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Fig. 4 | BMC Genomics

Fig. 4

From: Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development

Fig. 4

Novel implementation of three computational methods to generate a focused list of biologically-relevant Nr2e1-candidate-target genes. a Data mining from the literature allowed generation of a position-weight matrix representing the binding properties of NR2E1. The matrix and resulting logo are presented. b Flow chart describing the novel implementation of three computational methods to generate a focused list of biologically-relevant Nr2e1-candidate-target genes. DiscoverySpace was used to generate a compiled list of 1279 Refseq accession numbers, corresponding to genes differentially regulated between Wt and Nr2e1 frc/frc embryos. A customized oPOSSUM database of predicted conserved TFBS was created by first aligning all orthologous human-mouse genes using ORCAtk. During this alignment, 304 of the 1279 differentially regulated genes were excluded due to a lack of ortholog information or poor ORCAtk alignment quality. Then the remaining 975 genes with conserved promoter regions were scanned with the NR2E1 matrix (as well as all the vertebrate matrices from the JASPAR CORE collection of transcription factor binding site profiles). Of the 975 scanned genes, 770 contained conserved NR2E1 binding sites. These 770 Refseq accession numbers were submitted to a gene ontology (GO) term analysis using DAVID. From the DAVID analysis, 479 Refseq accession numbers were found to be enriched in GO term categories related to biological processes

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