Table 2A.
Top four pathways identified by WebGestalt Pathway Analysis in fetal livers.
| Wild type vs. tx-j | ||||
|---|---|---|---|---|
| Pathway | Wild type Mean RPKM | tx-j Mean RPKM | Percent Difference (Wild type relative to tx-j) | |
| Protein processing in endoplasmic reticulum (KEGG Pathway 04141) | ||||
| C = 169; O = 19; E = 3.36; R = 5.65; rawP = 1.52e-09; adjP = 4.71e-08 | ||||
| Tusc3 | tumor suppressor candidate 3 | 15.1 | 21.5 | 43% |
| Dnaja1 | DnaJ (Hsp40) homolog, subfamily A, member 1 | 11.6 | 16.4 | 41% |
| Hsph1 | heat shock 105kDa/110kDa protein 1 | 8.5 | 11.5 | 35% |
| Ube2e2 | ubiquitin-conjugating enzyme E2E 2 | 4.1 | 5.5 | 34% |
| Casp12 | caspase 12 | 0.2 | 0.3 | 31% |
| Map3k5 | mitogen-activated protein kinase kinase kinase 5 | 2.5 | 3.2 | 30% |
| Ube2d2a | ubiquitin-conjugating enzyme E2D 2A | 34.0 | 43.9 | 29% |
| Ube2g1 | ubiquitin-conjugating enzyme E2G 1 | 10.6 | 13.6 | 28% |
| Rbx1 | ring-box 1 | 21.0 | 25.9 | 24% |
| Dnajc10 | DnaJ (Hsp40) homolog, subfamily C, member 10 | 16.0 | 19.5 | 22% |
| Mbtps2 | membrane-bound transcription factor peptidase, site 2 | 2.3 | 2.8 | 22% |
| Bcap31 | B cell receptor associated protein 31 | 46.7 | 55.1 | 18% |
| Ube2e1 | ubiquitin-conjugating enzyme E2E 1 | 14.0 | 16.3 | 17% |
| Sar1a | SAR1 gene homolog A (S. cerevisiae) | 29.0 | 33.8 | 16% |
| Ern1 | endoplasmic reticulum (ER) to nucleus signalling 1 | 6.7 | 5.5 | −18% |
| Rnf5 | ring finger protein 5 | 27.1 | 21.5 | −20% |
| Sil1 | endoplasmic reticulum chaperone SIL1 homolog | 10.0 | 7.9 | −20% |
| Atf6b | activating transcription factor 6 β | 4.6 | 3.3 | −27% |
| Os9 | amplified in osteosarcoma | 25.7 | 18.6 | −28% |
| Ubiquitin mediated proteolysis (KEGG Pathway 04120) | ||||
| C = 140; O = 17; E = 2.78; R = 6.10; rawP = 3.35e-09; adjP = 6.92e-08 | ||||
| Ube2e2 | ubiquitin-conjugating enzyme E2E 2 | 4.1 | 5.5 | 34% |
| Klhl9 | kelch-like 9 (Drosophila) | 9.6 | 12.6 | 31% |
| Ube2d2a | ubiquitin-conjugating enzyme E2D 2A | 34.0 | 43.9 | 29% |
| Birc2 | baculoviral IAP repeat-containing 2 | 8.1 | 10.3 | 28% |
| Ube2g1 | ubiquitin-conjugating enzyme E2G 1 | 10.6 | 13.6 | 28% |
| Rchy1 | ring finger and CHY zinc finger domain containing 1 | 11.8 | 14.9 | 27% |
| Itch | itchy, E3 ubiquitin protein ligase | 13.9 | 17.5 | 25% |
| Rbx1 | ring-box 1 | 21.0 | 25.9 | 24% |
| Vhl | von Hippel-Lindau tumor suppressor | 4.9 | 5.9 | 21% |
| Xiap | X-linked inhibitor of apoptosis | 17.4 | 20.5 | 18% |
| Ube2e1 | ubiquitin-conjugating enzyme E2E 1 | 14.0 | 16.3 | 17% |
| Klhl13 | kelch-like 13 (Drosophila) | 10.9 | 12.6 | 16% |
| Wwp2 | WW domain containing E3 ubiquitin protein ligase 2 | 9.7 | 8.3 | −14% |
| Tceb2 | transcription elongation factor B (SIII), polypeptide 2 | 33.8 | 24.9 | −26% |
| Ube2o | ubiquitin-conjugating enzyme E2O | 20.3 | 14.9 | −27% |
| Cdc34 | cell division cycle 34 | 23.6 | 16.3 | −31% |
| Fzr1 | fizzy/cell division cycle 20 related 1 (Drosophila) | 15.2 | 9.5 | −38% |
