Results: 4

1.
FIG. 3.

FIG. 3. From: Transcriptional Profiling of Cross Pathway Control in Neurospora crassa and Comparative Analysis of the Gcn4 and CPC1 Regulons .

Functional category analysis of Gcn4p, CaGcn4p, and CPC1 targets. Target gene sets derived from S. cerevisiae Gcn4p transcriptional profiling and ChIP data (, , , ) were combined to generate a set of 747 Gcn4p target genes. A statistical analysis of C. albicans Gcn4p transcriptional profiling data () retrieved a set of 483 CaGcn4p target genes. The S. cerevisiae Gcn4p and C. albicans Gcn4p data sets were subjected to functional category analysis using FunCat (). The functional category analyses of the S. cerevisiae Gcn4p and C. albicans Gcn4p data sets were then compared to the functional category analysis of the set of 443 CPC1 target genes.

Chaoguang Tian, et al. Eukaryot Cell. 2007 June;6(6):1018-1029.
2.
FIG. 2.

FIG. 2. From: Transcriptional Profiling of Cross Pathway Control in Neurospora crassa and Comparative Analysis of the Gcn4 and CPC1 Regulons .

Computational identification of cis-element enrichment in predicted promoter regions of genes within the CPC1 regulon. The 500-bp upstream regions of the predicted translational start sites of 67 amino acid metabolism genes from the CPC1 target gene set were retrieved and evaluated by MDscan (), BioProspector (), and MEME () for motif prediction. By using the initial CPC1 matrix, the promoter regions of the 67 amino acid genes were evaluated by the PATSER program (). To identify additional CPC1 target genes in the N. crassa target gene set and the genome, predicted promoter regions were scanned using the CPC1 matrix. The logo using the CPC1 matrix was built using WebLogo (http://weblogo.berkeley.edu/logo.cgi).

Chaoguang Tian, et al. Eukaryot Cell. 2007 June;6(6):1018-1029.
3.
FIG. 1.

FIG. 1. From: Transcriptional Profiling of Cross Pathway Control in Neurospora crassa and Comparative Analysis of the Gcn4 and CPC1 Regulons .

Venn diagram of genes with differences in expression levels between the WT and the cpc-1 mutant. (A) Venn diagram showing overlap among genes that exhibit statistically significantly increased or altered expression levels in the WT (FGSC 2489) versus the cpc-1 mutant (FGSC 4264) in minimal medium after exposure to 3-AT. The 443 genes comprising set B, set D, set A, set F, and set C are defined as the CPC1 target gene set (regulon) (see the text for details). A functional category analysis of these 443 genes is given in Table S1 in the supplemental material. (B) Venn diagram showing overlap among genes whose expression levels in the WT (FGSC 2489) and the cpc-1 (FGSC 4264) mutant were reduced in minimal medium upon exposure to 3-AT. A functional category analysis of genes that showed reduced expression levels is given in Table S1 in the supplemental material.

Chaoguang Tian, et al. Eukaryot Cell. 2007 June;6(6):1018-1029.
4.
FIG. 4.

FIG. 4. From: Transcriptional Profiling of Cross Pathway Control in Neurospora crassa and Comparative Analysis of the Gcn4 and CPC1 Regulons .

Identification of common regulogs in the S. cerevisiae (sc), C. albicans (ca), and N. crassa (nc) genomes by computational analysis using cis-element scans compared to identification of common regulogs by transcriptional profiling. (A) In N. crassa, predicted promoter regions of 351 genes that contain the CPC1 cis-element were identified. Of these 351 genes, 103 have orthologs in S. cerevisiae, and of these 103 orthologs, 21 have a Gcn4p cis-element consensus in the promoter region (regulogs). Orthologs of 116 of the 351 N. crassa genes were identified in C. albicans. Of these 116 C. albicans genes, 30 have a CaGcn4p consensus cis-element in the predicted promoter region. In S. cerevisiae, 278 genes that contain a Gcn4p consensus cis-element in their promoter regions were identified. Of these 278 genes, 155 had orthologs identified in C. albicans, and of the 155 orthologs, 34 have a predicted CaGcn4p cis-element in predicted promoter regions. The overlap of all three data sets identified 17 orthologous gene pairs that maintained the conserved Gcn4p/CaGcn4p/CPC1 cis-element. (B) By transcriptional profiling, 443 genes were identified as CPC1 targets. The overlap between the 747-gene S. cerevisiae and N. crassa CPC1 data sets revealed 73 orthologous gene pairs (regulogs). The overlap between the N. crassa and C. albicans data sets identified 64 orthologous gene pairs, and the overlap between the S. cerevisiae and C. albicans data sets revealed 94 orthologous gene pairs. The overlap of all three data sets identified a conserved regulon of 32 orthologous genes present in all three species as determined by transcriptional profiling and ChIP.

Chaoguang Tian, et al. Eukaryot Cell. 2007 June;6(6):1018-1029.

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