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Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons

Rui Liu, Sridhar Hannenhalli* and Maja Bucan*

Author Affiliations

Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA

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Genome Biology 2009, 10:R72  doi:10.1186/gb-2009-10-7-r72

Published: 1 July 2009

Additional files

Additional data file 1:

Table S1 lists 107 presynaptic genes in corresponding expression clusters. Table S2 lists TFBSs identified in Rab3A MCEs. Table S3 lists 42 additional genes potentially regulated by Rab3A ECR1's CRM and their expression levels. Table S4 lists all primer sets used in this study.

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Additional data file 2:

Figure S1 shows Rab3A amplification in cDNA and genomic DNA (gDNA) samples. Figure S2 shows the screen of functional elements in the non-coding region of the Rab3A locus. Figure S3 shows fine mapping of the promoter region of Rab3A. Figure S4 shows the screen of the 1.5 kb upstream region of Rab3A for potential regulatory element(s). Figure S5 shows the screen and characterization of the first intron of Rab3A for regulatory element(s). Figure S6 shows the masking of MCE5 by the presence of MCE1 and MCE2 in Neuro2a cells. Figure S7 shows the statistical evaluation of the scoring strategy for MCEs.

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