Itemised list of Supplemental Material

1. Supplemental Materials and Methods

2. Supplemental References

3. Supplemental Table S1. Summary of pathological abnormalities observed

with variable penetrance in L597VBraf-expressing mice.

4. Supplemental Figures S1-7.

Fig. S1: Multiplex PCR genotyping of Braf+/LSL-L597V mouse ear samples

Fig. S2: H&E-stained sections of benign growths

Fig. S3: PCR to detect Cre-mediated recombination in MEFs

Fig. S4: Characterisation of the Erk pathway in MEFs: Dusp 6 knockdown and

p90RSK phosphorylation

Fig. S5: PCR to detection Cre-mediated recombination in lung

Fig. S6: Expression of D-type cyclins in primary MEFs.

Fig. S7: Heterodimer formation between L597VBRAF and CRAF in HEK293T

cells.

5. Supplemental Table S2. Summary of microarray data

6. Supplemental Table S3. whose expression is significantly altered in

V600EBraf, G12DKras and L597VBraf/G12DKras MEFs.

7. Supplemental Table S4. Genes whose expression is altered in

L597VBraf/G12DKras MEFs but not G12DKras or V600EBraf MEFs Supplemental Materials and Methods

Transfection of HEK293T cells

HEK293T cells were cultured in DMEM with 10% FCS and penicillin/streptomycin and transfected with lipofectamine 2000 using conditions recommended by the manufacturer (Invitrogen). Cells were either mock transfected or transfected with myc-tagged expression vectors for human WTBRAF or L597VBRAF. 48 hours after transfection, cells were harvested and lysates generated by previously reported methods (Huser et al. 2001). BRAF was immunoprecipitated using the

BRAF antibody (Santa Cruz Inc. #SC-5284).

Immunoblotting

Protein lysates were prepared by previously published methods (Huser et al. 2001).

Antibodies used were as follows: Cyclin d1 (Cell Signaling Tech. #2922), Cyclin d2

(Santa Cruz Inc. #SC-593), Cyclin d3 (Cell Signaling Tech. #2936), Gapdh (Millipore

#MAB374), CRAF (BD Biosciences #610153), BRAF (Santa Cruz Inc. #SC-5284),

MYC (Cell Signaling Tech. #2276), Gapdh (Millipore #MAB374), Erk2 (Santa Cruz

Inc. #SC-1647), Dusp6 (Abcam #AB76310) and phospho-Ser380 p90RSK (Cell

Signaling Tech. 9341S).

siRNA knockdown

ON-TARGETplus SMARTpool Dusp6 siRNA (Dharmacon) was used and transfected using lipofectamine 2000 as described in Materials and Methods of the main text.

Supplemental References

Ritt, D.A., Monson, D.M., Specht, S.I., Morrison, D.K. (2010) Impact of feedback phosphorylation and Raf heterodimerization on normal and mutant B-Raf signaling. Mol. Cell. Biol. 30: 806-819.

Supplemental Table S1. Summary of pathological abnormalities observed with variable penetrance in L597VBraf-expressing mice.

Pathology Braf+/Lox-L597V Braf+/+

a)Splenomegaly 17/31 (55%) 0/26 (0%)

Stroke 8/31 (26%) 0/26 (0%)

b)Growth in internal organs 3/31 (16%) 0/26 (0%)

c)Eye abnormalities 4/31 (13%) 0/26 (0%)

Uterine prolapse 4/31 (13%) 0/26 (0%)

d)Skin lesions 2/31 (6%) 0/26 (0%)

Overgrown incisors 4/31 (13%) 0/26 (0%)

a) Increased spleen weight by ~4-fold was observed in these mice b) These included: a small intestinal adenoma in one animal at 79 weeks, hyperplasia of the

lymphoid tissue in one animal at 73 weeks and hyperplasia of the smooth muscle of the uterus in

one animal at 23 weeks. c) Eye abnormalities included cataracts and watery eyes. d) Skin lesions were histologically confirmed as benign skin papillomas in two mice at 29 and 48

weeks of age.

Pathologies arising in mice of 6-80 weeks of age with the indicated genotypes are included in the table: all of these mice arose from Braf+/LSL-L597V x CMV-Cre+/o intercrosses and recombination efficiencies were as those indicated in Supplemental Figure 1.

+ + + - - - CMV-Cre + + - - + - LSL-L597V

BrafLox-L597V BrafWT

BrafLSL-L597V

Supplemental Figure S1. Multiplex PCR genotyping of Braf+/LSL-L597V mouse ear samples with and without the CMV-Cre transgene, utilizing three primers shown in Figure 1A. A B

C

Supplemental Figure S2. H&E-stained sections of benign growths arising in aged Braf+/Lox-L597V mice.

