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Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures.

Greco D, Volpicelli F, Di Lieto A, Leo D, Perrone-Capano C, Auvinen P, di Porzio U - PLoS ONE (2009)

Bottom Line: We integrate bioinformatics and functional genomics, together with developmental neurobiology.Moreover, we propose guidelines for the computational analysis of microarray gene expression data.Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland. dario.greco@helsinki.fi

ABSTRACT
In the mammalian central nervous system (CNS) an important contingent of dopaminergic neurons are localized in the substantia nigra and in the ventral tegmental area of the ventral midbrain. They constitute an anatomically and functionally heterogeneous group of cells involved in a variety of regulatory mechanisms, from locomotion to emotional/motivational behavior. Midbrain dopaminergic neuron (mDA) primary cultures represent a useful tool to study molecular mechanisms involved in their development and maintenance. Considerable information has been gathered on the mDA neurons development and maturation in vivo, as well as on the molecular features of mDA primary cultures. Here we investigated in detail the gene expression differences between the tissue of origin and ventral midbrain primary cultures enriched in mDA neurons, using microarray technique. We integrated the results based on different re-annotations of the microarray probes. By using knowledge-based gene network techniques and promoter sequence analysis, we also uncovered mechanisms that might regulate the expression of CNS genes involved in the definition of the identity of specific cell types in the ventral midbrain. We integrate bioinformatics and functional genomics, together with developmental neurobiology. Moreover, we propose guidelines for the computational analysis of microarray gene expression data. Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.

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Significant genes with an annotation in DAVID database.The numbers of significant genes with a reliable DAVID annotation in each re-annotation analysis are shown. The intersections show the amount of common genes between two or all the three analyses. Proportional-area Venn diagrams were built as suggested by Chow and Rodgers [55].
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pone-0004977-g001: Significant genes with an annotation in DAVID database.The numbers of significant genes with a reliable DAVID annotation in each re-annotation analysis are shown. The intersections show the amount of common genes between two or all the three analyses. Proportional-area Venn diagrams were built as suggested by Chow and Rodgers [55].

Mentions: In order to characterize the expanded mesencephalic neuronal primary cultures and their expression profiling, as well as to identify new genes involved in mDA neurons differentiation and maturation, we performed the microarray analysis. To fulfill our aim we used three independent re-annotation systems based on the alignment of each oligonucleotide probe present on the RAE230A chipset against the Entrez Gene (EG), RefSeq (RS), and Ensembl gene (ENS) databases. Based on the new identities for probes we performed three independent analyses abbreviated from now on as EG, RS, and ENS. According to the original annotation released by the manufacturer, the RAE230A chipset contains 15923 probe sets; after re-annotation the probes were re-arranged in 8676 (EG), 13224 (RS), and 7600 (ENS) probe sets. After moderated t-test, we obtained 1016 genes in EG (11.7% of all the screened genes), 1568 (9.8% of all the screened genes) genes in RS, and 862 (11.3% of all the screened genes) genes in ENS to be differentially expressed between MesE11 and MesPC with p-value<0.001 (Table 1). We annotated the gene lists using DAVID which is a gene-centered database where gene entities from several databases are uniquely stored [27]. We took advantage of this system for parsing the gene lists from the three analyses. As many as 987 genes from EG, 1038 genes in RS, and 567 genes in ENS respectively had a reliable DAVID identifier. Of these, 425 unique genes were shared between the three annotations (Figure 1). The RefSeq-based set showed the largest overlapping with the other two annotation systems. From the set of 425 common genes, 268 genes were upregulated in MesPC, and 157 were upregulated in MesE11 (Table S1). Functional classification of these groups of genes was carried out with the DAVID-based Fisher's exact test. Overall, the three annotations produced very consistent fold change estimation for all of the 425 common genes (average standard deviation = 0.04).


Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures.

Greco D, Volpicelli F, Di Lieto A, Leo D, Perrone-Capano C, Auvinen P, di Porzio U - PLoS ONE (2009)

Significant genes with an annotation in DAVID database.The numbers of significant genes with a reliable DAVID annotation in each re-annotation analysis are shown. The intersections show the amount of common genes between two or all the three analyses. Proportional-area Venn diagrams were built as suggested by Chow and Rodgers [55].
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2654915&req=5

pone-0004977-g001: Significant genes with an annotation in DAVID database.The numbers of significant genes with a reliable DAVID annotation in each re-annotation analysis are shown. The intersections show the amount of common genes between two or all the three analyses. Proportional-area Venn diagrams were built as suggested by Chow and Rodgers [55].
Mentions: In order to characterize the expanded mesencephalic neuronal primary cultures and their expression profiling, as well as to identify new genes involved in mDA neurons differentiation and maturation, we performed the microarray analysis. To fulfill our aim we used three independent re-annotation systems based on the alignment of each oligonucleotide probe present on the RAE230A chipset against the Entrez Gene (EG), RefSeq (RS), and Ensembl gene (ENS) databases. Based on the new identities for probes we performed three independent analyses abbreviated from now on as EG, RS, and ENS. According to the original annotation released by the manufacturer, the RAE230A chipset contains 15923 probe sets; after re-annotation the probes were re-arranged in 8676 (EG), 13224 (RS), and 7600 (ENS) probe sets. After moderated t-test, we obtained 1016 genes in EG (11.7% of all the screened genes), 1568 (9.8% of all the screened genes) genes in RS, and 862 (11.3% of all the screened genes) genes in ENS to be differentially expressed between MesE11 and MesPC with p-value<0.001 (Table 1). We annotated the gene lists using DAVID which is a gene-centered database where gene entities from several databases are uniquely stored [27]. We took advantage of this system for parsing the gene lists from the three analyses. As many as 987 genes from EG, 1038 genes in RS, and 567 genes in ENS respectively had a reliable DAVID identifier. Of these, 425 unique genes were shared between the three annotations (Figure 1). The RefSeq-based set showed the largest overlapping with the other two annotation systems. From the set of 425 common genes, 268 genes were upregulated in MesPC, and 157 were upregulated in MesE11 (Table S1). Functional classification of these groups of genes was carried out with the DAVID-based Fisher's exact test. Overall, the three annotations produced very consistent fold change estimation for all of the 425 common genes (average standard deviation = 0.04).

Bottom Line: We integrate bioinformatics and functional genomics, together with developmental neurobiology.Moreover, we propose guidelines for the computational analysis of microarray gene expression data.Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland. dario.greco@helsinki.fi

ABSTRACT
In the mammalian central nervous system (CNS) an important contingent of dopaminergic neurons are localized in the substantia nigra and in the ventral tegmental area of the ventral midbrain. They constitute an anatomically and functionally heterogeneous group of cells involved in a variety of regulatory mechanisms, from locomotion to emotional/motivational behavior. Midbrain dopaminergic neuron (mDA) primary cultures represent a useful tool to study molecular mechanisms involved in their development and maintenance. Considerable information has been gathered on the mDA neurons development and maturation in vivo, as well as on the molecular features of mDA primary cultures. Here we investigated in detail the gene expression differences between the tissue of origin and ventral midbrain primary cultures enriched in mDA neurons, using microarray technique. We integrated the results based on different re-annotations of the microarray probes. By using knowledge-based gene network techniques and promoter sequence analysis, we also uncovered mechanisms that might regulate the expression of CNS genes involved in the definition of the identity of specific cell types in the ventral midbrain. We integrate bioinformatics and functional genomics, together with developmental neurobiology. Moreover, we propose guidelines for the computational analysis of microarray gene expression data. Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.

Show MeSH