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Supplementary Table 1. (a) Basal alkylation sensitivity associated gene set (BASA) sorted by correlation (page 1 of 2) Present in Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) % accuracy Network MGMT O-6-methylguanine-DNA methyltransferase NM_002412 204880_at 0.95 0.74 69 Yes C21orf56 chromosome 21 open reading frame 56 AL136871 223360_at 0.86 0.54 56 No NQO2 NAD(P)H dehydrogenase, quinone 2 NM_000904 203814_s_at -0.71 -0.53 69 No glycerol-3-phosphate dehydrogenase 2 GPD2 (mitochondrial) U36310 210007_s_at -0.72 -0.59 63 Yes RAD54B RAD54 homolog B (S. cerevisiae) NM_012415 219494_at -0.72 -0.66 63 Yes PIAS2 protein inhibitor of activated STAT, 2 AF361054 1555514_a_at -0.73 -0.58 69 No FLJ12442 hypothetical protein FLJ12442 NM_022908 218051_s_at -0.73 -0.53 69 No TM4SF12 transmembrane 4 superfamily member 12 NM_012338 219274_at -0.76 -0.58 63 No LRRK1 leucine-rich repeat kinase 1 AW792857 1565627_a_at -0.76 -0.53 81 No ARSB arylsulfatase B AW168942 232197_x_at -0.77 -0.52 75 No PPP2R1B protein phosphatase 2 (formerly 2A) T79584 202883_s_at -0.78 -0.58 56 Yes MSC musculin (activated B-cell factor-1) AF060154 209928_s_at -0.78 -0.55 69 Yes LOC283130 hypothetical protein LOC283130 AI336233 236436_at -0.79 -0.58 69 No LAMC1 laminin, gamma 1 (formerly LAMB2) NM_002293 200771_at -0.79 -0.69 75 Yes FLJ12886 hypothetical protein FLJ12886 NM_019108 221335_x_at -0.81 -0.59 75 No discoidin, CUB and LCCL domain containing DCBLD1 1 NM_173674 1553768_a_at -0.81 -0.53 75 No CMIP c-Maf-inducing protein AI363061 224992_s_at -0.81 -0.54 63 Yes --- --- AI825302 238700_at -0.82 -0.64 63 No platelet/endothelial cell adhesion molecule PECAM1 (CD31 antigen) M37780 208983_s_at -0.82 -0.62 63 Yes FLJ32942 hypothetical protein FLJ32942 BG150433 227711_at -0.82 -0.61 75 No LOC284801 hypothetical protein LOC284801 AL531683 225762_x_at -0.83 -0.62 63 No guanine nucleotide binding protein (G GNB5 protein), beta 5 NM_006578 207124_s_at -0.83 -0.71 81 Yes sarcoglycan, beta (43kDa dystrophin- SGCB associated glycoprotein) U29586 205120_s_at -0.83 -0.68 63 Yes SFXN2 sideroflexin 2 AL530504 227560_at -0.83 -0.54 56 No SYPL synaptophysin-like protein AI768845 201259_s_at -0.84 -0.58 69 No DTNBP1 dystrobrevin binding protein 1 AF061734 223446_s_at -0.84 -0.68 75 Yes LOC203069 hypothetical protein LOC203069 AI081543 212866_at -0.84 -0.74 75 No MESDC2 mesoderm development candidate 2 AK026606 224675_at -0.85 -0.65 63 No FIGNL1 fidgetin-like 1 NM_022116 1552921_a_at -0.85 -0.71 69 Yes PHYH phytanoyl-CoA hydroxylase (Refsum disease) NM_006214 203335_at -0.85 -0.61 75 Yes Supplementary Table 1. (a) Basal alkylation sensitivity associated gene set (BASA) sorted by correlation (page 2 of 2) Present in Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) % accuracy Network TM4SF7 transmembrane 4 superfamily member 7 BC000389 209263_x_at -0.85 -0.68 75 No echinoderm microtubule associated protein EML4 like 4 NM_019063 220386_s_at -0.85 -0.60 81 No CKLFSF3 chemokine-like factor super family 3 AY166714 1555705_a_at -0.86 -0.58 69 No MGC45731 hypothetical protein MGC45731 AW003092 227080_at -0.86 -0.58 63 No phosphoinositide-3-kinase, regulatory PIK3R1 subunit, polypeptide 1 (p85 alpha) AI680192 212239_at -0.87 -0.76 63 No MAGEF1 melanoma antigen, family F, 1 NM_022149 218176_at -0.88 -0.72 81 Yes TMEM14A transmembrane protein 14A NM_014051 218477_at -0.88 -0.70 63 No ANKRD9 ankyrin repeat domain 9 AW194999 230972_at -0.90 -0.67 75 No MGC11266 hypothetical protein MGC11266 BE326728 226118_at -0.91 -0.70 63 Yes DTYMK deoxythymidylate kinase (thymidylate kinase) NM_012145 203270_at -0.91 -0.58 56 No CANP cancer-associated nucleoprotein AA960844 1557128_at -0.91 -0.50 63 No --- --- BE467688 231259_s_at -0.92 -0.52 56 No H2AFV H2A histone family, member V BF343852 212206_s_at -0.92 -0.70 69 No NET1 neuroepithelial cell transforming gene 1 NM_005863 201830_s_at -0.92 -0.58 56 Yes TSAP6 dudulin 2 NM_018234 218424_s_at -0.92 -0.70 75 Yes --- --- AA227879 235919_at -0.93 -0.58 56 No CKLF chemokine-like factor NM_016951 219161_s_at -0.94 -0.62 75 No MUTYH mutY homolog (E. coli) NM_012222 207727_s_at -0.97 -0.76 69 Yes ALL 94 Supplementary Table 1. (b) Basal alkylation sensitivity associated gene set (BASA) sorted by gene (page 1 of 2) Present in Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) % accuracy Network ANKRD9 ankyrin repeat domain 9 AW194999 230972_at -0.90 -0.67 75 No ARSB arylsulfatase B AW168942 232197_x_at -0.77 -0.52 75 No C21orf56 chromosome 21 open reading frame 56 AL136871 223360_at 0.86 0.54 56 No CANP cancer-associated nucleoprotein AA960844 1557128_at -0.91 -0.50 63 No CKLF chemokine-like factor NM_016951 219161_s_at -0.94 -0.62 75 No CKLFSF3 chemokine-like factor super family 3 AY166714 1555705_a_at -0.86 -0.58 69 No CMIP c-Maf-inducing protein AI363061 224992_s_at -0.81 -0.54 63 Yes discoidin, CUB and LCCL domain containing DCBLD1 1 NM_173674 1553768_a_at -0.81 -0.53 75 No DTNBP1 dystrobrevin binding protein 1 AF061734 223446_s_at -0.84 -0.68 75 Yes DTYMK deoxythymidylate kinase (thymidylate kinase) NM_012145 203270_at -0.91 -0.58 56 No echinoderm microtubule associated protein EML4 like 4 NM_019063 220386_s_at -0.85 -0.60 81 No FIGNL1 fidgetin-like 1 NM_022116 1552921_a_at -0.85 -0.71 69 Yes FLJ12442 hypothetical protein FLJ12442 NM_022908 218051_s_at -0.73 -0.53 69 No FLJ12886 hypothetical protein FLJ12886 NM_019108 221335_x_at -0.81 -0.59 75 No FLJ32942 hypothetical protein FLJ32942 BG150433 227711_at -0.82 -0.61 75 No guanine nucleotide binding protein (G GNB5 protein), beta 5 NM_006578 207124_s_at -0.83 -0.71 81 Yes glycerol-3-phosphate dehydrogenase 2 GPD2 (mitochondrial) U36310 210007_s_at -0.72 -0.59 63 Yes H2AFV H2A histone family, member V BF343852 212206_s_at -0.92 -0.70 69 No LAMC1 laminin, gamma 1 (formerly LAMB2) NM_002293 200771_at -0.79 -0.69 75 Yes LOC203069 hypothetical protein LOC203069 AI081543 212866_at -0.84 -0.74 75 No LOC283130 hypothetical protein LOC283130 AI336233 236436_at -0.79 -0.58 69 No LOC284801 hypothetical protein LOC284801 AL531683 225762_x_at -0.83 -0.62 63 No LRRK1 leucine-rich repeat kinase 1 AW792857 1565627_a_at -0.76 -0.53 81 No MAGEF1 melanoma antigen, family F, 1 NM_022149 218176_at -0.88 -0.72 81 Yes MESDC2 mesoderm development candidate 2 AK026606 224675_at -0.85 -0.65 63 No MGC11266 hypothetical protein MGC11266 BE326728 226118_at -0.91 -0.70 63 Yes MGC45731 hypothetical protein MGC45731 AW003092 227080_at -0.86 -0.58 63 No MGMT O-6-methylguanine-DNA methyltransferase NM_002412 204880_at 0.95 0.74 69 Yes MSC musculin (activated B-cell factor-1) AF060154 209928_s_at -0.78 -0.55 69 Yes MUTYH mutY homolog (E. coli) NM_012222 207727_s_at -0.97 -0.76 69 Yes Supplementary Table 1. (b) Basal alkylation sensitivity associated gene set (BASA) sorted by gene (page 2 of 2) Present in Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) % accuracy Network NET1 neuroepithelial cell transforming gene 1 NM_005863 201830_s_at -0.92 -0.58 56 Yes NQO2 NAD(P)H dehydrogenase, quinone 2 NM_000904 203814_s_at -0.71 -0.53 69 No platelet/endothelial cell adhesion molecule PECAM1 (CD31 antigen) M37780 208983_s_at -0.82 -0.62 63 Yes PHYH phytanoyl-CoA hydroxylase (Refsum disease) NM_006214 203335_at -0.85 -0.61 75 Yes PIAS2 protein inhibitor of activated STAT, 2 AF361054 1555514_a_at -0.73 -0.58 69 No phosphoinositide-3-kinase, regulatory PIK3R1 subunit, polypeptide 1 (p85 alpha) AI680192 212239_at -0.87 -0.76 63 No protein phosphatase 2 (formerly 2A), PPP2R1B regulatory subunit A (PR 65), beta isoform T79584 202883_s_at -0.78 -0.58 56 Yes RAD54B RAD54 homolog B (S. cerevisiae) NM_012415 219494_at -0.72 -0.66 63 Yes SFXN2 sideroflexin 2 AL530504 227560_at -0.83 -0.54 56 No sarcoglycan, beta (43kDa dystrophin- SGCB associated glycoprotein) U29586 205120_s_at -0.83 -0.68 63 Yes SYPL synaptophysin-like protein AI768845 201259_s_at -0.84 -0.58 69 No TM4SF12 transmembrane 4 superfamily member 12 NM_012338 219274_at -0.76 -0.58 63 No TM4SF7 transmembrane 4 superfamily member 7 BC000389 209263_x_at -0.85 -0.68 75 No TMEM14A transmembrane protein 14A NM_014051 218477_at -0.88 -0.70 63 No TSAP6 dudulin 2 NM_018234 218424_s_at -0.92 -0.70 75 Yes --- --- AI825302 238700_at -0.82 -0.64 63 No --- --- AA227879 235919_at -0.93 -0.58 56 No --- --- BE467688 231259_s_at -0.92 -0.52 56 No ALL 94 Supplementary Table 2. (a) Treated Ratio alkylation sensitivity associated gene set (TRASA) sorted by correlation (page 1 of 2) Gene Symbol Gene Title Representative Public ID Probeset ID R (train) R (all) low density lipoprotein receptor (familial LDLR hypercholesterolemia) NM_000527 202068_s_at 0.98 0.85 BCL2/adenovirus E1B 19kDa