Supplementary Table S1: All QTL Derived from the SM X NZB F2 Cross

Supplementary Tables

Supplementary Table S1: All QTL derived from the SM x NZB F2 cross

Position of marker (Mb) / Peak (cM) / CI (cM) / Nearest marker / High allele / Mode of inheritance
QTL / Chr / LOD
Obwq1 / 1 / 114.1 / 4.3 / 62 / (34-76) / D1Mit87 / NZB / Dom
Hdlq20 / 1 / 184.3 / 11.0 / 96 / (94-103) / D1Mit291 / NZB / Dom
Adip10 / 2 / 3.8 / 3.5 / 2 / (0-26) / D2Mit1 / SM / Add
Bwtq8 / 2 / 71.3 / 4.0 / 42 / (34-78) / D2Mit92 / NZB / Add
Hdlq21 / 3 / 10.0 / 4.0 / 56 / (34–60) / D3Mit11 / NZB / Add
Bwtq9 / 4 / 59.5 / 2.1 / 24 / (0-44) / D4Mit44 / NZB / Dom
Adip11 / 4 / 88.0 / 3.2 / 46 / (30-68) / D4Mit26 / SM / Dom
Adip12 / 4 / 140.7 / 2.6 / 70 / (52-80) / D4Mit312 / SM / Add
Hdlq22 / 5 / 30.3 / 5.2 / 18 / N/A / D5Mit228 / NZB / Add
Adip13 / 5 / 41.1 / 2.9 / 26 / (8-44) / D5Mit81 / NZB / Add
Obwq2 / 5 / 78.0 / 3.7 / 44 / (16-66) / D5Mit204 / NZB / Dom
Hdlq2 / 5 / 92.5 / 7.6 / 50 / N/A / D5Mit205 / NZB / Add
Lith17 / 5 / 111.4 / 5.4 / 60 / (40–68)‡ / D5Mit24 / SM / Add
Hdlq1 / 5 / 126.0 / 10.0 / 66 / (12–85) / D5Mit161 / NZB / Add
Lith18 / 5 / 138.5 / 3.9 / 76 / (70–80)‡ / D5Mit284 / SM / Add
Hdlq23* / 6 / 48.8 / 4.2 / 26 / (12–32) / D6Mit74 / NZB / Add
Obwq3 / 6 / 108.3 / 5.8 / 42 / (36-54) / D6Mit105 / SM / Rec
Hdlq24 / 6 / 143.6 / 6.3 / 66 / (54–70) / D6Mit259 / NZB / Add
Bwtq10 / 6 / 143.6 / 5.3 / 62 / (52-70) / D6Mit259 / NZB / Add
Lith19 / 8 / 4.3 / 5.3 / 0 / (0–10) / D8Mit155 / SM / Rec
Obq20 / 8 / 4.3 / 3.2 / 0 / (0-14) / D8Mit155 / NZB / Add
Lith20 / 9 / 71.7 / 2.7 / 44 / (33–50) / D9Mit73 / SM / Rec
Adip14 / 9 / 109.8 / 3.0 / 60 / (48-60) / D9Mit15 / Het / over-Dom
Lith21 / 10 / 25.6 / 2.9 / 24 / (10–40) / D10Mit214 / NZB / Rec
Adip15 / 10 / 92.2 / 3.2 / 52 / (46-66) / D10Mit10 / Het / over-Dom
Adip16 / 12 / 68.6 / 5.3 / 26 / (12-32) / D12Mit91 / SM / Dom
Bwtq11 / 12 / 115.0 / 4.3 / 54 / (42-58) / D12Mit19 / NZB / Add
Bwtq12 / 15 / 69.2 / 3.1 / 34 / (20-59) / D15Mit90 / NZB / Dom
Hdlq27* / 15 / 81.2 / 4.2 / 48 / (44–60) / D15Mit70 / NZB / Rec
Adip17 / 16 / 3.6 / 2.4 / 0 / (0-22) / D16Mit32 / SM / Add
Hdlq28 / 16 / 28.2 / 3.7 / 26 / (0–60) / D16Mit57 / NZB / Dom
Adip18 / 17 / 9.0 / 2.9 / 10 / (0-18) / D17Mit58 / NZB / Add
Obwq4 / 17 / 54.9 / 6.8 / 32 / (26-38) / D17Mit20 / NZB / Add
Hdlq30 / 18 / 68.7 / 4.2 / 48 / N/A / D18Mit9 / NZB / Add
Hdlq31 / 18 / 84.2 / 4.1 / 56 / (42–60) / D18Mit4 / NZB / Add
Obq21 / 18 / 84.2 / 2.5 / 54 / (22-56) / D18Mit4 / NZB / Dom
Obwq5 / 19 / 59.2 / 9.3 / 52 / (46-54) / D19Mit71 / NZB / Rec
Obq22 / X / 67.7 / 4.2 / 34 / (22-42) / DXMit1 / NZB/SM / Co-Dom

*Female specific QTL. N/A indicates QTL for which authors could not determine the interval for an individual QTL due to multiple linked QTL.‡95% confidence interval contain multiple linked loci. LOD scores are given with sex as an additive covariate except for the body weight and obesity phenotypes. Mb indicates millions of base pairs from the centromere (Build 36). Dom -dominance; Add - additive; Rec - recessive.