A. Small intestinal adenomatous polyp B. Skin papilloma C. Hyperplasia of lymphoid tissue. D. Hyperplasia of smooth muscle of the uterus.

Scale bars = 200 µm β-gal 0 hour 24 hours 48 hours 72 hours 96 hours . WT LV VE WT LV VE WT LV VE WT LV VE WT LV VE WT LV VE

BrafLox BrafWT

BrafLSL

Supplemental Figure S3. PCR to detect Cre-mediated recombination of BrafLSL-L597V and BrafLSL-V600E alleles in MEFs. Braf+/+, Braf+/LSL-L597V or BrafLSL-V600E MEFs were treated with AdCre for 0-96 hours or Adβgal for 96 hours, and genomic DNA was isolated. DNA was PCR genotyped using the three primers (A-C) indicated in Fig. 1A and described in Methods. Cre-mediated recombination is indicated by the appearance of the BrafLox band and the disappearance of the BrafLSL band. A high level of recombination was achieved within 24 hours, and recombination was virtually complete within 72 hours for both alleles.

A - Scr D P-Mek

P-Erk

Dusp6

Erk2

B 0 24 48 72 96 hr + AdCre WT LV VE WT LV VE WT LV VE WT LV VE WT LV VE P-Mek

P-Erk

P-p90Rsk

Erk2

Supplemental Figure S4. Characterisation of the Erk pathway in MEFs: Dusp6 knockdown and p90RSK phosphorylation.

A, Dusp6 siRNA knockdown in V600EBraf MEFs. To investigate control of the Erk pathway by Dusp6 in V600EBraf cells, immortalised VE MEFs were either untransfected (-) or transfected with Scrambled (Scr) or Dusp6 (D) siRNA. Protein lysates were western blotted and analysed with antibodies for phosphoMek, phosphoErk, Dusp6 and Erk2. As expected, phosphoErk levels were observed to increase significantly following Dusp6 knockdown while P-Mek levels were slightly reduced, possibly as a result of increased negative feedback regulation of the V600EBRAF/MEK pathway by ERK as previously documented (Ritt et al 2010). B, Analysis of the phosphorylation of the Erk target p90RSK. Protein lysates from Braf+/+, Braf+/LSL-L597V and Braf+/LSL-V600E MEFs treated with AdCre for 0-96 hours were western blotted and analysed with antibodies for phosphoMek, phosphoErk and phospho-p90RSK (Ser380). Erk phosphorylates and activates the C-terminal kinase domain of p90RSK which in turn autophosphorylates Ser380 and so phosphorylation of Ser380 of RSK is Erk- dependent. RSK phosphorylation was observed to correspond to levels of Mek/Erk activation with higher levels being observed in the VE cells compared to LV and WT cells at 48 and 72 hours following Cre-induced recombination. Levels of phosphoRSK were more similar at the 96 hour time point when phosphoErk levels were more similar between the LV and VE cells. A WT LV G12D VE G12D/LV

Braf BrafLox BrafWT

KrasLox-G12D Kras KrasWT

WT VE LV G12D G12D/LV B BrafLox Braf BrafWT

KrasLox-G12D Kras KrasWT

Supplemental Figure S5. PCR to detection Cre-mediated recombination of BrafLSL- L597V, BrafLSL-V600E and KrasLSL-G12D alleles in lung and MEFs. A, Genomic DNAs taken from lungs of Braf+/+ (WT), Braf+/LSL-L597V (LV), Kras+/LSL-G12D (GD), Kras+/LSL-G12D ;Braf+/LSL-L597V (G12D/LV) or Braf+/LSL-V600E (VE) mice treated with AdCre were PCR genotyped using the two primers (A,C) indicated in Figure 1A and described in Methods for Braf (top panel) and the two primers described in Methods for Kras (lower panel). B, Genomic DNAs taken from MEFs of Braf+/+ (WT), Braf+/LSL-L597V (LV), Kras+/LSL-G12D (G12D), Kras+/LSL-G12D;Braf+/LSL-L597V (G12D/LV) or Braf+/LSL-V600E (VE) mice treated with AdCre were PCR genotyped using the two primers (A,C) indicated in Figure 1A and described in Methods for Braf (top panel) and the two primers described in Methods for Kras (lower panel). G12D/ WT VE LV G12D LV

Cyclin d1

Cyclin d2

Cyclin d3

Gapdh

Supplemental Figure S6. Expression of D-type cyclins in primary MEFs. Protein lysates from pimary MEFs from WT, LV, VE, G12D and G12D/LV MEFs were prepared 96 hours after infection with AdCre and western blots were analysed with the indicated antibodies. While Cyclin D1 and Cyclin D2 levels were increased to similar levels in the VE, G12D and G12D samples compared to WT and LV samples, Cyclin D3 levels were higher in the G12D MEFs.

