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Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation.

Aid-Pavlidis T, Pavlidis P, Timmusk T - BMC Genomics (2009)

Bottom Line: Conventional microarray co-expression analysis is usually carried out by merging the datasets or by confirming the re-occurrence of significant correlations across datasets.Also, several transcription factor identified here have been reported to regulate BDNF expression in vitro and in vivo.The study demonstrates the potential of the "subset" approach in co-expression conservation analysis for studying the regulation of single genes and proposes novel regulators of BDNF gene expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 19086 Tallinn, Estonia. tamara.aid@gmail.com

ABSTRACT

Background: Alterations in brain-derived neurotrophic factor (BDNF) gene expression contribute to serious pathologies such as depression, epilepsy, cancer, Alzheimer's, Huntington and Parkinson's disease. Therefore, exploring the mechanisms of BDNF regulation represents a great clinical importance. Studying BDNF expression remains difficult due to its multiple neural activity-dependent and tissue-specific promoters. Thus, microarray data could provide insight into the regulation of this complex gene. Conventional microarray co-expression analysis is usually carried out by merging the datasets or by confirming the re-occurrence of significant correlations across datasets. However, co-expression patterns can be different under various conditions that are represented by subsets in a dataset. Therefore, assessing co-expression by measuring correlation coefficient across merged samples of a dataset or by merging datasets might not capture all correlation patterns.

Results: In our study, we performed meta-coexpression analysis of publicly available microarray data using BDNF as a "guide-gene" introducing a "subset" approach. The key steps of the analysis included: dividing datasets into subsets with biologically meaningful sample content (e.g. tissue, gender or disease state subsets); analyzing co-expression with the BDNF gene in each subset separately; and confirming co- expression links across subsets. Finally, we analyzed conservation in co-expression with BDNF between human, mouse and rat, and sought for conserved over-represented TFBSs in BDNF and BDNF-correlated genes. Correlated genes discovered in this study regulate nervous system development, and are associated with various types of cancer and neurological disorders. Also, several transcription factor identified here have been reported to regulate BDNF expression in vitro and in vivo.

Conclusion: The study demonstrates the potential of the "subset" approach in co-expression conservation analysis for studying the regulation of single genes and proposes novel regulators of BDNF gene expression.

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Novel regulatory elements in the BDNF gene. Highly conserved TFBSs in the BDNF locus as predicted by DiRE and CONFAC tools. Given TFBSs were also found to be over-represented in the BDNF-correlated genes. Histograms represent evolutionary conservation across 9 mammal species (adapted from UCSC Genome Browser at ) (39). The height of the histogram reflects the size of the conservation score. Conservation for each species is shown in grayscale using darker values to indicate higher levels of overall conservation. Missing sequences are highlighted by regions of yellow. Single line: no bases in the aligned species; double line: aligning species has one or more unalignable bases in the gap region. Transcribed regions (BDNF exons and 3'UTR) are highlighted in green; non-transcribed regions (BDNF promoters and introns) are highlighted in blue. Red ovals represent TFBSs mapped to the BDNF gene sequences. Mapped TFBSs have Matrix Similarity score >0.85 and Core Similarity score >0.99. Core elements of presented TFBSs have 100% of conservation across mammals. For the structure of human BDNF see Pruunsild et al., 2007 [11].
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Figure 3: Novel regulatory elements in the BDNF gene. Highly conserved TFBSs in the BDNF locus as predicted by DiRE and CONFAC tools. Given TFBSs were also found to be over-represented in the BDNF-correlated genes. Histograms represent evolutionary conservation across 9 mammal species (adapted from UCSC Genome Browser at ) (39). The height of the histogram reflects the size of the conservation score. Conservation for each species is shown in grayscale using darker values to indicate higher levels of overall conservation. Missing sequences are highlighted by regions of yellow. Single line: no bases in the aligned species; double line: aligning species has one or more unalignable bases in the gap region. Transcribed regions (BDNF exons and 3'UTR) are highlighted in green; non-transcribed regions (BDNF promoters and introns) are highlighted in blue. Red ovals represent TFBSs mapped to the BDNF gene sequences. Mapped TFBSs have Matrix Similarity score >0.85 and Core Similarity score >0.99. Core elements of presented TFBSs have 100% of conservation across mammals. For the structure of human BDNF see Pruunsild et al., 2007 [11].

Mentions: Using DiRE we discovered two regulatory regions at the human BDNF locus that were enriched in TFBSs (Figure 3) [see also Additional file 10: DiRE motif discovery results for BDNF and 84 conserved correlated genes]. The first regulatory region spans 218 bp and is located 622 bp upstream of human BDNF exon I transcription start site (TSS). The second putative regulatory region is 1625 bp long and located 2915 bp downstream of the BDNF stop-codon. Analysis of mouse and rat gene lists produced similar results. Significant over-representation of binding sites for WT1, KROX, ZNF219, NFkB, SOX, CREB, OCT, MYOD and MEF2 transcription factors was reported by DiRE in BDNF and BDNF-correlated genes when all the genes were analyzed as one cluster [see Additional file 10: DiRE motif discovery results for BDNF and 84 conserved correlated genes]. Also, the following cluster-specific over-representation of TFBSs was detected: i) CNS - KROX; ii) endocrine - TAL1beta/TCF4, ETS2, SOX5, and ARID5B (known as MRF2); iii) gastrointestinal - MMEF2, and SREBF1; iv) genitourinary - ATF4/CREB, and GTF3 (TFIII) (Table 3) [see also Additional file 11: DiRE motif discovery results for conserved BDNF-correlated genes clustered by tissue-specific expression].


Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation.

