Article Figures & Data
Figures
- Figure 1
Flow-chart overview of experimental steps taken, plus the findings from each step.
- Figure 2
Genomic locations of all detected open field behavioral QTL. Bars indicate 1.8-LOD drop confidence intervals.
- Figure 3
Part of LOD curves and scatterplots of trait vs. gene expression for selected candidates GABRB2, RABGGTB, STK17A and SFRP4, and LOC770352. Bars indicate 1.8-LOD intervals, extended to the closest marker.
Tables
- Table 1 Candidate gene expression levels predicting behavior
Mouse HS open field LOD scores (additive model) Chr Trait QTL C.I. (Mb) eQTL PhQTL pos Gene P-value NEO leo.nb score Model P-value Marker Latency Total activity Time in center Marker 2 Time in center zone trial 2 45.5–51.9 SFRP4 2@426 0.04 NA NA rs2709114 — — — rs13481716 2 Time in center zone trial 2 45.5–51.9 STK17A 2@426 0.004 NA NA rs1181601 — — — rs6253368 3 Minimum total movement 25.1–27 RSPH9 3@277 0.03 0.823 5.48E-06 rs3778493 4.7 7.8 — UT_17_45.56 3 Minimum total movement 25.1–27 C1orf107/DIEXF 3@277 0.003 0.368 0.804 rs7549523 — — — rs3684501 8 Total velocity average 23.9–26.6 RABGGTB 8@194.0 0.05 NA NA rs7555627 — — — rs3656403 10 Total velocity average 4.3–6.8 ADAM10 10@101 0.03 0.44 0.396 rs2242321 — — — rs13480265 10 Total velocity average 4.3–6.8 APBA2 10@101 0.01 0.0421 0.0719 rs7680321 — 7.7 — rs3717846 10 Total velocity trial 1 14.4–17.4 LOC770352 10@185.0 0.002 0.943 0.687 rs1480617 — — 4.5 rs13476065 10 Total movement average 14.4–17.4 LOC770352 10@185.0 0.0002 1.07 0.956 rs1480617 — — 4.5 rs13476065 10 Minimum total movement 14.4–17.4 LOC770352 10@182.0 0.003 0.874 0.925 rs1480617 — — 4.5 rs13476065 10 Total movement trial 2 7.6–15.0 LOC770352 10@64.0 0.0012 0.747 0.878 rs1480617 — — 4.5 rs13476065 10 Maximum total movement 14.4–17.4 LOC770352 10@185.0 0.0003 1.13 0.985 rs1480617 — — 4.5 rs13476065 10 Total velocity trial 1 4.3–6.8 APBA2 10@99.0 0.004 0.977 0.131 rs7680321 — 7.7 — rs3717846 10 Total velocity trial 1 4.3–6.8 ADAM10 10@99.0 0.04 0.515 0.37 rs2242321 — — — rs13480265 10 Total movement trial 1 4.3–6.8 LOC770352 10@99.0 0.008 0.815 0.852 rs7680321 — — 4.5 rs13476065 10 Total movement average 4.3–6.8 APBA2 10@99.0 0.02 −0.966 0.0002 rs7680321 — 7.7 — rs3717846 13 Total velocity trial 2 1.5–4.1 GABRB2 13@32.0 0.0014 NA NA rs4302629 5.1 5.1 — rs6225242 17 Total velocity average 1–2.5 SLC31A1 17@1 0.004 NA NA rs786978 — — — rs3690581 17 Total velocity trial 1 1–2.5 SLC31A1 17@1 0.003 NA NA rs786978 — — — rs3690581 Chromosome (Chr) and QTL confidence interval are given for the trait that each eQTL significantly correlated with. The phenotypic QTL position (PhQTL pos) is also given in centimorgans. The P-value of the correlation, after Bonferroni correction, is also provided (Gene P-value). The causality modeling scores are also indicated for each gene, as are the WTCCC P-values for each gene region. The association of each gene with the mouse HS cross is also given, with the LOD scores of the gene location for each of the three different open field tests provided.
- Table 2 Candidate genes trait correlations and ranking vs. all eQTL
Gene Trait Overall rank (of 535 eQTL) Trait–gene correlation P-value ADAM10 Average velocity 52 0.027 ADAM10 Velocity trial 1 35 0.018 APBA2 Average total movement 34 0.024 APBA2 Average velocity 27 0.010 APBA2 Velocity trial 1 11 0.002 C1orf107/DIEXF Minimum total movement 7 0.003 GABRB2 Velocity trial 2 7 0.006 LOC770352 Total movement trial 1 11 0.004 LOC770352 Total movement trial 2 2 0.001 LOC770352 Maximum total movement 1 <0.001 LOC770352 Minimum total movement 4 0.001 LOC770352 Average total movement 2 <0.001 LOC770352 Velocity trial 1 13 0.002 RABGGTB Average velocity 23 0.008 RSPH9 Minimum total movement 39 0.033 SFRP4 Time in center trial 2 24 0.018 SLC31A1 Average velocity 17 0.004 SLC31A1 Velocity trial 1 15 0.003 STK17A Time in center trial 2 1 0.002 - Table 3 Association of the nine genes tested in the GWASs
Bipolar: Schizophrenia: Major depressive disorder: PGCBD 2011 study SWGPCCa 2014 PGCMDD Gene P-value Marker P-value Marker P-value Marker SFRP4 0.0001* rs7807315 NS — NS — STK17A NS — NS — NS — RSPH9 NS — 0.00009# rs72859036 NS — DIEXF NS — NS — NS — RABGGTB NS — NS — NS — ADAM10 NS — 0.00001* rs6494035 NS — APBA2 NS — NS — NS — GABRB2 NS — NS — NS — SLC31A1 NS — NS — NS — Significant (*) and suggestive (#) P-values are given for each gene, along with the marker showing the highest association in the gene interval. In the case of RSPH9 and ADAM10 the distance of the marker from the gene is also given.
↵a Schizophrenia Working Group of the Psychiatric Genomics Consortium.
Supporting Information for Johnsson et al., 2015
Supporting Information
- Figure S1 - Scatter plots of behavioural phenotypes between the first and second trials. (.pdf, 389 KB)
- Figure S2 - Scatter plots of the remaining candidate genes. (.pdf, 467 KB)
- Figure S3 - LOD graphs of overlapping candidate eQTL and QTL. (.pdf, 283 KB)
- Table S1 - Pearson Correlations between open-field measurements from trial 1(A) and trial 2 (B) measurements. (.pdf, 302 KB)
- Table S2 - Behavioural QTL for open field behaviour. Chromosome, position (in cM), Lod score, r-squared (in %), additive and dominance values are given, as well as the confidence intervals (C.I.) as defined by a 1.8 LOD drop. (.pdf, 1,010 KB)
- Table S3 - cis and trans eQTL. (.pdf, 411 KB)
- Table S4 - Number of eQTL correlated with traits for which candidate genes identified. (.pdf, 301 KB)
- File S1 - Supplemental methods. (.pdf, 312 KB)