- WT LV

CRAF IP: BRAF BRAF

CRAF

WCL BRAF

MYC

Supplemental Figure S7. L597VBRAF forms a heterodimer with CRAF following overexpression in HEK293T cells. HEK293T cells were either mock-transfected (-) or transfected with vectors expressing myc-tagged WTBRAF or L597VBRAF. Protein lysates were immunoprecipitated for BRAF and immunoprecipitates analysed for BRAF and CRAF. Whole cell lysates (WCL) were also analysed with antibodies for BRAF, CRAF or the myc-tag.

Supplemental Table S3. Genes whose expression is significantly altered in V600EBraf, G12DKras and L597VBraf/G12DKras MEFs compared to Braf+/+ MEFs

Fold change Fold change Fold change Name Gene Description ID (V600E over WT) (G12D over WT) (LV/G12D over WT) Gap43 growth associated protein 43 14432 16.60 11.70 10.20 Etv1 ets variant gene 1 14009 15.60 10.90 11.40 Etv1 /// Gm5454 ets variant gene 1 /// predicted gene 5454 14009 /// 432800 13.80 10.80 9.62 Olfr1318 /// Olfr1317 olfactory receptor 1318 /// olfactory receptor 1317 258022 /// 258440 12.70 9.95 6.93 Sh3bgrl2 SH3 domain binding glutamic acid-rich protein like 2 212531 9.87 2.88 4.37 Ramp3 receptor (calcitonin) activity modifying protein 3 56089 9.75 8.14 6.74 Pde3b phosphodiesterase 3B, cGMP-inhibited 18576 9.23 18.90 9.27 Pdgfra platelet derived growth factor receptor, alpha polypeptide 18595 8.50 6.28 6.11 Lrrtm2 leucine rich repeat transmembrane neuronal 2 107065 8.36 7.70 9.43 Tmeff2 transmembrane protein with EGF-like and two follistatin-like domains 2 56363 7.19 4.45 3.98 Gpm6b glycoprotein m6b 14758 6.67 6.88 7.99 Rgs2 regulator of G-protein signaling 2 19735 6.21 5.12 2.72 Man1a mannosidase 1, alpha 17155 6.08 4.74 3.75 Grem1 gremlin 1 23892 5.72 6.21 4.22 sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, Sema5a (semaphorin) 5A 20356 5.70 2.96 3.41 Myct1 myc target 1 68632 5.58 20.70 9.40 Aig1 androgen-induced 1 66253 5.09 3.81 3.80 Fez1 fasciculation and elongation protein zeta 1 (zygin I) 235180 4.47 3.93 3.91 Cacnb2 calcium channel, voltage-dependent, beta 2 subunit 12296 4.46 2.81 3.93 Errfi1 ERBB receptor feedback inhibitor 1 74155 4.41 3.59 4.27 Ctsh cathepsin H 13036 4.26 3.94 3.17 Abcb1a ATP-binding cassette, sub-family B (MDR/TAP), member 1A 18671 4.21 3.28 2.78 Flrt2 fibronectin leucine rich transmembrane protein 2 399558 4.03 3.62 2.36 Slc5a3 solute carrier family 5 (inositol transporters), member 3 53881 4.02 2.52 3.46 Gm10454 predicted gene 10454 331484 3.87 2.04 2.13 Fam110c family with sequence similarity 110, member C 104943 3.82 3.44 3.45 Chic1 cysteine-rich hydrophobic domain 1 12212 3.82 1.92 2.20 Pcdh7 protocadherin 7 54216 3.76 2.38 2.36 9030425E11Rik RIKEN cDNA 9030425E11 gene 71566 3.61 3.46 3.42 Dusp6 dual specificity phosphatase 6 67603 3.20 2.32 2.32 Spry2 sprouty homolog 2 (Drosophila) 24064 3.18 2.47 2.62 Uaca uveal autoantigen with coiled-coil domains and ankyrin repeats 72565 3.13 2.73 3.32 Tuba8 tubulin, alpha 8 53857 3.03 4.49 3.59 Eps8 epidermal growth factor receptor pathway substrate 8 13860 2.99 3.22 3.35 Ptpre protein tyrosine phosphatase, receptor type, E 19267 2.91 1.93 2.48 Nr2f1 nuclear receptor subfamily 2, group F, member 1 13865 2.89 3.78 3.47 Osbpl6 oxysterol binding protein-like 6 99031 2.79 2.72 3.16 Etv5 ets variant gene 5 104156 2.73 2.64 2.64 Spred1 sprouty protein with EVH-1 domain 1, related sequence 114715 2.68 1.59 1.83 Laptm4b lysosomal-associated protein transmembrane 4B 114128 2.67 1.52 1.92 Spry4 sprouty homolog 4 (Drosophila) 24066 2.61 1.72 2.01 Sdpr serum deprivation response 20324 2.60 1.94 1.99 Hdgfrp3 hepatoma-derived growth factor, related protein 3 29877 2.57 2.79 2.89 Ap1s2 adaptor-related protein complex 1, sigma 2 subunit 108012 2.56 2.14 2.05 Cebpd CCAAT/enhancer binding protein (C/EBP), delta 