regulation. The reported involvement of Cdon, Celsr1, Dbi, Eomes, Neurog2, Notch1, Pcnt, Sox3, Tead2, and Tgif2 in neural development or diseases resulting from the disruption of neurogenesis validates these candidate genes. Taken together, our knowledge-based discovery method has validated the involvement of many genes already known to be involved in neocortical development and extended the potential number of genes by 100's, many of which are involved in functions related to cell proliferation but others of which are potential candidates for involvement in the regulation of neocortical development. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-08-21 2014-08-21T00:00:00Z 2015-10-07T10:45:21Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10400.7/375 |
url |
http://hdl.handle.net/10400.7/375 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
ViedCM,FreudenbergF,WangY,RaposoAASF,FengDandNowakowski RS (2014)Amulti-resourcedataintegrationapproach:identificationofcandidate genesregulatingcellproliferationduringneocorticaldevelopment.Front.Neurosci. 8:257. doi:10.3389/fnins.2014.00257 10.3389/fnins.2014.00257 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Frontiers Research Foundation |
publisher.none.fl_str_mv |
Frontiers Research Foundation |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
|
_version_ |
1799130572199559168 |