Article Figures & Data
Figures
- Figure 1.
The eQTL locations of probes of the three genes Tet methylcytosine dioxygenase (Tet2), B-cell lymphoma 2 (Bcl2), and solute carrier family 23 member 2 (Slc23a2) on different chromosomes. The number identifier of the chromosomes is on the top of each individual graph, while the Mb of the physical distance is indicated at the bottom. The pink lines (indicated by the red arrow) indicate the threshold of significance level, and the gray lines (indicated by the gray arrow) indicate the threshold of the level suggestive of expression quantitative trait locus (eQTL). Blue traces indicate LSR scores by chromosome, while red and green traces (on each individual chromosome) indicate regions where B6 or D2 alleles tended to increase the expression level of the gene, respectively. The top line is all eQTL from probes (probe numbers are on top of each graph) of Bcl2. The bottom left is eQTL from probes of Slc23a2. The bottom right is the eQTL from Tet2.
- Figure 2.
Gene network and pathway composed of one probe of Tet methylcytosine dioxygenase (Tet2), eight probes of B-cell lymphoma 2 (Bcl2), and six probes of solute carrier family 23 member 2 (Slc23a2). A: The network graphs. The 16 nodes in the graph show the selected traits. The 15 curved edges between the nodes were filtered from the total of 15 edges. Only Pearson correlation coefficients greater than 0.43 or less than −0.43 are displayed. B: The positive correlation between the expression level of a probe of Tet2 (probe 1455300) and that of a probe of Slc23a2 (probe 1445983). C: The negative association between a probe of Bcl2 (1443874) and a probe of Slc23a2 (probe 1421912). D: A probe of Slc23a2 (1417330) shows negative correlation with one Bcl2 probe (1437122). E: A probe of Slc23a2 (1417330) was positively correlated with a probe (1426054) of Bcl2. F: A probe of Slc23a2 (1417330) was positively correlated with a probe (1422938) of Bcl2.
- Figure 3.
Key genes and the connection among genes of the full list. The 92 nodes show the selected traits. Only nodes with edges are displayed. The 216 edges between the nodes, filtered from the 4,186 total edges and drawn as lines, show Pearson correlation coefficients greater than 0.5 or less than −0.5. Different color of lines represents different R values between the two genes as explained in the Materials and Methods section.
- Figure 4.
Alternative gene networks and pathways composed of additional relevant genes. In A and G, different color of lines represents different R values between the two genes as explained in the Materials and Methods section of the manuscript. In B, C, D, E, F and H, mouse strain names are written in blue color. A: The two alternative pathways between B-cell lymphoma 2 (Bcl2), and six probes of solute carrier family 23 member 2 (Slc23a2) (marked as P1, light blue, and P2, red). B: The expression level of a probe of Bcl2 (probe 1440770) was negatively correlated with that of a probe of BCL2-associated athanogene 4 (Bag4) (probe 1439024). C: A probe of Bag4 (1439024) was positively correlated with a probe of BCL2-like 13 (1429539). D: A probe of BCL2-like 13 (Bcl2l13) (1429539) was negatively correlated with a probe of myeloid leukemia cell differentiation protein (Mcl1) (1416881). E: A probe of Mcl1 (1416881) was positively correlated with a probe of beclin 1 (Becn1) (1460320). F: A probe of Becn1 (1460320) was negatively correlated to a probe of Slc23a2 (1442983). G: The alternative pathway between Bcl2 and Tet2 (indicated by arrows). H: The expression level of Mcl1 (probe 1456381) was positively correlated to that of Tet2 (probe 1455300).
- Figure 5.
Association between the most correlated genes from the top 100 identified from Tet methylcytosine dioxygenase (Tet2), eight probes of B-cell lymphoma 2 (Bcl2), and six probes of solute carrier family 23 member 2 (Slc23a2) and functional analysis of the 25 selected genes. A: Genes according to different functional groups identified by GO analysis from 25 selected genes out of the top 100 and Bcl2 and Tet2. These genes only have functional roles in two functional categories: biological processes and cellular components. B: Genes identified for biological processes. Some further functions in the database are not listed. C: Genes identified for correlation with cellular components. D: Association between Bcl2, Slc23a2, and the eight most highly correlated genes from the top 100 genes identified from Tet2. The expression levels of Slc23a2 were highly correlated to these eight genes. E: Association between Tet2, Slc23a2 and the five most highly correlated genes from the top 100 genes identified from Bcl2. Numbers listed vertically on the circular lines are the R values at different positions. Circular lines indicate the positions of different R values.
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