12609 2.50 2.01 1.82 Svip small VCP/p97-interacting protein 75744 2.39 1.95 1.88 recombination signal binding protein for immunoglobulin kappa J Rbpj region 19664 2.32 2.45 2.14 Mtmr10 myotubularin related protein 10 233315 2.31 1.96 2.64 Spa17 sperm autoantigenic protein 17 20686 2.28 3.22 2.18 Gm9869 predicted gene 9869 791387 2.28 2.20 2.75 Acot1 acyl-CoA thioesterase 1 26897 2.24 1.70 1.69 Trib2 tribbles homolog 2 (Drosophila) 217410 2.17 3.27 2.89 Etv5 ets variant gene 5 104156 2.15 2.54 2.46 Rapgef2 Rap guanine nucleotide exchange factor (GEF) 2 76089 2.09 1.90 1.96 Mef2a myocyte enhancer factor 2A 17258 2.09 1.90 1.72 Hmga2 high mobility group AT-hook 2 15364 2.03 1.62 1.84 Mast4 microtubule associated serine/threonine kinase family member 4 328329 1.96 1.71 1.56 Spred2 sprouty-related, EVH1 domain containing 2 114716 1.91 1.64 1.62 Cd14 CD14 antigen 12475 1.83 2.36 1.99 Mark1 MAP/microtubule affinity-regulating kinase 1 226778 1.78 2.24 2.07 Btbd3 BTB (POZ) domain containing 3 228662 1.76 1.73 2.35 Rap2a RAS related protein 2a 76108 1.74 1.49 1.56 Socs6 suppressor of cytokine signaling 6 54607 1.73 1.50 1.58 Ddef2 development and differentiation enhancing factor 2 211914 1.72 1.52 1.59 B3galt1 UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1 26877 1.72 1.74 1.72 Katnal2 katanin p60 subunit A-like 2 71206 1.63 1.71 1.63 Imp3 IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) 102462 1.62 1.48 1.57 Rhebl1 Ras homolog enriched in brain like 1 69159 1.61 1.41 1.41 Tspan11 tetraspanin 11 68498 1.61 2.40 1.99 Nfe2l2 nuclear factor, erythroid derived 2, like 2 18024 1.58 1.43 1.47 Obfc1 oligonucleotide/oligosaccharide-binding fold containing 1 108689 1.55 1.58 1.64 Plekha5 pleckstrin homology domain containing, family A member 5 109135 1.54 1.53 1.41 Cd46 CD46 antigen, complement regulatory protein 17221 1.53 1.66 1.54 Sdccag8 serologically defined colon cancer antigen 8 76816 1.52 1.29 1.24 Gata2 GATA binding protein 2 14461 1.51 1.93 1.80 non-metastatic cells 7, protein expressed in (nucleoside-diphosphate Nme7 kinase) 171567 1.50 1.35 1.52 Ift81 intraflagellar transport 81 homolog (Chlamydomonas) 12589 1.43 1.51 1.38 Ccnd1 cyclin D1 12443 1.41 1.42 1.42 4833442J19Rik RIKEN cDNA 4833442J19 gene 320204 1.39 1.62 1.79 MTERF domain containing 2 /// sushi, nidogen and EGF-like domains Mterfd2 /// Sned1 1 69821 /// 208777 1.37 1.35 1.34 Pvrl3 poliovirus receptor-related 3 58998 1.33 1.33 1.37 B3galt6 UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6 117592 1.30 1.31 1.42 Paqr4 progestin and adipoQ receptor family member IV 76498 0.79 0.82 0.73 Dip2b DIP2 disco-interacting protein 2 homolog B (Drosophila) 239667 0.77 0.77 0.71 methylmalonic aciduria (cobalamin deficiency) cblD type, with Mmadhc homocystinuria 109129 0.74 0.74 0.81 adaptor protein, phosphotyrosine interaction, PH domain and leucine Appl1 zipper containing 1 72993 0.73 0.73 0.75 Flnc filamin C, gamma 68794 0.71 0.65 0.62 Thbs4 thrombospondin 4 21828 0.70 0.73 0.72 Ufsp2 UFM1-specific peptidase 2 192169 0.70 0.67 0.60 Fam38b2 family with sequence similarity 38, member B2 667742 0.68 0.66 0.65 Gm7795 predicted gene 7795 665806 0.68 0.67 0.69 Aldh18a1 aldehyde dehydrogenase 18 family, member A1 56454 0.67 0.68 0.69 Adra1d adrenergic receptor, alpha 1d 11550 0.67 0.69 0.75 Entpd5 ectonucleoside triphosphate diphosphohydrolase 5 12499 0.66 0.59 0.64 Tsc22d2 TSC22 domain family, member 2 72033 0.66 0.68 0.58 Ugp2 UDP-glucose pyrophosphorylase 2 216558 0.65 0.69 0.69 Slc9a9 solute carrier family 9 (sodium/hydrogen exchanger), member 9 331004 0.63 0.60 0.61 Tmeff1 transmembrane protein with EGF-like and two follistatin-like domains 1 230157 0.62 0.68 0.68 Zfp791 zinc finger protein 791 244556 0.62 0.60 0.58 Tns3 