Top five associated network functions of all the genes regulated by single metabolite generated by IPA.

<p>Top five associated network functions of all the genes regulated by single metabolite generated by IPA.</p

Top five associated network functions of genes exclusively regulated by single metabolite generated by IPA.

<p>Top five associated network functions of genes exclusively regulated by single metabolite generated by IPA.</p

IPA diagrams of the top associated network generated for genes exclusively regulated by each metabolite in hP29SN stromal cells.

<p>(A) Genes regulated by 1α,25(OH)₂D₃ in Cardiovascular System Development and Function, Tissue Development, Organismal Development. (B) Genes regulated by 25(OH)D₃ in Cell Death and Survival, Gene Expression, Tissue Morphology. (C) Genes regulated by 25(OH)D₃ in Cell Death and Survival, Cellular Growth and Proliferation, Cell Cycle. (D) Genes regulated by 24R,25(OH)₂D₃ in Cell Morphology, Cellular Function and Maintenance, DNA Replication, Recombination, and Repair. Green indicates gene down-regulation and pink to red indicate gene up-regulation (the more intensive the color, the higher the expression level). An asterisk (*) indicates that multiple identifiers in the microarray set map to a single gene.</p

Validation of gene expression by qRT-PCR.

<p>(A–C) Gene expression in hP29SN stromal cells. <i>CH25H</i>: cholesterol 25-hydroxylase; <i>SSBP2</i>: single-stranded DNA binding protein 2; <i>VHL</i>: von Hippel-Lindau tumor suppressor; <i>IGF1</i>: insulin-like growth factor; <i>EGFR</i>: epidermal growth factor receptor; <i>LAMB1</i>: laminin subunit β1; <i>RAB7</i>: RAB7A, member RAS oncogene family; <i>MED1</i>: mediator complex subunit 1. (D) Fold changes of gene expression in hP29SN detected by either qRT-PCR or microarray are plotted and linear regression is shown by a solid line. (E–F) The expression of endothelial lipase (<i>Lipg</i>) and tumor necrosis factor receptor superfamily, member 11b (<i>Tnfrsf11b</i>) in m<i>Cyp27b1</i>^−/− fibroblasts was measured by qRT-PCR. Randomly selected two sets of experiments were pooled to generate final two sets of RNA samples for both microarray and qRT-PCR. Results are expressed as means ± SD.</p

Top five canonical pathways generated by IPA constructed from genes exclusively regulated by single metabolite.

<p>Top five canonical pathways generated by IPA constructed from genes exclusively regulated by single metabolite.</p

Gene expression profiles.

<p>Hierarchical clustering of the differentially expressed genes in (A) hP29SN stromal cells and (B) m<i>Cyp27b1</i>^−/− fibroblasts after vitamin D₃ treatments. Colored-bands represent the change of the corresponding gene expression, green indicating down-regulation and red up-regulation. The key for deciphering of the color is shown below the clustering image. Venn diagrams of co-expressed and uniquely regulated genes by vitamin D₃ metabolites in (C) hP29SN and (D) m<i>Cyp27b1</i>^−/− fibroblasts.</p

IPA diagrams of the top associated network generated for all the regulated genes in m<i>Cyp27b1</i>^−/− fibroblasts.

<p>(A) Genes regulated by 1α,25(OH)₂D₃ in Cardiovascular System Development and Function, Organismal Development, Cancer. (B) Genes regulated by 25(OH)D₃ in Humoral Immune Response, Inflammatory Response, Cellular Development. (C) Genes regulated by 25(OH)D₃ in Cancer, Cellular Growth and Proliferation, Connective Tissue Disorders. (D) Genes regulated by 24R,25(OH)₂D₃ in Hematological System Development and Function, Hematopoiesis, Tissue Morphology. Green indicates gene down-regulation and pink to red indicate gene up-regulation (the more intensive the color, the higher the expression level). An asterisk (*) indicates that multiple identifiers in the microarray set map to a single gene.</p