Aid-Pavlidis T, Pavlidis P, Timmusk T - BMC Genomics (2009)

Novel regulatory elements in the BDNF gene. Highly conserved TFBSs in the BDNF locus as predicted by DiRE and CONFAC tools. Given TFBSs were also found to be over-represented in the BDNF-correlated genes. Histograms represent evolutionary conservation across 9 mammal species (adapted from UCSC Genome Browser at ) (39). The height of the histogram reflects the size of the conservation score. Conservation for each species is shown in grayscale using darker values to indicate higher levels of overall conservation. Missing sequences are highlighted by regions of yellow. Single line: no bases in the aligned species; double line: aligning species has one or more unalignable bases in the gap region. Transcribed regions (BDNF exons and 3'UTR) are highlighted in green; non-transcribed regions (BDNF promoters and introns) are highlighted in blue. Red ovals represent TFBSs mapped to the BDNF gene sequences. Mapped TFBSs have Matrix Similarity score >0.85 and Core Similarity score >0.99. Core elements of presented TFBSs have 100% of conservation across mammals. For the structure of human BDNF see Pruunsild et al., 2007 [11].
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2748098&req=5

Figure 3: Novel regulatory elements in the BDNF gene. Highly conserved TFBSs in the BDNF locus as predicted by DiRE and CONFAC tools. Given TFBSs were also found to be over-represented in the BDNF-correlated genes. Histograms represent evolutionary conservation across 9 mammal species (adapted from UCSC Genome Browser at ) (39). The height of the histogram reflects the size of the conservation score. Conservation for each species is shown in grayscale using darker values to indicate higher levels of overall conservation. Missing sequences are highlighted by regions of yellow. Single line: no bases in the aligned species; double line: aligning species has one or more unalignable bases in the gap region. Transcribed regions (BDNF exons and 3'UTR) are highlighted in green; non-transcribed regions (BDNF promoters and introns) are highlighted in blue. Red ovals represent TFBSs mapped to the BDNF gene sequences. Mapped TFBSs have Matrix Similarity score >0.85 and Core Similarity score >0.99. Core elements of presented TFBSs have 100% of conservation across mammals. For the structure of human BDNF see Pruunsild et al., 2007 [11].
Mentions: Using DiRE we discovered two regulatory regions at the human BDNF locus that were enriched in TFBSs (Figure 3) [see also Additional file 10: DiRE motif discovery results for BDNF and 84 conserved correlated genes]. The first regulatory region spans 218 bp and is located 622 bp upstream of human BDNF exon I transcription start site (TSS). The second putative regulatory region is 1625 bp long and located 2915 bp downstream of the BDNF stop-codon. Analysis of mouse and rat gene lists produced similar results. Significant over-representation of binding sites for WT1, KROX, ZNF219, NFkB, SOX, CREB, OCT, MYOD and MEF2 transcription factors was reported by DiRE in BDNF and BDNF-correlated genes when all the genes were analyzed as one cluster [see Additional file 10: DiRE motif discovery results for BDNF and 84 conserved correlated genes]. Also, the following cluster-specific over-representation of TFBSs was detected: i) CNS - KROX; ii) endocrine - TAL1beta/TCF4, ETS2, SOX5, and ARID5B (known as MRF2); iii) gastrointestinal - MMEF2, and SREBF1; iv) genitourinary - ATF4/CREB, and GTF3 (TFIII) (Table 3) [see also Additional file 11: DiRE motif discovery results for conserved BDNF-correlated genes clustered by tissue-specific expression].

Bottom Line: Conventional microarray co-expression analysis is usually carried out by merging the datasets or by confirming the re-occurrence of significant correlations across datasets.Also, several transcription factor identified here have been reported to regulate BDNF expression in vitro and in vivo.The study demonstrates the potential of the "subset" approach in co-expression conservation analysis for studying the regulation of single genes and proposes novel regulators of BDNF gene expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 19086 Tallinn, Estonia. tamara.aid@gmail.com

ABSTRACT

Background: Alterations in brain-derived neurotrophic factor (BDNF) gene expression contribute to serious pathologies such as depression, epilepsy, cancer, Alzheimer's, Huntington and Parkinson's disease. Therefore, exploring the mechanisms of BDNF regulation represents a great clinical importance. Studying BDNF expression remains difficult due to its multiple neural activity-dependent and tissue-specific promoters. Thus, microarray data could provide insight into the regulation of this complex gene. Conventional microarray co-expression analysis is usually carried out by merging the datasets or by confirming the re-occurrence of significant correlations across datasets. However, co-expression patterns can be different under various conditions that are represented by subsets in a dataset. Therefore, assessing co-expression by measuring correlation coefficient across merged samples of a dataset or by merging datasets might not capture all correlation patterns.

Results: In our study, we performed meta-coexpression analysis of publicly available microarray data using BDNF as a "guide-gene" introducing a "subset" approach. The key steps of the analysis included: dividing datasets into subsets with biologically meaningful sample content (e.g. tissue, gender or disease state subsets); analyzing co-expression with the BDNF gene in each subset separately; and confirming co- expression links across subsets. Finally, we analyzed conservation in co-expression with BDNF between human, mouse and rat, and sought for conserved over-represented TFBSs in BDNF and BDNF-correlated genes. Correlated genes discovered in this study regulate nervous system development, and are associated with various types of cancer and neurological disorders. Also, several transcription factor identified here have been reported to regulate BDNF expression in vitro and in vivo.

Conclusion: The study demonstrates the potential of the "subset" approach in co-expression conservation analysis for studying the regulation of single genes and proposes novel regulators of BDNF gene expression.

Show MeSH
Related in: MedlinePlus