tensin 3 319939 0.60 0.64 0.57 Mmp14 matrix metallopeptidase 14 (membrane-inserted) 17387 0.60 0.71 0.64 Nol3 nucleolar protein 3 (apoptosis repressor with CARD domain) 78688 0.60 0.63 0.62 ENSMUST00000083407 ------0.58 0.55 0.58 microtubule associated monoxygenase, calponin and LIM domain Mical1 containing 1 171580 0.56 0.67 0.59 Gjb4 gap junction protein, beta 4 14621 0.56 0.70 0.64 Dysf dysferlin 26903 0.56 0.51 0.51 4930402E16Rik RIKEN cDNA 4930402E16 gene 319518 0.56 0.67 0.63 Farp2 FERM, RhoGEF and pleckstrin domain protein 2 227377 0.55 0.54 0.66 Zfp185 zinc finger protein 185 22673 0.55 0.59 0.59 Chd9 chromodomain helicase DNA binding protein 9 109151 0.54 0.58 0.54 Vamp5 vesicle-associated membrane protein 5 53620 0.53 0.58 0.53 Tmem123 transmembrane protein 123 71929 0.53 0.70 0.66 Gtpbp8 GTP-binding protein 8 (putative) 66067 0.52 0.52 0.63 solute carrier family 1 (neuronal/epithelial high affinity glutamate Slc1a1 transporter, system Xag), member 1 20510 0.51 0.50 0.49 Zfp9 zinc finger protein 9 22750 0.51 0.54 0.54 Usp49 ubiquitin specific peptidase 49 224836 0.50 0.69 0.65 Cxcl1 chemokine (C-X-C motif) ligand 1 14825 0.50 0.61 0.50 Me3 malic enzyme 3, NADP(+)-dependent, mitochondrial 109264 0.50 0.60 0.45 Foxo1 forkhead box O1 56458 0.46 0.46 0.48 Nuak1 NUAK family, SNF1-like kinase, 1 77976 0.45 0.58 0.39 Ifih1 interferon induced with helicase C domain 1 71586 0.43 0.37 0.45 TAF9B RNA polymerase II, TATA box binding protein (TBP)- Taf9b associated factor 407786 0.43 0.59 0.47 Dclk1 doublecortin-like kinase 1 13175 0.42 0.62 0.62 Mtss1l metastasis suppressor 1-like 244654 0.42 0.52 0.54 Myo7a myosin VIIA 17921 0.40 0.58 0.42 Stard13 StAR-related lipid transfer (START) domain containing 13 243362 0.39 0.41 0.43 Arhgef10 Rho guanine nucleotide exchange factor (GEF) 10 234094 0.39 0.57 0.48 Tifa TRAF-interacting protein with forkhead-associated domain 211550 0.37 0.49 0.38 Fhdc1 FH2 domain containing 1 229474 0.36 0.47 0.49 ENSMUST00000055026 ------0.33 0.24 0.32 Pla2g16 phospholipase A2, group XVI 225845 0.33 0.52 0.48 Rnd3 Rho family GTPase 3 74194 0.33 0.58 0.45 Cdsn corneodesmosin 386463 0.32 0.34 0.31 Pcp4l1 Purkinje cell protein 4-like 1 66425 0.31 0.31 0.33 Cpa4 carboxypeptidase A4 71791 0.31 0.35 0.32 Col5a2 collagen, type V, alpha 2 12832 0.30 0.44 0.31 Limch1 LIM and calponin homology domains 1 77569 0.30 0.29 0.34 Lgr4 leucine-rich repeat-containing G protein-coupled receptor 4 107515 0.28 0.31 0.38 Fam46a family with sequence similarity 46, member A 212943 0.26 0.25 0.27 Aldh1l2 aldehyde dehydrogenase 1 family, member L2 216188 0.23 0.19 0.30 Bhlhe41 basic helix-loop-helix family, member e41 79362 0.23 0.24 0.24 Fam129a family with sequence similarity 129, member A 63913 0.22 0.29 0.22 Fam46a family with sequence similarity 46, member A 212943 0.22 0.23 0.26 Nid2 nidogen 2 18074 0.21 0.43 0.30 Creb3l1 cAMP responsive element binding protein 3-like 1 26427 0.21 0.22 0.18 Gca grancalcin 227960 0.18 0.29 0.21 Mtap2 microtubule-associated protein 2 17756 0.17 0.19 0.25 Igf1 insulin-like growth factor 1 16000 0.17 0.24 0.15 sema domain, immunoglobulin domain (Ig), short basic domain, Sema3e secreted, (semaphorin) 3E 20349 0.17 0.29 0.19 Epha3 Eph receptor A3 13837 0.15 0.16 0.15 Gm10808 predicted gene 10808 100038470 0.12 0.22 0.12 Tgfb2 transforming growth factor, beta 2 21808 0.11 0.23 0.16 Rcan2 regulator of calcineurin 2 53901 0.11 0.17 0.16 Fmod fibromodulin 14264 0.10 0.10 0.09 Ccdc80 coiled-coil domain containing 80 67896 0.09 0.27 0.14 a disintegrin-like and metallopeptidase (reprolysin type) with Adamts5 thrombospondin type 1 motif, 5 (aggrecanase-2) 23794 0.08 0.30 0.26 Serpinb1a serine (or cysteine) peptidase inhibitor, clade B, member 1a 66222 0.06 0.23 0.12

