Table 1. The details of gene and pathway enrichment in the modules.
| Modules | Gene count | Wistar-snp | GK-snp | Coding-synonymous | Missense | Significantly up-regulated genes | Significantly down-regulated genes | Top10 pathways | |
|---|---|---|---|---|---|---|---|---|---|
| All | M1 | 99 | 25 | 164 | 94 | 70 | Bad(1:0;1;0)#; Gstm4(2:0;2;0); Pik3c2b(10:8;2;0); Nt5c3b(1:1;0;0); | Entpd2(0:0;0;0); Itgb4(3:2;1;0); Ppp1r3c(4:3;1;0); Aldh7a1(1:0;1;0); Gstp1(1:1;0;0); Mapk12(0:0;0;0); Alox5(0:0;0;0); Akr1b1(1:0;1;0); Prim1(1:0;1;0); | rno00230:Purine metabolism, rno04914:Progesterone-mediated oocyte maturation, rno04916:Melanogenesis, rno00240:Pyrimidine metabolism, rno04912:GnRH signaling pathway, rno04722:Neurotrophin signaling pathway, rno04910:Insulin signaling pathway, rno04540:Gap junction, rno04270:Vascular smooth muscle contraction, rno04720:Long-term potentiation |
| M2 | 86 | 23 | 113 | 55 | 58 | Gstm4(2:0;2;0); Ifit1(3:1;2;0); Pla2g12a(0:0;0;0); Eif3c(5:4;1;0); | Aldh7a1(1:0;1;0); Gstp1(1:1;0;0); Tdp2(1:0;1;0); Alox5(0:0;0;0); Glb1(0:0;0;0); Tm7sf2(1:0;1;0); Akr1b1(1:0;1;0); Nit2(1:0;1;0); Hmgcs2(1:0;1;0); | rno00980:Metabolism of xenobiotics by cytochrome P450, rno00982:Drug metabolism, rno00480:Glutathione metabolism, rno00650:Butanoate metabolism, rno00590:Arachidonic acid metabolism, rno00830:Retinol metabolism, rno00591:Linoleic acid metabolism, rno04730:Long-term depression, rno00592:alpha-Linolenic acid metabolism, rno00380:Tryptophan metabolism | |
| 4 weeks | M1 | 105 | 28 | 174 | 96 | 78 | Bad(1:0;1;0); Ifit1(3:1;2;0); | Entpd2(0:0;0;0); Mrpl44(3:2;1;0); Ppp1r3c(4:3;1;0); Tdp2(1:0;1;0); Mapk12(0:0;0;0); Prim1(1:0;1;0); | rno00230:Purine metabolism, rno00240:Pyrimidine metabolism, rno04722:Neurotrophin signaling pathway, rno04912:GnRH signaling pathway, rno04370:VEGF signaling pathway, rno04910:Insulin signaling pathway, rno04916:Melanogenesis, rno05223:Non-small cell lung cancer, rno04540:Gap junction, rno04012:ErbB signaling pathway |
| M2 | 140 | 39 | 229 | 129 | 100 | Rrp9(9:7;2;0); Eif3c(5:4;1;0); Gstm4(2:0;2;0); Ifit1(3:1;2;0); Pik3c2b(10:8;2;0); | Mrpl44(3:2;1;0); Aldh7a1(1:0;1;0); Tdp2(1:0;1;0); Mapk12(0:0;0;0); Col6a2(7:5;2;0); Gstp1(1:1;0;0); Mlycd(1:0;1;0); Akr1b1(1:0;1;0); Hmgcs2(1:0;1;0); | rno04620:Toll-like receptor signaling pathway, rno05215:Prostate cancer, rno05212:Pancreatic cancer, rno04622:RIG-I-like receptor signaling pathway, rno05222:Small cell lung cancer, rno04914:Progesterone-mediated oocyte maturation, rno05200:Pathways in cancer, rno04920:Adipocytokine signaling pathway, rno04010:MAPK signaling pathway, rno05214:Glioma | |