QTL prefixes: Hdlq - HDL; Lith - gallstones, presence, weight or both; Obwq - lean body weight and specific fad pads; Bwtq– lean body weight; Obq - fat pad weight with sex as an additive covariate; Adip - fat pad weight with sex and body weight as additive covariates.

Supplementary Table S2: Complete candidate gene list based on mRNA difference (M), protein difference (P) or sequence differences (S) for Hdlq20 on Chr 1.

Evidence
Gene / Mb / M1 / P2 / S3
Fmo13 / 168.3 / x
Nos1ap / 172.2 / x
Olfml2b / 172.5 / x
Dusp12 / 172.7 / x
Fcrlb / 172.7 / x
Fcrla / 172.8 / x
Apoa2 / 173.1 / 4.1
Arhgap30 / 173.2 / x
Usf1 / 173.3 / x
Slamf9 / 174.3 / x
Igsf9 / 174.3 / x
Kmo / 177.5 / x
Opn3 / 177.5 / x
Fh1 / 177.5 / -2.8 / x
Chml / 177.5 / x
4930511H01Rik / 177.6 / x
Exo1 / 177.7 / x
Pld5 / 177.8 / x
Cep170 / 178.6 / x
Sdccag8 / 178.7 / x
MGC68323 / 182.2 / x
BC031781 / 182.7 / x
Lefty1 / 182.8 / x
6530421E24Rik / 183.3 / x

Candidate genes listed are in QTL regions that are not identical by descent between SM and NZB. M = mRNA, P = protein, and S = sequence differences. Protein and mRNA fold changes are given where a positive value indicates up-regulation and a negative indicates down-regulation in NZB relative to SM.

1Fold changes for mRNA are significant (Fs<1x10-4), while for proteins2 they are suggestive (P<0.1). Further details are give in Supplementary Tables S4 and S5.

3Genes that contain known or extrapolated codon changing SNPs leading to potential functional differences indicated by an ‘x’.

Supplementary Table S3: Complete candidate gene list based on mRNA difference (M), protein difference (P) or sequence differences (S) for Hdlq1 on Chr 5.

Evidence
Gene / Mb / M1 / P2 / S3
Acads / 115.3 / -2.6 / x
2410014A08Rik / 115.4 / 1.8
1500001A10Rik / 116.7 / x
Taok3 / 117.5 / x
BC023744 / 117.6 / x
Tbx3 / 119.9 / x
Oas2 / 121.0 / x
Oas3 / 121.0 / x
Oas1c / 121.1 / x
Hpd / 123.4 / x
Lrrc43 / 123.8 / x
B3gnt4 / 123.8 / x
Vps33a / 123.8 / x
Rsn / 123.9 / x
2810006K23Rik / 124.6 / x
Sbno1 / 124.6 / x
Ccdc92 / 125.1 / x
Scarb1 / 125.6 / -2.1
Ubc / 125.7 / x
1444439_at / 125.7 / 2.3
Dhx37 / 125.7 / x
Tmem132b / 125.9 / x
Tmem132d / 128.3 / x
Rimbp2 / 129.1 / x
2410018M08Rik / 130.2 / x
Asl / 130.3 / x
0610007L01Rik / 130.5 / -1.5

See legend for Supplementary Table S2.

Supplementary Table S4: Complete candidate gene list based on mRNA difference (M), protein difference (P) or sequence differences (S) for Hdlq24 on Chr 6.

