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Gene expression in the rat brain: high similarity but unique differences between frontomedial-, temporal- and occipital cortex.

Stansberg C, Ersland KM, van der Valk P, Steen VM - BMC Neurosci (2011)

Bottom Line: A large proportion of these 65 genes appear to be involved in signal transduction, including the ion channel Fxyd6, the neuropeptide Grp and the nuclear receptor Rorb.We also find that the majority of these genes display increased expression levels around birth and show distinct preferences for certain cortical layers and cell types in rodents.Since specific patterns of expression often are linked to equally specialised biological functions, we propose that these cortex sub-region enriched genes are important for proper functioning of the cortical regions in question.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dr E. Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Norway. Christine.Stansberg@uib.no

ABSTRACT

Background: The six-layered neocortex of the mammalian brain may appear largely homologous, but is in reality a modular structure of anatomically and functionally distinct areas. However, global gene expression seems to be almost identical across the cerebral cortex and only a few genes have so far been reported to show regional enrichment in specific cortical areas.

Results: In the present study on adult rat brain, we have corroborated the strikingly similar gene expression among cortical areas. However, differential expression analysis has allowed for the identification of 30, 24 and 11 genes enriched in frontomedial -, temporal- or occipital cortex, respectively. A large proportion of these 65 genes appear to be involved in signal transduction, including the ion channel Fxyd6, the neuropeptide Grp and the nuclear receptor Rorb. We also find that the majority of these genes display increased expression levels around birth and show distinct preferences for certain cortical layers and cell types in rodents.

Conclusions: Since specific patterns of expression often are linked to equally specialised biological functions, we propose that these cortex sub-region enriched genes are important for proper functioning of the cortical regions in question.

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Related in: MedlinePlus

Functional characterisation of the 65 genes regionally enriched in cortex subregions. Panther was used to search for over-represented biological processes and molecular functions among the sub-regionally enriched cortex-genes. The heat map demonstrates the significance of over- and under-represented Panther categories in the entire set of 65 cortical genes (column 2), the 30 FMCx genes (column 3), the 24 TCx genes (column 4) and the 11 OCx genes (column 5). The colour intensity displays the statistical significance (negative log p-value) of over- and under-represented functional categories. Red colour signifies an over-representation of genes mapping to a certain term, blue colour an under-representation and white a representation as expected, based on the overall distribution on the array. Numbers presented on the heat map indicate the percentage of genes within a gene set that map to the given category, e.g. 38% of the 65 regional genes map to the biological process 'signal transduction'. The first column states the overall distribution of a term among the 25,170 genes with detectable expression in the data set, e.g. 13.6% of the 65 regional genes were expected to map to 'signal transduction', hence this category is significantly over-represented among our regional genes. Exp, expected (based on overall distribution on array); Cx, cortex; FCx, fronto-medial cortex; TCx, temporal cortex; OCx, occipital cortex; #, number of genes in each gene set; %, percentage of genes.
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Figure 6: Functional characterisation of the 65 genes regionally enriched in cortex subregions. Panther was used to search for over-represented biological processes and molecular functions among the sub-regionally enriched cortex-genes. The heat map demonstrates the significance of over- and under-represented Panther categories in the entire set of 65 cortical genes (column 2), the 30 FMCx genes (column 3), the 24 TCx genes (column 4) and the 11 OCx genes (column 5). The colour intensity displays the statistical significance (negative log p-value) of over- and under-represented functional categories. Red colour signifies an over-representation of genes mapping to a certain term, blue colour an under-representation and white a representation as expected, based on the overall distribution on the array. Numbers presented on the heat map indicate the percentage of genes within a gene set that map to the given category, e.g. 38% of the 65 regional genes map to the biological process 'signal transduction'. The first column states the overall distribution of a term among the 25,170 genes with detectable expression in the data set, e.g. 13.6% of the 65 regional genes were expected to map to 'signal transduction', hence this category is significantly over-represented among our regional genes. Exp, expected (based on overall distribution on array); Cx, cortex; FCx, fronto-medial cortex; TCx, temporal cortex; OCx, occipital cortex; #, number of genes in each gene set; %, percentage of genes.

Mentions: In the same rat model, we have previously shown that functional annotations of genes preferably expressed in a certain brain region reflect the functional specialisation of the given area [20]. We therefore mapped the regionally enriched cortex genes, both the entire set of 65 cortical genes and each regional set individually, to the Panther annotation categories to search for significant over-representations of particular functional groups compared to the overall distribution of the 25,170 genes detected on the AB1700 Rat Genome Survey array (Figure 6). At first glance it is interesting to note that only 23% of the 65 genes examined were so far un-annotated, with no known function. This is far less than expected based on the overall distribution of un-annotated genes on the microarray (~50%) (Figure 6).


