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

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

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

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

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

<i>In situ</i> hybridization for HPV16-miR-H1-1 and HPV16-miR-H2-1.

<p>(A) Hematoxylin-eoxin (HE) staining, immunohistochemical staining for p16, and <i>in situ</i> (italics) hybridization for scramble (negative control), U6 (positive control), human miR-205 (positive control for cervical tissue), HPV16-miR-H1-1 (16-miR-H1-1) and HPV16-miR-H2-1 (16-miR-H2-1). Shown are two cervical intraepithelial neoplasia grade 1 (CIN 1) samples (samples 10 and 28), one squamous cell carcinoma (SCC) (sample 102), as well as normal squamous epithelium (SE) (sample 104) and normal columnar epithelium (CE) (sample 104). Arrows point to positive signals. (B) Areas of selected picture fields shown in higher magnification to depict localization and positive hybridization signal. Same numbering is used as in (A).</p

Locations and putative target sites of HPV 16 encoded microRNAs.

<p>Locations of HPV16-miR-H1-1 and HPV16-miR-H2-1 in the viral genome are shown as black bars and the predicted secondary structures are given next to the bars. For each miRNA, the seed sequences and predicted target sequences in the HPV genome are shown.</p

Predicted viral miRNA candidate.

<p>Each row presents one candidate miRNA with name, reference genome, pre-miRNA location in the genome, total read counts of pre-miRNA, viral gene annotation in corresponding region, strand information and mature miRNA sequence. Some miRNAs were shown in more than one isolate/subtype papillomavirus genomes. ^§ Prediction results from second round.</p