Evidence
Gene / Mb / M1 / P2 / S3
Pparg / 115.4 / x
Tsen2 / 115.5 / x
2510049J12Rik / 115.6 / x
Raf1 / 115.6 / x
Tmem40 / 115.7 / x
Cand2 / 115.8 / x
BC060267 / 115.8 / x
Mbd4 / 115.8 / 1.7 / x
D6Wsu116e / 116.2 / x
Anubl1 / 116.3 / x
Olfr212 / 116.5 / x
Olfr213 / 116.5 / x
Rassf4 / 116.6 / -8.2
Bms1l / 118.4 / x
Ankrd26 / 118.5 / x
Cacna1c / 118.6 / x
5730412N02Rik / 119.3 / x
Adipor2 / 119.3 / 1.9 / x
Il17r / 120.4 / x
Tmem16b / 125.7 / x
Ndufa9 / 126.8 / -2.6
Efcab4b / 127.6 / x
5930416I19Rik / 128.3 / x
Foxm1 / 128.3 / x
Nrip2 / 128.4 / x
Itfg2 / 128.4 / x
1446868_at / 128.4 / -1.7
Pzp / 128.5 / x
BC048546 / 128.5 / 4.1 / x
Klrb1a / 128.6 / x
Clec2h / 128.6 / 3.1 / x
Klrb1c / 128.7 / x
A630024B12Rik / 129.0 / x
Clec7a / 129.4 / 2.0 / x
Klrc1 / 129.6 / x
Klrc3 / 129.6 / x
Klri2 / 129.7 / x
Gm156 / 129.7 / x
Klra3 / 130.3 / x
Klra1 / 130.3 / x
Klra2 / 131.2 / x
Styk1 / 131.3 / x
Tas2r130 / 131.6 / x
Tas2r107 / 131.6 / x
Tas2r104 / 131.7 / x
Tas2r114 / 131.7 / x
Prb1 / 132.2 / x
A630073D07Rik / 132.6 / x
Tas2r121 / 132.7 / x
Tas2r115 / 132.7 / x
Tas2r124 / 132.7 / x
Tas2r102 / 132.7 / x
Tas2r117 / 132.8 / x
Tas2r123 / 132.8 / x
Tas2r116 / 132.8 / x
Tas2r110 / 132.8 / x
Tas2r113 / 132.9 / x
Tas2r125 / 132.9 / x
Tas2r129 / 132.9 / x
Tas2r131 / 132.9 / x
Tas2r109 / 132.9 / x
1446155_at / 133.0 / -5.4
Tas2r140 / 133.0 / x
Kap / 133.8 / x
Bcl2l14 / 134.4 / x
Lrp6 / 134.4 / x
Mansc1 / 134.6 / x
Dusp16 / 134.7 / 2.4
Gpr19 / 134.8 / x
Cdkn1b / 134.9 / x
Apold1 / 134.9 / x
Hebp1 / 135.1 / x
8430419L09Rik / 135.2 / -2.3 / x
Pbp2 / 135.3 / x
E330021D16Rik / 136.4 / x
Igbp1b / 138.6 / x

See legend for Supplementary Table S2.

Supplementary Table S5: Complete candidate gene list based on mRNA difference (M), protein difference (P) or sequence differences (S) for Lith17 on Chr 5.

Evidence
Gene / Mb / M1 / P2 / S3
Igj / 89.6 / 21.4
BC038311 / 91.3 / x
Cxcl5 / 91.8 / x
Scarb2 / 93.6 / x
4932413O14Rik / 93.7 / x
5730467H21Rik / 94.1 / x
Ccni / 94.3 / x
C87414 / 94.7 / x
Mrpl1 / 96.5 / x
Fras1 / 96.6 / x
Bmp2k / 97.3 / -1.7 / x
1700007G11Rik / 98.6 / x
Hnrpd / 100.2 / -1.4
2310057D15Rik / 100.3 / x
Plac8 / 100.8 / 1.9
C230008H04Rik / 103.1 / x
Slc10a6 / 103.9 / x
Dhrs8 / 104.2 / -2.8
Hsd17b13 / 104.2 / x
LOC666279 / 104.4 / x
Spp1 / 104.7 / x
Pkd2 / 104.7 / -1.4 / x
BC005561 / 104.8 / x
D930016D06Rik / 104.8 / -2.0
5830443L24Rik / 105.3 / x
BC057170 / 105.3 / x
Mpa2l / 105.5 / 4.5
Lrrc8d / 106.1 / x
Zfp326 / 106.2 / x
Evi5 / 108.1 / x
Dgkq / 108.9 / x
Idua / 108.9 / x
Golga3 / 110.4 / x
Pgam5 / 110.5 / x
Pole / 110.6 / x
Noc4l / 110.9 / x
Ddx51 / 110.9 / x
Ep400 / 110.9 / x
Chek2 / 111.1 / x
Mn1 / 111.7 / 4.0 / x
Tfip11 / 112.6 / x
Hps4 / 112.6 / x
Asphd2 / 112.6 / x
Sez6l / 112.7 / x
Myo18b / 112.9 / x
Adrbk2 / 113.2 / x
Crybb3 / 113.3 / x
Rutbc2 / 113.5 / x
Selpl / 114.1 / x
Ssh1 / 114.2 / x
Acacb / 114.5 / x
Myo1h / 114.6 / x
4930519G04Rik / 115.1 / x
Tcf1 / 115.2 / x
Acads / 115.3 / -2.6 / x
2410014A08Rik / 115.4 / 1.8
Rnf10 / 115.5 / x
Sfrs9 / 115.6 / x
Dnclc1 / 115.6 / 2.1
2010003O18Rik / 115.6 / x
Gcn1l1 / 115.9 / x
1500001A10Rik / 116.7 / x
2900006A08Rik / 117.4 / -1.5 / x
BC023744 / 117.6 / x
Tbx3 / 119.9 / x
Oas2 / 121.0 / x
Oas3 / 121.0 / x
Oas1c / 121.1 / x
Trafd1 / 121.6 / x

See legend for Supplementary Table S2.

Supplementary Table S6: Complete candidate gene list based on mRNA difference (M), protein difference (P) or sequence differences (S) for Lith19 on Chr 8.

