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. 2006 Aug 28;26(21):7913–7928. doi: 10.1128/MCB.01220-06

FIG. 1.

FIG. 1.

DNA array analysis of wild-type versus HDAC1-deficient ES cell lines. (A) Summary of DNA array results. Total numbers of genes found on Affymetrix GeneChip Mu74 microarray analysis are presented as nonregulated (black) and deregulated (light gray) genes. The dark gray bar represents the number of positively regulated genes, and the white bar represents the number of negatively regulated genes in HDAC1-deficient ES cells. (B) Molecular networks of putative HDAC1 target genes. Putative HDAC1 target genes were overlaid onto a global molecular network developed from information contained in the Ingenuity Pathways Knowledge Base. Networks of putative HDAC1 target genes were then algorithmically generated based on their connectivity. The networks are ranked according to their scores, and the five highest-ranking networks of upregulated and downregulated genes are displayed. The numbers of genes in each network are shown in brackets. (C) Functional classification of HDAC1 target genes. The probe sets corresponding to all deregulated transcripts were analyzed using Ingenuity Pathways Analysis (Ingenuity Systems) for molecular and cellular functions. Different categories are ranked according to the numbers of associated genes. Gray bars represent genes that are upregulated in HDAC1 KO cells, and white bars represent genes that are downregulated in HDAC1 KO cells. The probability that each biological function and/or disease assigned to the data set is due to chance alone is indicated as a P value for each category (shown on the right-hand side of each bar). (D) Chromosomal distribution of deregulated genes. Black bars, total numbers of genes on the indicated chromosomes relative to the total number of genes in the mouse genome; white bars, numbers of genes on the indicated chromosomes present on the array relative to the total number of genes present on the array; gray bars, numbers of deregulated genes on the indicated chromosomes relative to the total number of deregulated genes. Chromosomes X and Y are excluded, since the cell lines were of opposite sexes.