A comparative genomics approach to identifying the plasticity transcriptome

doi:10.1186/1471-2202-8-20

BMC Neuroscience

Volume 8

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Research article

A comparative genomics approach to identifying the plasticity transcriptome

Andreas R Pfenning¹ , Russell Schwartz¹^,2 and Alison L Barth²^,3

¹Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA

²Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA

³Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA 15213, USA

author email corresponding author email

BMC Neuroscience 2007, 8:20doi:10.1186/1471-2202-8-20


Published:	13 March 2007

Additional files

Additional File 1:

Table of all identified CREB and zif268 target genes in mouse. The file includes all mouse genes that were searched indicating the number of identified CREB or zif268 target sites in each gene. Also noted is the score for each site, the mRNA, the gene ID, and a gene description.

Format: TXT Size: 1.5MB Download file

Additional File 2:

Table of all identified CREB and zif268 target genes in human. The file includes all human genes that were searched indicating the number of identified CREB or zif268 target sites in each gene. Also noted is the score for each site, the mRNA, the gene ID, and a gene description.

Format: TXT Size: 1.6MB Download file

Additional File 3:

Table of all identified CREB and zif268 target genes in rat. The file includes all rat genes that were searched indicating the number of identified CREB or zif268 target sites in each gene. Also noted is the score for each site, the mRNA, the gene ID, and a gene description.

Format: TXT Size: 494KB Download file

Additional File 4:

Table of all identified CREB and zif268 target genes in the mouse-human homologene dataset. The file includes all mouse-human homologous genes that were searched, indicating the number of identified CREB or zif268 target sites in each gene. Also noted is the gene ID and a gene description.

Format: TXT Size: 32KB Download file

Additional File 5:

Position and sequence of CREB and zif268 binding sites in mouse promoter regions. Mouse genes that had one or more CREB and zif268 binding sites are listed in table format, with the precise nucleotide sequence corresponding to the binding site and the relative position of this sequence within the promoter region indicated. Genes are identified by gene ID, symbol, and gene descriptor.

Format: TXT Size: 213KB Download file

Additional File 6:

Position and sequence of CREB and zif268 binding sites in human promoter regions. Human genes that had one or more CREB and zif268 binding sites are listed in table format, with the precise nucleotide sequence corresponding to the binding site and the relative position of this sequence within the promoter region indicated. Genes are identified by gene ID, symbol, and gene descriptor.

Format: TXT Size: 215KB Download file

Additional File 7:

Position and sequence of CREB and zif268 binding sites in rat promoter regions. Rat genes that had one or more CREB and zif268 binding sites are listed in table format, with the precise nucleotide sequence corresponding to the binding site and the relative position of this sequence within the promoter region indicated. Genes are identified by gene ID, symbol, and gene descriptor.

Format: TXT Size: 79KB Download file

Additional File 8:

Gene functions associated with CREB and zif268 targets. A list of the broad gene ontology classifications where CREB or zif268 targets showed an over- or underrepresentation, according to the GOstat ontology classifier.

Format: XLS Size: 19KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 9:

CREB or zif268 target genes in overrepresented gene ontology categories. The specific genes that were placed in over- or underrepresented gene onotologies using the GOstat resource are listed according to ontology classification.

Format: XLS Size: 301KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 10:

Comparative genomics as a metric for transcription factor targets quality. Transcription factor binding site searches were done with varying correction scores that correspond to the specificity of the search. The log of the specificity is subtracted from every subsequence scored by the program to correct for sequence length (see Methods). A higher specificity means a smaller number of higher quality binding sites are used. The predicted fraction of true positives or positive predictive value is defined as (true positives)/(true positives + false positives). This measure is estimated as (observed sites - expected sites)/(observed sites). The observed sites are the targets verified by comparative genomics while the expected sites are the number of binding sites one would find by chance if comparing independent human/mouse datasets.

Format: PDF Size: 275KB Download file

This file can be viewed with: Adobe Acrobat Reader