Evidence
Gene / Mb / M1 / P2 / S3
Arhgef18 / 3.4 / x
1700019B03Rik / 3.5 / x
Mcoln1 / 3.5 / -1.6 / x
Fcer2a / 3.7 / x
Cd209a / 3.7 / x
Cd209e / 3.8 / x
2610208M17Rik / 4.1 / x
Map2k7 / 4.2 / -1.9
B130050I23Rik / 4.2 / x
BC068157 / 4.2 / x
Ccl25 / 4.3 / -1.8 / x
Lass4 / 4.5 / x
9130221J18Rik / 5.1 / 2.8
Slc10a2 / 5.1 / 5.2
Efnb2 / 8.6 / x
Cln8 / 14.9 / x
Arhgef10 / 14.9 / -2.5 / x
Kbtbd11 / 15.0 / x
Myom2 / 15.1 / 3.1 / x

See legend for Supplementary Table S2.

Supplementary Table S7: Complete candidate gene list based on mRNA difference (M), protein difference (P) or sequence differences (S) for Lith21 on Chr 10.

Evidence
Gene / Mb / M1 / P2 / S3
Nhsl1 / 18.7 / x
Tnfaip3 / 19.3 / x
Ifngr1 / 19.7 / x
Map3k5 / 24.3 / -2.6 / x
Ctgf / 24.3 / x
Enpp1 / 24.5 / x
Enpp3 / 24.7 / -6.6
4833416E15Rik / 25.2 / 2.0
1438359_at / 25.9 / x
Gm623 / 18.2 / x

See legend for Supplementary Table S2.

Supplementary Table S8: Complete candidate gene list based on mRNA difference (M), protein difference (P) or sequence differences (S) for Obwq3 on Chr 6.

Evidence
Gene / Mb / M1 / P2 / S3
Nup210 / 91.0 / x
Fbln2 / 91.2 / x
Ppp4r2 / 100.8 / x
Pdzrn3 / 101.1 / x
Cntn6 / 104.7 / x
5031434C07Rik / 112.3 / x
Ogg1 / 113.3 / x
Hrh1 / 114.4 / x
Pparg / 115.4 / x
Tsen2 / 115.5 / x
2510049J12Rik / 115.6 / x
Raf1 / 115.6 / x
Tmem40 / 115.7 / x
Cand2 / 115.8 / x
BC060267 / 115.8 / x
Mbd4 / 115.8 / 1.7 / x
D6Wsu116e / 116.2 / x
Anubl1 / 116.3 / x
Rassf4 / 116.6 / -8.2
Bms1l / 118.4 / x
Ankrd26 / 118.5 / x
Cacna1c / 118.6 / x
Dcp1b / 119.2 / x
5730412N02Rik / 119.3 / x
Adipor2 / 119.3 / 1.9 / x
Il17r / 120.4 / x

See legend for Supplementary Table 2.

Supplementary Table S9: Complete candidate gene list based on mRNA difference (M), protein difference (P) or sequence differences (S) for Obwq4 on Chr 17.

Evidence
Gene / Mb / M1 / P2 / S3
Notch4 / 34.2 / x
Pbx2 / 34.2 / x
Fkbpl / 34.3 / x
Crebl1 / 34.3 / x
Ng23 / 34.6 / x
Msh5 / 34.6 / x
Ly6g6e / 34.7 / x
Bat2 / 34.8 / x
Lst1 / 34.8 / 2.6
Ltb / 34.8 / x
H2-D1 / 34.9 / -6.7
H2-Q8 / 35.0 / x
Cdsn / 35.2 / x
2300002M23Rik / 35.2 / x
Dpcr1 / 35.2 / x
2310061I04Rik / 35.5 / x
2610110G12Rik / 35.5 / x
H2-T23 / 35.6 / -2.4
H2-Bl / 35.7 / x
H2-T10 / 35.7 / -1.8
2410017I17Rik / 35.8 / x
LOC667977 / 35.8 / x
H2-T3 / 35.8 / x
Trim39 / 35.9 / x
H2-M10.1 / 35.9 / x
H2-M10.3 / 36.0 / x
H2-M10.4 / 36.1 / x
H2-M1 / 36.3 / x
H2-M10.6 / 36.4 / x
Trim26 / 36.5 / x
Trim10 / 36.5 / x
Ppp1r11 / 36.6 / x
D130003B22Rik / 36.6 / x
Olfr93 / 36.8 / x
Olfr99 / 36.9 / x
Olfr102 / 36.9 / x
Olfr107 / 37.0 / x
Gpr115 / 42.1 / x
Gpr110 / 42.8 / x
Tdrd6 / 43.1 / x
Enpp5 / 43.5 / x
Supt3h / 44.5 / x
Vegfa / 45.5 / x
Mad2l1bp / 45.6 / x
Yipf3 / 45.7 / x
Tjap1 / 45.7 / x
G1p2 / 45.9 / 1.9
Slc22a7 / 45.9 / x
BC048355 / 46.0 / x
Ptk7 / 46.0 / x
Rpl7l1 / 46.1 / 2.9
Klhdc3 / 46.1 / x
Pex6 / 46.2 / x
Gnmt / 46.2 / x
Guca1b / 46.9 / x
Guca1a / 46.9 / x
1700001C19Rik / 46.9 / -3.3 / x
1437584_at / 46.9 / -2.2
Tbn / 47.0 / x
Pgc / 47.2 / x
Mdfi / 47.3 / x
Foxp4 / 47.3 / x
Treml2 / 47.8 / x
Bzrpl1 / 47.9 / x
Kif6 / 49.2 / x
LOC668470 / 49.4 / x
2310015N21Rik / 49.5 / x
A130033B22 / 51.9 / x
Efhb / 52.9 / x
Sgol1 / 53.1 / x
4932415M13Rik / 53.2 / x
Sult1c2 / 53.3 / x
Sult1c1 / 53.4 / x
Zfp119 / 55.5 / x
Tnfsf9 / 56.8 / x