interacting BNIP3 protein 3 U15174 201848_s_at 0.94 0.86 --- --- AI375915 1555852_at 0.93 0.73 ZNF395 zinc finger protein 395 /// F-box protein 16 BC001237 223216_x_at 0.93 0.82 SCD stearoyl-CoA desaturase (delta-9-desaturase) AB032261 200832_s_at 0.93 0.76 histone 2, H2aa /// similar to Histone H2A.o HIST2H2AA (H2A/o) (H2A.2) (H2a-615) /// histone H2A/r NM_003516 218280_x_at 0.92 0.67 CTA-126B4.3 CGI-96 protein AL022316 202937_x_at 0.92 0.48 ING2 inhibitor of growth family, member 2 NM_001564 205981_s_at 0.91 0.75 PRO1843 hypothetical protein PRO1843 NM_018507 219599_at 0.90 0.38 --- --- AK026764 226348_at 0.89 0.72 C10orf75 Chromosome 10 open reading frame 75 AU151788 232230_at 0.88 0.68 LOC440731 hypothetical LOC440731 AI286239 237563_s_at 0.88 0.50 BCL2/adenovirus E1B 19kDa interacting BNIP3L protein 3-like /// BCL2/adenovirus
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    www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1.
  • Análise Integrativa De Perfis Transcricionais De Pacientes Com

    Análise Integrativa De Perfis Transcricionais De Pacientes Com

    UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas.
  • Supplementary Table S2

    Supplementary Table S2

    1-high in cerebrotropic Gene P-value patients Definition BCHE 2.00E-04 1 Butyrylcholinesterase PLCB2 2.00E-04 -1 Phospholipase C, beta 2 SF3B1 2.00E-04 -1 Splicing factor 3b, subunit 1 BCHE 0.00022 1 Butyrylcholinesterase ZNF721 0.00028 -1 Zinc finger protein 721 GNAI1 0.00044 1 Guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1 GNAI1 0.00049 1 Guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1 PDE1B 0.00069 -1 Phosphodiesterase 1B, calmodulin-dependent MCOLN2 0.00085 -1 Mucolipin 2 PGCP 0.00116 1 Plasma glutamate carboxypeptidase TMX4 0.00116 1 Thioredoxin-related transmembrane protein 4 C10orf11 0.00142 1 Chromosome 10 open reading frame 11 TRIM14 0.00156 -1 Tripartite motif-containing 14 APOBEC3D 0.00173 -1 Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D ANXA6 0.00185 -1 Annexin A6 NOS3 0.00209 -1 Nitric oxide synthase 3 SELI 0.00209 -1 Selenoprotein I NYNRIN 0.0023 -1 NYN domain and retroviral integrase containing ANKFY1 0.00253 -1 Ankyrin repeat and FYVE domain containing 1 APOBEC3F 0.00278 -1 Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F EBI2 0.00278 -1 Epstein-Barr virus induced gene 2 ETHE1 0.00278 1 Ethylmalonic encephalopathy 1 PDE7A 0.00278 -1 Phosphodiesterase 7A HLA-DOA 0.00305 -1 Major histocompatibility complex, class II, DO alpha SOX13 0.00305 1 SRY (sex determining region Y)-box 13 ABHD2 3.34E-03 1 Abhydrolase domain containing 2 MOCS2 0.00334 1 Molybdenum cofactor synthesis 2 TTLL6 0.00365 -1 Tubulin tyrosine ligase-like family, member 6 SHANK3 0.00394 -1 SH3 and multiple ankyrin repeat domains 3 ADCY4 0.004 -1 Adenylate cyclase 4 CD3D 0.004 -1 CD3d molecule, delta (CD3-TCR complex) (CD3D), transcript variant 1, mRNA.