Supplemental Table S4. Genes whose expression is altered in L597VBraf/G12DKras MEFs compared to Braf/+/+ MEFs but not G12DKras or V600EBraf MEFs

Fold change Gene name Gene Description Entrez ID (LV/G12D over WT) 1100001E04Rik RIKEN cDNA 1100001E04 gene 75404 15.00 B3gnt5 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5 108105 4.67 ENSMUST00000101869 ------3.64 ENSMUST00000101806 ------3.36 Pde1a phosphodiesterase 1A, calmodulin-dependent 18573 3.30 Jph1 junctophilin 1 57339 3.07 Hmga1 high mobility group AT-hook 1 15361 2.59 C130071C03Rik RIKEN cDNA C130071C03 gene 320203 2.44 Gpr85 G protein-coupled receptor 85 64450 2.27 Gnb4 guanine nucleotide binding protein (G protein), beta 4 14696 2.26 Il1rapl1 interleukin 1 receptor accessory protein-like 1 331461 2.21 ENSMUST00000083192 ------2.01 Mfsd2 major facilitator superfamily domain containing 2 76574 2.00 Id3 inhibitor of DNA binding 3 15903 1.89 Jph1 junctophilin 1 57339 1.85 Snrnp35 small nuclear ribonucleoprotein 35 (U11/U12) 76167 1.79 Atf7ip2 activating transcription factor 7 interacting protein 2 75329 1.77 Sms /// Gm8234 spermine synthase /// spermine synthase pseudogene 20603 /// 666680 1.72 Sms spermine synthase 20603 1.71 Frat2 frequently rearranged in advanced T-cell lymphomas 2 212398 1.64 Nup210l nucleoporin 210-like 77595 1.63 Ube2t ubiquitin-conjugating enzyme E2T (putative) 67196 1.61 Fastkd2 FAST kinase domains 2 75619 1.60 Reps1 RalBP1 associated Eps domain containing protein 19707 1.59 Plch1 phospholipase C, eta 1 269437 1.53 Ccdc56 coiled-coil domain containing 56 52469 1.50 V1rh9 vomeronasal 1 receptor, H9 171252 1.50 amyotrophic lateral sclerosis 2 (juvenile) region, candidate 12 Als2cr12 (human) 108812 1.49 1810009A15Rik RIKEN cDNA 1810009A15 gene 66276 1.48 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N- Galnt12 acetylgalactosaminyltransferase 12 230145 1.48 Nubp1 /// Fam18a nucleotide binding protein 1 /// family with sequence similarity 18, member A 26425 /// 383103 1.46 Rps21 /// Gm5963 ribosomal protein S21 /// predicted gene 5963 66481 /// 546663 1.46 Dtymk deoxythymidylate kinase 21915 1.45 Dph5 DPH5 homolog (S. cerevisiae) 69740 1.44 TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated Taf10 /// Gm4799 factor /// predicted gene 4799 24075 /// 216185 1.42 Nit2 nitrilase family, member 2 52633 1.41 Olfr98 /// Olfr97 olfactory receptor 98 /// olfactory receptor 97 258503 /// 258505 1.41 Gm12642 predicted gene 12642 384125 1.41 Eps15 epidermal growth factor receptor pathway substrate 15 13858 1.40 Nif3l1 Ngg1 interacting factor 3-like 1 (S. pombe) 65102 1.39 Agfg1 ArfGAP with FG repeats 1 15463 1.39 BC030336 cDNA sequence BC030336 233812 1.39 Gm7712 predicted gene 7712 665612 1.38 Sox7 SRY-box containing gene 7 20680 1.36 Aarsd1 /// Astn2 alanyl-tRNA synthetase domain containing 1 /// astrotactin 2 69684 /// 56079 1.35 Kbtbd4 kelch repeat and BTB (POZ) domain containing 4 67136 1.35 ENSMUST00000093726 ------1.35 BC025082 /// ENSMUST00000099111 ------1.35 Blmh bleomycin hydrolase 104184 1.34 Vegfb vascular endothelial growth factor B 22340 1.34 ENSMUST00000082996 ------1.34 