See legend for Supplementary Table S2.

Supplementary Table S10: Complete candidate gene list based on mRNA difference (M), protein difference (P) or sequence differences (S) for Obwq5 on Chr 19.

Evidence
Gene / Mb / M1 / P2 / S3
1110018J23Rik / 53.9 / x
Nrap / 56.4 / x
Dclre1a / 56.5 / -2.3
Casp7 / 56.5 / x
Tdrd1 / 56.9 / x
Ablim1 / 57.1 / x
AI450540 / 57.4 / -1.6 / x
Atrnl1 / 57.7 / 3.4
Slc18a2 / 59.3 / x

See legend for Supplementary Table S2.

.

1

1

Supplementary Table S11: Validation of 10 Affymetrix probes sets using TaqMan assays. Chosen probe sets had an FDR<0.0001 and a conservative fold difference of ≤4.0.

Affy Probe ID / Fold change NZB to SM
Affymetric TaqMan / Gene Symbol / p-value
Taqman / FDR
Affy
1418872_at / -3.8 / -82.9* / Abcb1b / 0.00E+00 / 0.00000
1421741_at / 3.5 / 5.0 / Cyp3a16 / 1.37E-06 / 0.00005
1417968_a_at / 2.0 / 2.1 / Mbd1 / 4.43E-08 / 0.00000
1418595_at / 1.9 / 7.0* / S3-12 / 4.01E-05 / 0.00045
1450109_s_at / -1.9 / -1.5 / Abcc2 / 3.10E-07 / 0.00002
1416029_at / 1.9 / 2.2 / Tieg1 / 5.81E-06 / 0.00012
1418167_at / 1.9 / 2.2 / Tcfap4 / 1.42E-06 / 0.00005
1425745_a_at / 3.2 / 8.0* / Tacc2 / 0.00E+00 / 0.00000
1431056_a_at / -3.7 / -4.9 / Lpl / 4.43E-08 / 0.00000
1420491_at / 1.8 / 1.5 / Eif2s1 / 1.37E-06 / 0.00005

P-value is the calculated permutation p-value.FDR is the false discovery rate. *All genes on both platforms had fold changes that were significant and in the same direction. However, fold differences between microarrays and real-time are not always the same for various reasons. Commonly this is because the probes differ between platforms because one probe may be better designed than the other to the target gene.

