Cargando…

A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development

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 ava...

Descripción completa

Detalles Bibliográficos
Autores principales: Vied, Cynthia M., Freudenberg, Florian, Wang, Yuting, Raposo, Alexandre A. S. F., Feng, David, Nowakowski, Richard S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139594/
https://www.ncbi.nlm.nih.gov/pubmed/25191221
http://dx.doi.org/10.3389/fnins.2014.00257
_version_ 1782331374867316736
author Vied, Cynthia M.
Freudenberg, Florian
Wang, Yuting
Raposo, Alexandre A. S. F.
Feng, David
Nowakowski, Richard S.
author_facet Vied, Cynthia M.
Freudenberg, Florian
Wang, Yuting
Raposo, Alexandre A. S. F.
Feng, David
Nowakowski, Richard S.
author_sort Vied, Cynthia M.
collection PubMed
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.
format Online
Article
Text
id pubmed-4139594
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-41395942014-09-04 A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development Vied, Cynthia M. Freudenberg, Florian Wang, Yuting Raposo, Alexandre A. S. F. Feng, David Nowakowski, Richard S. Front Neurosci Genetics 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. Frontiers Media S.A. 2014-08-21 /pmc/articles/PMC4139594/ /pubmed/25191221 http://dx.doi.org/10.3389/fnins.2014.00257 Text en Copyright © 2014 Vied, Freudenberg, Wang, Raposo, Feng and Nowakowski. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Vied, Cynthia M.
Freudenberg, Florian
Wang, Yuting
Raposo, Alexandre A. S. F.
Feng, David
Nowakowski, Richard S.
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
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_short A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development
title_sort multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139594/
https://www.ncbi.nlm.nih.gov/pubmed/25191221
http://dx.doi.org/10.3389/fnins.2014.00257
work_keys_str_mv AT viedcynthiam amultiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment
AT freudenbergflorian amultiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment
AT wangyuting amultiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment
AT raposoalexandreasf amultiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment
AT fengdavid amultiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment
AT nowakowskirichards amultiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment
AT viedcynthiam multiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment
AT freudenbergflorian multiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment
AT wangyuting multiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment
AT raposoalexandreasf multiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment
AT fengdavid multiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment
AT nowakowskirichards multiresourcedataintegrationapproachidentificationofcandidategenesregulatingcellproliferationduringneocorticaldevelopment