Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals
Computer analysis of gene expression in the nervous system plays a fundamental role in biology, genetics, and neurosciences. We studied molecular and genetic mechanisms of enhanced aggressiveness in comparison with tolerant behaviour using experimental animal models developed at the Institute of Cyt...
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Series: | Journal of Integrative Bioinformatics |
Online Access: | https://doi.org/10.1515/jib-2016-292 |
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doaj-6ce4ce4d71dc4733b53f800eef5515162021-09-06T19:40:32ZengDe GruyterJournal of Integrative Bioinformatics1613-45162016-10-0113411510.1515/jib-2016-292jib-2016-292Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animalsBabenko Vladimir N.0Bragin Anatoly O.1Spitsina Anastasia M.2Chadaeva Irina V.3Galieva Elvira R.4Orlova Galina V.5Medvedeva Irina V.6Orlov Yuriy L.7Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, www.bionet.nsc.ru Russian FederationInstitute of Cytology and Genetics SB RAS, 630090Novosibirsk, www.bionet.nsc.ru, Russian FederationNovosibirsk State University, 630090Novosibirsk, lcg.nsu.ru, Russian FederationInstitute of Cytology and Genetics SB RAS, 630090Novosibirsk, www.bionet.nsc.ru, Russian FederationInstitute of Cytology and Genetics SB RAS, 630090Novosibirsk, www.bionet.nsc.ru, Russian FederationInstitute of Cytology and Genetics SB RAS, 630090Novosibirsk, www.bionet.nsc.ru, Russian FederationNovosibirsk State University, 630090Novosibirsk, lcg.nsu.ru, Russian FederationInstitute of Cytology and Genetics SB RAS, 630090Novosibirsk, www.bionet.nsc.ru Russian FederationComputer analysis of gene expression in the nervous system plays a fundamental role in biology, genetics, and neurosciences. We studied molecular and genetic mechanisms of enhanced aggressiveness in comparison with tolerant behaviour using experimental animal models developed at the Institute of Cytology and Genetics SB RAS. Grey rats (Rattus norvegicus) have been subjected to selection during several generations in two directions - friendly, tolerant behaviour towards man (tame grey rats) and increased aggressive behaviour. We used samples from hypothalamus, mesencephalic tegmentum and periaqueductum grey matter from brain areas of grey rats genetically selected by behaviour in many generations. The set of computer tools and data processing pipelines helped to find genes and gene regulation patterns related to behaviour patterns. RNAprofiling experiments revealed the lists of differentially expressed genes in the contrast samples as well as differentially spliced isoforms. The gene ontology categories of protein transport, phosphoproteins, and nucleotide binding are presented together with categories of transmission of nerve impulses and neuron development were identified. Differential alternative splicing events found in the brain areas studied are statistically significant. We discuss role of alternative splicing events for neurospecific genes in behaviour patterns as well as extension of brain transcriptomics profiling.https://doi.org/10.1515/jib-2016-292 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Babenko Vladimir N. Bragin Anatoly O. Spitsina Anastasia M. Chadaeva Irina V. Galieva Elvira R. Orlova Galina V. Medvedeva Irina V. Orlov Yuriy L. |
spellingShingle |
Babenko Vladimir N. Bragin Anatoly O. Spitsina Anastasia M. Chadaeva Irina V. Galieva Elvira R. Orlova Galina V. Medvedeva Irina V. Orlov Yuriy L. Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals Journal of Integrative Bioinformatics |
author_facet |
Babenko Vladimir N. Bragin Anatoly O. Spitsina Anastasia M. Chadaeva Irina V. Galieva Elvira R. Orlova Galina V. Medvedeva Irina V. Orlov Yuriy L. |
author_sort |
Babenko Vladimir N. |
title |
Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals |
title_short |
Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals |
title_full |
Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals |
title_fullStr |
Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals |
title_full_unstemmed |
Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals |
title_sort |
analysis of differential gene expression by rna-seq data in brain areas of laboratory animals |
publisher |
De Gruyter |
series |
Journal of Integrative Bioinformatics |
issn |
1613-4516 |
publishDate |
2016-10-01 |
description |
Computer analysis of gene expression in the nervous system plays a fundamental role in biology, genetics, and neurosciences. We studied molecular and genetic mechanisms of enhanced aggressiveness in comparison with tolerant behaviour using experimental animal models developed at the Institute of Cytology and Genetics SB RAS. Grey rats (Rattus norvegicus) have been subjected to selection during several generations in two directions - friendly, tolerant behaviour towards man (tame grey rats) and increased aggressive behaviour. We used samples from hypothalamus, mesencephalic tegmentum and periaqueductum grey matter from brain areas of grey rats genetically selected by behaviour in many generations. The set of computer tools and data processing pipelines helped to find genes and gene regulation patterns related to behaviour patterns. RNAprofiling experiments revealed the lists of differentially expressed genes in the contrast samples as well as differentially spliced isoforms. The gene ontology categories of protein transport, phosphoproteins, and nucleotide binding are presented together with categories of transmission of nerve impulses and neuron development were identified. Differential alternative splicing events found in the brain areas studied are statistically significant. We discuss role of alternative splicing events for neurospecific genes in behaviour patterns as well as extension of brain transcriptomics profiling. |
url |
https://doi.org/10.1515/jib-2016-292 |
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