Supplementary Table S12: Differentially expressed genes in the 9 QTL

HDL / Gallstones / Obesity / Gene Symbol / Chr / Bp / FC / q-value
X / D1Ertd471e / 1 / 168,151,385 / 2.4 / 0
X / Rgs5 / 1 / 171,492,178 / -2.9 / 0
X / 1417466_at / 1 / 171,530,582 / -1.9 / 0.00003
X / Fcgr3 / 1 / 172,887,836 / 1.8 / 0
X / Apcs / 1 / 174,730,635 / 2.5 / 0
X / Sult1d1 / 5 / 88,629,190 / -1.8 / 0.00001
X / Sult1e1 / 5 / 88,650,498 / -4.7 / 0
X / Igj / 5 / 89,595,073 / 21.4 / 0
X / 1455383_at / 5 / 93,666,192 / -8.0 / 0
X / Bmp2k / 5 / 97,309,282 / -1.7 / 0
X / Hnrpd / 5 / 100,201,178 / -1.4 / 0
X / Hnrpdl / 5 / 100,274,820 / -1.5 / 0
X / Plac8 / 5 / 100,794,027 / 1.9 / 0
X / Dhrs8 / 5 / 104,230,625 / -2.8 / 0
X / Pkd2 / 5 / 104,745,848 / -1.4 / 0
X / D930016D06Rik / 5 / 104,792,319 / -2.0 / 0
X / Mpa2l / 5 / 105,455,206 / 4.5 / 0
X / Golga3 / 5 / 110,466,185 / -1.5 / 0
X / Mn1 / 5 / 111,695,180 / 4.0 / 0
X / X / 2410014A08Rik / 5 / 115,405,353 / 1.8 / 0
X / X / Dnclc1 / 5 / 115,559,420 / 2.1 / 0
X / X / 2900006A08Rik / 5 / 117,535,696 / -1.5 / 0
X / X / Sds / 5 / 120,739,502 / -1.9 / 0
X / X / Cutl2 / 5 / 122,119,003 / -2.6 / 0
X / X / 9130017A15Rik / 5 / 122,577,723 / -2.6 / 0
X / Scarb1 / 5 / 125,566,063 / -2.1 / 0
X / Bri3bp / 5 / 125,730,953 / 1.6 / 0.00002
X / 1444439_at / 5 / 125,745,380 / 2.3 / 0
X / 0610007L01Rik / 5 / 130,507,053 / -1.5 / 0.00001
X / Klf15 / 6 / 90,428,079 / -1.8 / 0
X / 9430029L20Rik / 6 / 91,421,703 / -2.2 / 0
X / Irak2 / 6 / 113,659,859 / 2.1 / 0
X / X / Mbd4 / 6 / 115,807,799 / 1.7 / 0
X / X / Rassf4 / 6 / 116,598,614 / -8.2 / 0
X / X / 2900097C17Rik / 6 / 117,682,126 / 3.6 / 0
X / X / Adipor2 / 6 / 119,320,874 / 1.9 / 0.00002
X / 1446868_at / 6 / 128,409,213 / -1.7 / 0.00002
X / BC048546 / 6 / 128,505,382 / 4.1 / 0
X / Clec2h / 6 / 128,628,003 / 3.1 / 0
X / Clec7a / 6 / 129,427,266 / 2.0 / 0
X / 1446155_at / 6 / 133,077,299 / -5.4 / 0
X / Dusp16 / 6 / 134,701,160 / 2.4 / 0
X / 8430419L09Rik / 6 / 135,163,726 / -2.3 / 0
X / Arhgdib / 6 / 136,887,714 / 1.3 / 0.00001
X / Slco1a1 / 6 / 141,870,007 / 2.4 / 0.00003
X / Mcoln1 / 8 / 3,513,025 / -1.6 / 0
X / Xpot / 8 / 3,998,349 / -1.8 / 0
X / Map2k7 / 8 / 4,250,748 / -1.9 / 0
X / Ccl25 / 8 / 4,349,618 / -1.8 / 0
X / 9130221J18Rik / 8 / 5,083,193 / 2.8 / 0
X / Slc10a2 / 8 / 5,085,774 / 5.2 / 0
X / 4933411D12Rik / 8 / 13,120,188 / -1.3 / 0.00003
X / 1455745_at / 8 / 14,900,635 / -1.8 / 0
X / Arhgef10 / 8 / 14,979,836 / -2.5 / 0
X / Myom2 / 8 / 15,133,173 / 3.1 / 0
X / Rps12 / 10 / 23,474,611 / 1.4 / 0
X / Ctgf / 10 / 24,284,928 / -2.6 / 0
X / 4833416E15Rik / 10 / 24,327,316 / -6.6 / 0
X / 1438359_at / 10 / 25,217,359 / 2.0 / 0.00003
X / Ptprk / 10 / 27,953,365 / -1.7 / 0.00008
X / Hddc2 / 10 / 31,002,797 / 1.9 / 0
X / Tpd52l1 / 10 / 31,021,782 / -2.9 / 0
X / Sult3a1 / 10 / 33,553,350 / -3.8 / 0
X / Slc16a10 / 10 / 39,765,178 / -2.1 / 0.00003
X / Foxo3a / 10 / 41,870,260 / -1.8 / 0
X / 1455418_at / 10 / 52,961,857 / -2.2 / 0
X / septin 10 / 10 / 58,559,434 / 2.2 / 0
X / Neu1 / 17 / 34,539,328 / 1.9 / 0
X / D17H6S56E-5 / 17 / 34,605,192 / 2.9 / 0.00002
X / Bat4 / 17 / 34,732,667 / 1.5 / 0
X / Lst1 / 17 / 34,793,154 / 2.6 / 0
X / H2-D1 / 17 / 34,871,169 / -6.7 / 0
X / LOC386462 / 17 / 35,047,241 / -1.9 / 0
X / Tubb5 / 17 / 35,442,831 / 1.6 / 0.00002
X / 1441797_at / 17 / 35,604,557 / -2.2 / 0
X / H2-T23 / 17 / 35,637,739 / -2.4 / 0
X / H2-T10 / 17 / 35,725,171 / -1.8 / 0
X / Pla2g7 / 17 / 43,031,763 / 2.0 / 0
X / Cyp39a1 / 17 / 43,130,333 / -62.2 / 0
X / G1p2 / 17 / 45,870,111 / 1.9 / 0
X / Klc4 / 17 / 46,093,812 / 1.3 / 0.00001
X / Rpl7l1 / 17 / 46,237,077 / 2.9 / 0
X / 1700001C19Rik / 17 / 46,876,063 / -3.3 / 0
X / 1437584_at / 17 / 46,982,415 / -2.2 / 0
X / Dclre1a / 19 / 56,582,410 / -2.3 / 0
X / AI450540 / 19 / 57,441,480 / -1.6 / 0
X / Atrnl1 / 19 / 58,185,951 / 3.4 / 0

Multiple Affymetrix probe sets exist for many genes; however details are only given for representative probe sets. Differentially expressed genes are shown for the 95% CI of each QTL after removing regions that are identical by descent. ‘X’ – Indicates the phenotypes with which the probes are associated.