| Lysosome (KEGG Pathway 04142) | ||||
| C = 123; O = 15; E = 2.45; R = 6.13; rawP = 2.62e-08; adjP = 4.06e-07 | ||||
| Ctsk | cathepsin K | 0.7 | 1.2 | 76% |
| Hexb | hexosaminidase B | 18.3 | 24.1 | 32% |
| Atp6v1h | ATPase, H+ transporting, lysosomal V1 subunit H | 12.1 | 15.9 | 31% |
| Gla | galactosidase, α | 1.8 | 2.4 | 30% |
| Ap4e1 | adaptor-related protein complex AP-4, ϵ 1 | 2.2 | 2.9 | 29% |
| Ppt1 | palmitoyl-protein thioesterase 1 | 9.6 | 11.9 | 24% |
| Lamp2 | lysosomal-associated membrane protein 2 | 43.1 | 52.2 | 21% |
| Laptm4a | lysosomal-associated protein transmembrane 4A | 56.1 | 67.6 | 21% |
| Cd164 | CD164 antigen | 66.5 | 79.5 | 20% |
| Asah1 | N-acylsphingosine amidohydrolase 1 | 22.1 | 25.8 | 17% |
| Manba | mannosidase, beta A, lysosomal | 4.5 | 5.2 | 17% |
| Cd63 | CD63 antigen | 21.0 | 24.4 | 16% |
| Gusb | glucuronidase, beta | 10.4 | 12.1 | 16% |
| Napsa | napsin A aspartic peptidase | 2.8 | 2.2 | −22% |
| Abcb9 | ATP-binding cassette, sub-family B (MDR/TAP), member 9 | 0.4 | 0.2 | −47% |
| Huntington's disease (KEGG Pathway 05016) | ||||
| C = 197; O = 18; E = 3.92; R = 4.59; rawP = 1.04e-07; adjP = 1.29e-06 | ||||
| Atp5g3 | ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9) | 172.2 | 237.1 | 38% |
| Ndufb6 | NADH dehydrogenase 1 beta subcomplex, 6 | 25.9 | 34.2 | 32% |
| Cox5a | cytochrome c oxidase, subunit Va | 67.1 | 88.2 | 32% |
| Tfam | transcription factor A, mitochondrial | 9.0 | 11.8 | 31% |
| Ndufs4 | NADH dehydrogenase Fe-S protein 4 | 22.1 | 28.5 | 29% |
| Vdac3 | voltage-dependent anion channel 3 | 64.0 | 80.0 | 25% |
| Ndufab1 | NADH dehydrogenase 1, alpha/beta subcomplex, 1 | 8.7 | 10.6 | 22% |
| Ndufb2 | NADH dehydrogenase 1 beta subcomplex, 2 | 4.3 | 5.2 | 20% |
| Atp5j | ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F | 86.2 | 102.1 | 18% |
| Ndufc1 | NADH dehydrogenase 1, subcomplex unknown, 1 | 15.1 | 17.7 | 17% |
| Uqcrc2 | ubiquinol cytochrome c reductase core protein 2 | 102.6 | 119.8 | 17% |
| Ndufb5 | NADH dehydrogenase 1 beta subcomplex, 5 | 20.3 | 23.6 | 16% |
| Ap2a1 | adaptor protein complex AP-2, alpha 1 subunit | 9.6 | 7.5 | −22% |
| Gpx1 | glutathione peroxidase 1 | 474.7 | 331.8 | −30% |
| Dctn1 | dynactin 1 | 5.3 | 3.5 | −33% |
| Bbc3 | BCL2 binding component 3 | 1.9 | 1.2 | −36% |
| Ndufs7 | NADH dehydrogenase Fe-S protein 7 | 9.3 | 5.7 | −39% |
| Polr2i | polymerase (RNA) II (DNA directed) polypeptide I | 4.4 | 2.6 | −42% |
| Number of reference genes in the category (C) | ||||
| Number of differentially expressed genes in reference category (O) | ||||
| Expected number in the category (E) | ||||
| Ratio of enrichment (F) | ||||
| P-value from hypergeometric test (rawP) | ||||
| P-value adjusted by the multiple test adjustment (adjP) | ||||
| RPKM: Reads per kilobase of transcript per million mapped reads | ||||
| *Percent difference = [(tx-j - wild type)/wild type]*100 | ||||