Gene expression in the rat brain: high similarity but unique differences between frontomedial-, temporal- and occipital cortex.

Stansberg C, Ersland KM, van der Valk P, Steen VM - BMC Neurosci (2011)

Functional characterisation of the 65 genes regionally enriched in cortex subregions. Panther was used to search for over-represented biological processes and molecular functions among the sub-regionally enriched cortex-genes. The heat map demonstrates the significance of over- and under-represented Panther categories in the entire set of 65 cortical genes (column 2), the 30 FMCx genes (column 3), the 24 TCx genes (column 4) and the 11 OCx genes (column 5). The colour intensity displays the statistical significance (negative log p-value) of over- and under-represented functional categories. Red colour signifies an over-representation of genes mapping to a certain term, blue colour an under-representation and white a representation as expected, based on the overall distribution on the array. Numbers presented on the heat map indicate the percentage of genes within a gene set that map to the given category, e.g. 38% of the 65 regional genes map to the biological process 'signal transduction'. The first column states the overall distribution of a term among the 25,170 genes with detectable expression in the data set, e.g. 13.6% of the 65 regional genes were expected to map to 'signal transduction', hence this category is significantly over-represented among our regional genes. Exp, expected (based on overall distribution on array); Cx, cortex; FCx, fronto-medial cortex; TCx, temporal cortex; OCx, occipital cortex; #, number of genes in each gene set; %, percentage of genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 6: Functional characterisation of the 65 genes regionally enriched in cortex subregions. Panther was used to search for over-represented biological processes and molecular functions among the sub-regionally enriched cortex-genes. The heat map demonstrates the significance of over- and under-represented Panther categories in the entire set of 65 cortical genes (column 2), the 30 FMCx genes (column 3), the 24 TCx genes (column 4) and the 11 OCx genes (column 5). The colour intensity displays the statistical significance (negative log p-value) of over- and under-represented functional categories. Red colour signifies an over-representation of genes mapping to a certain term, blue colour an under-representation and white a representation as expected, based on the overall distribution on the array. Numbers presented on the heat map indicate the percentage of genes within a gene set that map to the given category, e.g. 38% of the 65 regional genes map to the biological process 'signal transduction'. The first column states the overall distribution of a term among the 25,170 genes with detectable expression in the data set, e.g. 13.6% of the 65 regional genes were expected to map to 'signal transduction', hence this category is significantly over-represented among our regional genes. Exp, expected (based on overall distribution on array); Cx, cortex; FCx, fronto-medial cortex; TCx, temporal cortex; OCx, occipital cortex; #, number of genes in each gene set; %, percentage of genes.
Mentions: In the same rat model, we have previously shown that functional annotations of genes preferably expressed in a certain brain region reflect the functional specialisation of the given area [20]. We therefore mapped the regionally enriched cortex genes, both the entire set of 65 cortical genes and each regional set individually, to the Panther annotation categories to search for significant over-representations of particular functional groups compared to the overall distribution of the 25,170 genes detected on the AB1700 Rat Genome Survey array (Figure 6). At first glance it is interesting to note that only 23% of the 65 genes examined were so far un-annotated, with no known function. This is far less than expected based on the overall distribution of un-annotated genes on the microarray (~50%) (Figure 6).

Bottom Line: A large proportion of these 65 genes appear to be involved in signal transduction, including the ion channel Fxyd6, the neuropeptide Grp and the nuclear receptor Rorb.We also find that the majority of these genes display increased expression levels around birth and show distinct preferences for certain cortical layers and cell types in rodents.Since specific patterns of expression often are linked to equally specialised biological functions, we propose that these cortex sub-region enriched genes are important for proper functioning of the cortical regions in question.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dr E. Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Norway. Christine.Stansberg@uib.no

ABSTRACT

Background: The six-layered neocortex of the mammalian brain may appear largely homologous, but is in reality a modular structure of anatomically and functionally distinct areas. However, global gene expression seems to be almost identical across the cerebral cortex and only a few genes have so far been reported to show regional enrichment in specific cortical areas.

Results: In the present study on adult rat brain, we have corroborated the strikingly similar gene expression among cortical areas. However, differential expression analysis has allowed for the identification of 30, 24 and 11 genes enriched in frontomedial -, temporal- or occipital cortex, respectively. A large proportion of these 65 genes appear to be involved in signal transduction, including the ion channel Fxyd6, the neuropeptide Grp and the nuclear receptor Rorb. We also find that the majority of these genes display increased expression levels around birth and show distinct preferences for certain cortical layers and cell types in rodents.

Conclusions: Since specific patterns of expression often are linked to equally specialised biological functions, we propose that these cortex sub-region enriched genes are important for proper functioning of the cortical regions in question.

Show MeSH
Related in: MedlinePlus