Journal: Scientific Reports
Article Title: Combined Transcriptomics and Chemical-Genetics Reveal Molecular Mode of Action of Valproic acid, an Anticancer Molecule using Budding Yeast Model
doi: 10.1038/srep35322
Figure Lengend Snippet: ( a ) Experimental design for microarray analysis. A large number of genes were differentially expressed (filtered on expression) upon VA treatment compared to that of untreated cells. BH-FDR stands for Benjamini–Hochberg false discovery rate and p < 0.05 was considered statistically significant. ( b ) A hierarchically clustered heatmap is generated using the averaged relative expression (log 2 ) values from two independent biological repeats of both untreated (UN) and VA treated, on the scale of red (induced)-blue (repressed). Each column in heatmap represents the normalized average values of untreated (UN) and VA transcriptome, and each row represents the genes (entities). ( c ) Functional classification of VA transcriptome ( p < 0.05, Fold change ≥2) into the MIPS (Munich International Center for Protein Sequences) categories. The enrichment of each category was represented as % of genes altered upon VA treatment compared to the whole number of genes present in each category. ‘*’ indicates the significantly enriched functional categories. ( d ) Analysis of VA induced (≥2 fold) transcriptome for overrepresented (enriched) biological processes using a Biological Networks Gene Ontology (BiNGO) tool reveal a biological network of significantly enriched Gene Ontology (GO) categories [Hypergeometric test ( p < 0.05) and corrected for Benjamini-Hochberg False Discovery Rate (FDR)]. Each node in the network represents a term of biological process (cluster of genes) whereas the edges represent the interaction between different nodes (biological processes). The nodes in yellow color show the significant enrichment of term. As the significance ( p -value) of enrichment increases, the color of node goes from yellow to orange. Node size in the network is relative to the number of nodes with that GO-term in the query set.
Article Snippet: Afterward, GeneChips were washed, stained in the Fluidics Station 450 (Affymetrix) and scanned using the GeneArray 3000 7G microarray scanner.
Techniques: Microarray, Expressing, Generated, Functional Assay
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![( a ) Experimental design for <t>microarray</t> analysis. A large number of genes were differentially expressed (filtered on expression) upon VA treatment compared to that of untreated cells. BH-FDR stands for Benjamini–Hochberg false discovery rate and p < 0.05 was considered statistically significant. ( b ) A hierarchically clustered heatmap is generated using the averaged relative expression (log 2 ) values from two independent biological repeats of both untreated (UN) and VA treated, on the scale of red (induced)-blue (repressed). Each column in heatmap represents the normalized average values of untreated (UN) and VA transcriptome, and each row represents the genes (entities). ( c ) Functional classification of VA transcriptome ( p < 0.05, Fold change ≥2) into the MIPS (Munich International Center for Protein Sequences) categories. The enrichment of each category was represented as % of genes altered upon VA treatment compared to the whole number of genes present in each category. ‘*’ indicates the significantly enriched functional categories. ( d ) Analysis of VA induced (≥2 fold) transcriptome for overrepresented (enriched) biological processes using a Biological Networks Gene Ontology (BiNGO) tool reveal a biological network of significantly enriched Gene Ontology (GO) categories [Hypergeometric test ( p < 0.05) and corrected for Benjamini-Hochberg False Discovery Rate (FDR)]. Each node in the network represents a term of biological process (cluster of genes) whereas the edges represent the interaction between different nodes (biological processes). The nodes in yellow color show the significant enrichment of term. As the significance ( p -value) of enrichment increases, the color of node goes from yellow to orange. Node size in the network is relative to the number of nodes with that GO-term in the query set.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_2167/pmc05062167/pmc05062167__srep35322-f2.jpg)