| 8 weeks | M1 | 93 | 28 | 180 | 105 | 75 | Bad(1:0;1;0); Gstm4(2:0;2;0); Pik3c2b(10:8;2;0); | Entpd2(0:0;0;0); Itgb4(3:2;1;0); Ppp1r3c(4:3;1;0); Aldh7a1(1:0;1;0); Mapk12(0:0;0;0); Orc5(0:0;0;0); Dpyd(0:0;0;0); Akr1b1(1:0;1;0); Prim1(1:0;1;0); | rno00230:Purine metabolism, rno00240:Pyrimidine metabolism, rno04916:Melanogenesis, rno04540:Gap junction, rno04914:Progesterone-mediated oocyte maturation, rno04912:GnRH signaling pathway, rno04020:Calcium signaling pathway, rno03030:DNA replication, rno04070:Phosphatidylinositol signaling system, rno04270:Vascular smooth muscle contraction |
| M2 | 144 | 44 | 223 | 136 | 87 | Rrp9(9:7;2;0); Acad9(3:2;1;0); Eif3c(5:4;1;0); Bad(1:0;1;0); Gstm4(2:0;2;0); Ifit1(3:1;2;0); H2afz(0:0;0;0); | Mrpl44(3:2;1;0); Aldh7a1(1:0;1;0); Tdp2(1:0;1;0); Tm7sf2(1:0;1;0); Nit2(1:0;1;0); Pdlim5(2:2;0;0); Ppp1r3c(4:3;1;0); Gstp1(1:1;0;0); Pccb(0:0;0;0); Mlycd(1:0;1;0); Akr1b1(1:0;1;0); Hmgcs2(1:0;1;0); Acat1(1:1;0;0); | rno00620:Pyruvate metabolism, rno00640:Propanoate metabolism, rno00650:Butanoate metabolism, rno04910:Insulin signaling pathway, rno00280:Valine, leucine and isoleucine degradation, rno04620:Toll-like receptor signaling pathway, rno00310:Lysine degradation, rno03010:Ribosome, rno00330:Arginine and proline metabolism, rno00410:beta-Alanine metabolism | |
| 12 weeks | M1 | 118 | 28 | 190 | 107 | 83 | Bad(1:0;1;0); Gstm4(2:0;2;0); Ifit1(3:1;2;0); Pik3c2b(10:8;2;0); | Entpd2(0:0;0;0); Mrpl44(3:2;1;0); Itgb4(3:2;1;0); Ppp1r3c(4:3;1;0); Aldh7a1(1:0;1;0); Tdp2(1:0;1;0); Mapk12(0:0;0;0); Mlycd(1:0;1;0); Akr1b1(1:0;1;0); Prim1(1:0;1;0); | rno00230:Purine metabolism, rno04916:Melanogenesis, rno04914:Progesterone-mediated oocyte maturation, rno00240:Pyrimidine metabolism, rno04540:Gap junction, rno04270:Vascular smooth muscle contraction, rno04910:Insulin signaling pathway, rno04730:Long-term depression, rno04912:GnRH signaling pathway, rno04114:Oocyte meiosis |
| M2 | 134 | 36 | 202 | 116 | 86 | Acad9(3:2;1;0); Gstm4(2:0;2;0); Ifit1(3:1;2;0); Pla2g12a(0:0;0;0); | Itgb4(3:2;1;0); Aldh7a1(1:0;1;0); Tdp2(1:0;1;0); Mapk12(0:0;0;0); Prim1(1:0;1;0); RGD735029(2:0;2;0); Vegfb(0:0;0;0); Ppp1r3c(4:3;1;0); Alox5(0:0;0;0); Mlycd(1:0;1;0); Akr1b1(1:0;1;0); Hmgcs2(1:0;1;0); | rno05215:Prostate cancer, rno04370:VEGF signaling pathway, rno04920:Adipocytokine signaling pathway, rno04620:Toll-like receptor signaling pathway, rno05220:Chronic myeloid leukemia, rno05200:Pathways in cancer, rno05222:Small cell lung cancer, rno04730:Long-term depression, rno05212:Pancreatic cancer, rno05221:Acute myeloid leukemia |
#Gene (mutations: coding-synonymous; missense; indel). For example, Bad has 1 mutation, consists of 0 coding-synonymous, 1 missense and 0 indel.