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Supplementary Table S13: Differentially expressed proteins with corresponding microarray data

Protein Symbol / Representative Peptide / Protein MW / Protein PI / P# / Normalized FC to S1:S2* / Corresponding microarray data
Chr / Mb / N1:S2 / N2:S2 / p-Value / Affy Prode ID / N:S FC* / Fdradj
Il1r2 / LEGEPVVLR / 1 / 40.0 / 58772 / 8.03 / 1 / -1.39 / -1.82 / 0.074 / 1419532_at / -1.04 / 0.396
Pthr2 / FLLFFSLR / 1 / 65.2 / 37036 / 9.16 / 1 / -1.96 / -3.85 / 0.094 / 1452129_at / -1.57 / 0.001
Apoa2 / AYFEKTHEQLTPLVR / 1 / 173.1 / 12799 / 6.56 / 4 / 5.70 / 2.54 / 0.077 / 1417950_a_at / 1.02 / 0.488
Fh1 / IYELAAGGTAVGTGLNTR / 1 / 177.5 / 59275 / 9.12 / 2 / -2.13 / -3.45 / 0.073 / 1424828_a_at / -1.51 / 0.000
Hsd11b1 / IMEFFSLR / 1 / 194.9 / 35363 / 8.58 / 1 / -1.96 / -3.85 / 0.094 / 1449038_at / -1.23 / 0.001
Ivd / LYEIGAGTSEVRR / 2 / 118.5 / 50523 / 8.67 / 3 / -1.37 / -1.49 / 0.016 / 1418238_at / -1.36 / 0.003
Hao1 / SGANDQETLADNIQAFSR / 2 / 134.2 / 44520 / 7.60 / 2 / -5.56 / -3.85 / 0.024 / 1420420_at / -1.08 / 0.170
Smarca5 / TAMALQRR / 4 / 144.7 / 128835 / 8.27 / 1 / 1.71 / 1.32 / 0.091 / 1424206_at / -1.71 / 0.000
Lrrc47 / ESGEGEEEVADSAR / 4 / 152.9 / 69100 / 8.38 / 1 / 3.29 / 2.37 / 0.038 / 1428451_at / -1.16 / 0.044
Acads / ITEIYEGTSEIQR / 5 / 115.3 / 48318 / 8.96 / 2 / -2.50 / -2.70 / 0.014 / 1460216_at / -1.09 / 0.131
Por / ALVPMFVR / 5 / 136.0 / 83225 / 5.34 / 1 / -1.67 / -2.78 / 0.092 / 1416933_at / -1.68 / 0.001
Atp5j2 / DFTPSGIAGAFR / 5 / 145.4 / 11824 / 9.95 / 1 / -1.52 / -1.56 / 0.008 / 1416269_at / -1.04 / 0.421
Cyp3a41 / QGLLQPEKPIVLK / 5 / 145.8 / 65154 / 8.93 / 1 / -1.59 / -2.17 / 0.087 / 1419704_at / -1.08 / 0.265
Ndufa9 / AIAQASKEAGVER / 6 / 126.8 / 42526 / 9.55 / 1 / -2.94 / -2.27 / 0.026 / 1416663_at / -1.15 / 0.037
Oat / LAPPLVIKEDEIR / 7 / 132.4 / 52537 / 6.19 / 2 / -2.50 / -3.33 / 0.020 / 1416452_at / -1.11 / 0.234
Prdx2 / QITVNDLPVGR / 8 / 87.9 / 23920 / 5.20 / 2 / -1.75 / -2.08 / 0.057 / 1418506_a_at / 2.93 / 0.000
Jph3 / SLGEAGQR / 8 / 124.6 / 173957 / 4.91 / 2 / -1.79 / -2.13 / 0.043 / 1443724_at / 1.04 / 0.430
Olfr868 / AIVLDPCR / 9 / 19.9 / 405148 / 5.02 / 1 / -1.67 / -2.78 / 0.092 / **none** / N/A / N/A
Pccb / GFVDDIIQPSSTR / 9 / 100.8 / 62447 / 7.59 / 1 / -1.82 / -1.96 / 0.031 / 1450969_at / 1.07 / 0.252
Syne1 / SSVTSTGNQLLR / 10 / 4.8 / 255057 / 5.39 / 1 / -1.61 / -2.27 / 0.094 / 1421545_a_at / 1.17 / 0.001
Shmt1 / AGXIFYRK / 11 / 60.6 / 57068 / 6.47 / 1 / -1.82 / -1.79 / 0.009 / 1425179_at / -1.11 / 0.068
Prr6 / CGVQSFYTPR / 11 / 62.3 / 11321 / 7.77 / 1 / -1.37 / -1.85 / 0.084 / 1428706_at / -1.37 / 0.000
Psmb6 / LAAIQESGVER / 11 / 70.3 / 26313 / 4.97 / 1 / -1.49 / -2.33 / 0.098 / 1448822_at / 1.67 / 0.000
