Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D

  1. Susan L Coort1⇑
  1. 1Department of Bioinformatics – BiGCaT, NUTRIM School of Nutrition and Metabolism in Translational Research, Maastricht University, Maastricht, The Netherlands
  2. 2Institute of Metabolism and Systems Research, The University of Birmingham, Birmingham, UK
  3. 3Maastricht Centre for System Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
  1. Correspondence should be addressed to S L Coort: susan.coort{at}maastrichtuniversity.nl
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    Figure 1

    Common altered pathways in 1,25(OH)2D-treated THP-1, DCs and monocytes. Heat map representing Z-scores for pathways significantly altered by 1,25(OH)2D after performing a pathway analysis on datasets for THP-1, DCs and monocytes treated with 1,25(OH)2D. Z-Scores >1.96 indicate that more genes are significantly altered in this pathway compared to the complete dataset.

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    Figure 2

    1,25(OH)2D-regulated genes in THP-1 cells, DCs and monocytes. Venn diagrams showing numbers of common and cell-specific genes regulated by 1,25(OH)2D in THP-1 cells, DCs and monocytes. Genes with an absolute log2 fold-change >0.26 and adjusted P value <0.05 were considered as regulated.

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    Figure 3

    ClueGO gene ontology analysis of common 1,25(OH)2D-regulated bioenergetics genes in THP-1 cells, DCs and monocytes. Cytoscape analysis showing overrepresented bioenergetic pathways for 1,25(OH)2D-treated THP-1 cells, DCs and monocytes. Colors represent the GO group, each node is a GO biological process and the edges shows the connectivity between each node based on the connection of the genes that contain. The size of the nodes depends on the amount of genes that are grouped. Nodes with no connections are colored in gray.

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    Figure 4

    Effect of 1,25(OH)2D on genes associated with the electron transport chain. Visualization of changes in gene expression after 1,25(OH)2D treatment in THP-1 cells, DCs and monocytes. Log2 fold changes are shown as a gradient from blue (downregulated) to red (upregulated) over white (unchanged). Adjusted P-values <0.05 are shown in green.

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    Figure 5

    Effect of 1,25(OH)2D on genes associated with oxidative phosphorylation. Visualization of changes in gene expression after 1,25(OH)2D treatment in THP-1 cells, DCs and monocytes. Log2 fold changes are shown as a gradient from blue (downregulated) to red (upregulated) over white (unchanged). Adjusted P-values <0.05 are shown in green.

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    Figure 6

    Effect of 1,25(OH)2D on genes associated with the TCA cycle. Visualization of changes in gene expression after 1,25(OH)2D treatment in THP-1 cells, DCs and monocytes. Log2 fold changes are shown as a gradient from blue (downregulated) to red (upregulated) over white (unchanged). Adjusted P-values <0.05 are shown in green.

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    Figure 7

    Effect of 1,25(OH)2D on the expression of genes associated with cell proliferation in THP-1 cells. WikiPathways representation of (A) cell cycle; (B) DNA replication pathways. Visualization of changes in gene expression after 1,25(OH)2D treatment in THP-1 cells. Log2 fold changes are shown as a gradient from blue (downregulated) to red (upregulated) over white (unchanged). Adjusted P-values <0.05 are shown in green.

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  1. doi: 10.1530/JME-17-0186 J Mol Endocrinol 60 95-108
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