A030009H04Rik RIKEN cDNA A030009H04 gene 80515 1.33 Zfp422 zinc finger protein 422 67255 1.32 Spire2 spire homolog 2 (Drosophila) 234857 1.32 Zfp114 zinc finger protein 114 232966 1.31 MIT, microtubule interacting and transport, domain containing 1 /// Mitd1 /// Lipt1 lipoyltransferase 1 69028 /// 623661 1.30 Gm7059 predicted gene 7059 631266 1.30 Fam171a1 family with sequence similarity 171, member A1 269233 1.30 ribosomal protein S8 /// ribosomal protein S8 pseudogene /// predicted gene 20116 /// 629732 /// Rps8 /// Gm6998 /// Gm11353 11353 791412 1.30 Cnih4 cornichon homolog 4 (Drosophila) 98417 1.29 peptidylprolyl isomerase (cyclophilin)-like 3 /// Ngg1 interacting factor 3-like Ppil3 /// Nif3l1 1 (S. pombe) 70225 /// 65102 1.28 Ndufa2 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2 17991 1.28 Tfb2m transcription factor B2, mitochondrial 15278 1.27 ribosomal protein S8 /// ribosomal protein S8 pseudogene /// predicted gene 20116 /// 629732 /// Rps8 /// Gm6998 /// Gm11353 11353 791412 1.27 Rps8 /// Gm11353 ribosomal protein S8 /// predicted gene 11353 20116 /// 791412 1.27 ribosomal protein S8 /// ribosomal protein S8 pseudogene /// predicted gene 20116 /// 629732 /// Rps8 /// Gm6998 /// Gm11353 11353 791412 1.27 Wdr73 WD repeat domain 73 71968 1.27 Amd-ps6 S-adenosylmethionine decarboxylase, pseudogene 6 666251 1.27 ribosomal protein S8 /// ribosomal protein S8 pseudogene /// predicted gene 20116 /// 629732 /// Rps8 /// Gm6998 /// Gm5121 /// Gm11353 5121 /// predicted gene 11353 330948 /// 791412 1.26 ribosomal protein S8 /// ribosomal protein S8 pseudogene /// predicted gene 20116 /// 629732 /// Rps8 /// Gm6998 /// Gm5121 /// Gm11353 5121 /// predicted gene 11353 330948 /// 791412 1.26 TSID# 10572958 (chr8, 79718594-79718760) ------1.26 ribosomal protein S8 /// ribosomal protein S8 pseudogene /// predicted gene 20116 /// 629732 /// Rps8 /// Gm6998 /// Gm11353 11353 791412 1.25 ribosomal protein S8 /// ribosomal protein S8 pseudogene /// predicted gene 20116 /// 629732 /// Rps8 /// Gm6998 /// Gm5121 /// Gm11353 5121 /// predicted gene 11353 330948 /// 791412 1.25 D730045B01Rik RIKEN cDNA D730045B01 gene 77867 1.25 Sumo1 SMT3 suppressor of mif two 3 homolog 1 (yeast) 22218 1.24 Det1 de-etiolated homolog 1 (Arabidopsis) 76375 1.24 Ap3s2 adaptor-related protein complex 3, sigma 2 subunit 11778 1.22 Akap10 A kinase (PRKA) anchor protein 10 56697 1.20 Rpl3 ribosomal protein L3 27367 1.19 Alpi alkaline phosphatase, intestinal 76768 0.83 Adcy1 adenylate cyclase 1 432530 0.82 Tfg Trk-fused gene 21787 0.82 Sar1a SAR1 gene homolog A (S. cerevisiae) 20224 0.81 Brwd1 bromodomain and WD repeat domain containing 1 93871 0.81 Gm10440 predicted gene 10440 330086 0.81 Gm10044 predicted gene 10044 218695 0.80 March8 membrane-associated ring finger (C3HC4) 8 71779 0.79 6330407J23Rik RIKEN cDNA 6330407J23 gene 67412 0.78 Olfr272 olfactory receptor 272 258836 0.78 Plb1 phospholipase B1 665270 0.78 Tm9sf4 transmembrane 9 superfamily protein member 4 99237 0.77 ENSMUST00000118039 /// GENSCAN00000040067 ------0.76 Rab33b RAB33B, member of RAS oncogene family 19338 0.76 Ttpa tocopherol (alpha) transfer protein 50500 0.76 Tmem214 transmembrane protein 214 68796 0.76 Slc35b4 solute carrier family 35, member B4 58246 0.76 Megf6 multiple EGF-like-domains 6 230971 0.75 LOC622307 similar to LOC360919 protein 622307 0.75 Tmcc1 transmembrane and coiled coil domains 1 330401 0.75 Gm6040 predicted gene 6040 574083 0.75 Terf2ip telomeric repeat binding factor 2, interacting protein 57321 0.75 solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, Slc1a1 system Xag), member 1 20510 0.74 Adam10 a disintegrin and metallopeptidase domain 10 11487 0.74 5033414D02Rik RIKEN cDNA 5033414D02 gene 67759 0.73 Tmem111 transmembrane protein 111 66087 0.73 Trip4 thyroid hormone receptor interactor 4 56404 0.73 Pja2 praja 2, RING-H2 motif containing 224938 0.72 Heatr5b HEAT repeat containing 5B 320473 0.72 Scn2a1 sodium channel, voltage-gated, type II, alpha 1 110876 0.72 1700113H08Rik RIKEN cDNA 1700113H08 gene 76640 0.71 Stat2 signal transducer and activator of transcription 2 20847 0.71 Serpinb9d serine (or cysteine) peptidase inhibitor, clade B, member 9d 20726 0.69 Tcra T-cell receptor alpha chain 21473 0.68 E130311K13Rik RIKEN cDNA E130311K13 gene 329659 0.67 Gm505 predicted gene 505 244666 0.67 mmu-let-7d ------0.65 Dgkh diacylglycerol kinase, eta 380921 0.65 Lgals2 lectin, galactose-binding, soluble 2 107753 0.65 TSID# 10352554 (chr1, 188500621-188500755) ------0.64 Ids iduronate 2-sulfatase 15931 0.64 Entpd4 ectonucleoside triphosphate diphosphohydrolase 4 67464 0.63 potassium large conductance calcium-activated channel, subfamily M, beta Kcnmb1 member 1 16533 0.62 Gm2a GM2 ganglioside activator protein 14667 0.62 Scn2a1 sodium channel, voltage-gated, type II, alpha 1 110876 0.62 Cyp3a44 cytochrome P450, family 3, subfamily a, polypeptide 44 337924 0.62 Ccdc65 coiled-coil domain containing 65 105833 0.59 Atp11a ATPase, class VI, type 11A 50770 0.59 Stbd1 starch binding domain 1 52331 0.57 Thbs2 thrombospondin 2 21826 0.55 Ust uronyl-2-sulfotransferase 338362 0.53 Hspa2 heat shock protein 2 15512 0.53 phosphatidylserine decarboxylase, pseudogene 1 /// phosphatidylserine Pisd-ps1 /// Pisd-ps3 decarboxylase, pseudogene 3 236604 /// 66776 0.52 Arrdc4 arrestin domain containing 4 66412 0.52 Aff3 AF4/FMR2 family, member 3 16764 0.50 Atp6v0a1 ATPase, H+ transporting, lysosomal V0 subunit A1 11975 0.49 Ube2h /// Gm2058 ubiquitin-conjugating enzyme E2H /// predicted gene 2058 22214 /// 100039133 0.49 Pmepa1 prostate transmembrane protein, androgen induced 1 65112 0.48 ubiquitin-conjugating enzyme E2H /// predicted gene 2058 /// similar to 22214 /// 100039133 /// Ube2h /// Gm2058 /// LOC100047093 Ubiquitin-conjugating enzyme UbcH2 100047093 0.48 Abcg2 ATP-binding cassette, sub-family G (WHITE), member 2 26357 0.45 Txnip thioredoxin interacting protein 56338 0.42 Txndc16 thioredoxin domain containing 16 70561 0.37 Fam114a1 family with sequence similarity 114, member A1 68303 0.37 Fkbp14 FK506 binding protein 14 231997 0.33 Pdgfrl platelet-derived growth factor receptor-like 68797 0.33 Itga11 integrin alpha 11 319480 0.25 TSID# 10513774 (chr4, 65014577-65014847) ------0.10