Kpnb1 / AAVENLPTFLVELSR / 11 / 97.0 / 104474 / 4.68 / 1 / -1.56 / -2.13 / 0.075 / 1416925_at / -1.20 / 0.048
Spnb1 / ILPDILR / 12 / 77.5 / 65940 / 6.18 / 1 / -1.39 / -1.61 / 0.088 / 1450556_at / 1.14 / 0.013
none / EPESTLRALR / 12 / 80.5 / 32016 / 8.93 / 1 / 2.04 / 1.45 / 0.082 / none / N/A / N/A
Dmgdh / DGLLFGPYESQEK / 13 / 94.8 / 77032 / 6.42 / 4 / -2.08 / -2.27 / 0.070 / 1452311_at / -1.44 / 0.000
Kif13b / SSGLQPQGAPEVR / 14 / 63.7 / 234753 / 5.46 / 1 / 5.85 / 3.59 / 0.028 / 1453276_at / -1.06 / 0.226
Eif3s6 / QMXSTRDGR / 15 / 43.0 / 72557 / 6.24 / 1 / -2.08 / -2.86 / 0.034 / 1434523_x_at / -1.11 / 0.034
Cacna1i / ASLSPATRR / 15 / 80.2 / 27255 / 9.74 / 1 / -2.08 / -3.03 / 0.042 / none / N/A / N/A
cystatin / MPGGLSRAR / 16 / 35.1 / 12512 / 7.79 / 1 / -1.49 / -1.49 / 0.085 / 1449909_at / 1.01 / 0.521
Pggt1b / EACLAGLR / 18 / 46.4 / 57004 / 6.37 / 1 / -2.44 / -2.86 / 0.046 / 1429769_at / -1.20 / 0.026
Rbm21 / GVFAIVEMGDISAR / 19 / 9.0 / 100363 / 5.56 / 1 / 3.29 / 2.37 / 0.038 / 1451106_at / 1.09 / 0.134
SLC-family / TAVAPIER / ** / 36492 / 9.73 / 1 / -2.13 / -3.03 / 0.032 / N/A / N/A / N/A
AHCY-family / ALDIAENEMPGLMR / ** / 52380 / 5.98 / 2 / -2.33 / -5.56 / 0.092 / N/A / N/A / N/A
ribosomal / VERADGYEPPVQESV / ** / 35539 / 9.75 / 2 / -1.32 / -1.32 / 0.060 / none / N/A / N/A
ribosomal / IALTDNSLIAR / ** / 34490 / 10.90 / 5 / 1.80 / 1.47 / 0.072 / none / N/A / N/A
unnamed / LLDPLLR / *** / 347308 / 7.10 / 1 / -1.39 / -1.61 / 0.088 / none / N/A / N/A
unnamed / VYTQVEFKR / *** / 22542 / 8.98 / 2 / 4.95 / 2.99 / 0.055 / none / N/A / N/A
unnamed / EIQSALR / *** / 96505 / 9.42 / 1 / -1.96 / -2.56 / 0.035 / none / N/A / N/A
unnamed / ETAQVLR / *** / 46668 / 5.25 / 1 / -1.96 / -2.56 / 0.035 / none / N/A / N/A
unnamed / ADLGTDRIGR / *** / 9730 / 8.50 / 1 / -7.69 / -20.00 / 0.046 / none / N/A / N/A
unnamed / EDNPWGSR / *** / 180089 / 7.71 / 1 / -1.49 / -1.49 / 0.085 / none / N/A / N/A
unnamed / EIQASLR / *** / 15600 / 9.51 / 1 / -1.96 / -2.56 / 0.035 / none / N/A / N/A
unnamed / ELQALSR / *** / 15423 / 6.62 / 1 / -1.96 / -2.56 / 0.035 / none / N/A / N/A

*S1 and S2 represent the two biological replicates of SM liver samples; N1 and N2 represent the two NZB samples. FDRadj is the fold discovery adjusted p-value. The FDR was calculated for the protein data but was 0.99 for all samples. This did not provide any basis to distinguish the protein changes from each other, and therefore the p values provided in the table are more meaningful. P# - indicates the number of different peptides identified for each protein. FC – is fold change, where a negative number indicates greater quantity in the SM strain relative to NZ. ** Multiple non unique chromosomal locations identified, ***no locations identified.

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