Supplementary Table 3. Genes Deregulated by OTA in Both The

Supplementary Table 3. Genes deregulated by OTA in both the COR and OM, as identified using global gene expression analysis Function Genbank EntrezGene Gene Gene Name COR OM Accession No. ID Symbol Fold change Regulation Fold change Regulation DNA damage and DNA damage repair Base-excision repair NM_012601 24561 Mpg N-methylpurine-DNA glycosylase 1.95 down 2.28 down Nucleotide-excision repair NM_001107146 304528 Rfc5 replication factor C (activator 1) 5 1.70 down 1.88 down NM_001013195 361698 Pold4 polymerase (DNA-directed), delta 4 2.56 down 2.49 down p53-associated factors NM_080782 114851 Cdkn1a cyclin-dependent kinase inhibitor 1A 2.46 up 6.58 up NM_001108099 314856 Mdm2 Mdm2 p53 binding protein homolog (mouse) 2.10 up 2.04 up XM_341690 361409 Rfwd3 ring finger and WD repeat domain 3 2.14 down 1.64 down APEX nuclease (multifunctional DNA Response to DNA damage stimulus NM_024148 79116 Apex1 1.87 down 1.67 down repair enzyme) 1 NM_012557 24361 Fancc Fanconi anemia, complementation group C 1.98 down 3.27 down NM_133405 170917 Cry2 cryptochrome 2 (photolyase-like) 2.05 up 2.18 up Oxidative stress Superoxide metabolic processes A_44_P1030225 25080 Apoa4 apolipoprotein A-IV 2.64 up 6.12 up A_44_P247997 24361 Fancc Fanconi anemia, complementation group C 1.98 down 3.27 down Oxidative phosphorylation A_44_P414273 25250 Cox8b cytochrome c oxidase, subunit VIIIb 16.12 down 11.02 down A_44_P554332 25309 Cycs cytochrome c, somatic 1.77 down 1.59 down Hydrogen peroxide metabolic processes A_44_P554454 58819 Txnrd1 thioredoxin reductase 1 1.63 down 1.87 down sepiapterin reductase Nitric oxide biosynthetic processes A_42_P746212 29270 Spr (7,8-dihydrobiopterin:NADP+ 1.86 down 2.32 down oxidoreductase) Glutathione biosynthetic processes A_43_P12737 24439 Hagh hydroxyacyl glutathione hydrolase 1.74 down 2.80 down A_44_P219628 116568 Ggt1 gamma-glutamyltransferase 1 2.31 down 2.19 down glutamate-cysteine ligase, catalytic A_44_P228874 25283 Gclc 10.44 down 8.23 down subunit A_44_P254767 25458 Gss glutathione synthetase 2.97 down 3.33 down Glutathione metabolic processes A_42_P624195 24421 Gsta3 glutathione S-transferase A3 1.65 down 2.42 down A_43_P13342 24426 Gstp1 glutathione S-transferase pi 1 3.42 down 3.52 down A_42_P701582 25260 Gstt1 glutathione S-transferase theta 1 1.70 down 2.03 down A_44_P194256 29487 Gstt2 glutathione S-transferase, theta 2 1.78 down 2.54 down A_44_P283561 171341 Mgst1 microsomal glutathione S-transferase 1 2.09 down 2.06 down A_44_P512874 24962 Cth cystathionase (cystathionine gamma-lyase) 2.56 down 4.19 down Response to oxidative stress A_44_P156513 81802 Stx3 syntaxin 3 2.05 up 1.74 up A_44_P311126 24854 Clu clusterin 1.66 up 2.96 up A_44_P428455 170520 Cygb cytoglobin 1.78 up 2.06 up A_42_P577129 24817 Hnf1a HNF1 homeobox A 2.17 down 3.49 down nicotinate phosphoribosyltransferase A_44_P1049252 315085 Naprt1 2.08 down 2.13 down domain containing 1 A_44_P126868 58950 Fkbp1b FK506 binding protein 1b 3.15 down 3.59 down A_44_P142016 29192 Psen1 presenilin 1 1.83 down 2.21 down nudix (nucleoside diphosphate linked A_44_P250575 290365 Nudt15 1.59 down 1.57 down moiety X)-type motif 15 A_44_P347250 298298 Dhcr24 24-dehydrocholesterol reductase 2.24 down 2.18 down A_44_P635089 303828 Etv5 ets variant 5 3.12 down 3.08 down Cell cycle regulation RGD RGD1561797 (CDC28 protein kinase Regulation of G phase A_44_P446817 499655 1561797 1.58 up 1.59 up 1 regulatory subunit 1B) (Cks1b) A_42_P522899 59086 Tgfb1 transforming growth factor, beta 1 1.58 up 1.88 up Function Genbank EntrezGene Gene Gene Name COR OM Accession No. ID Symbol Fold change Regulation Fold change Regulation

Regulation of G1/S phase A_44_P807777 399489 E2f1 E2F transcription factor 1 1.89 down 1.56 down TAF10 RNA polymerase II, TATA box A_44_P193221 293345 Taf10 2.02 down 1.82 down binding protein (TBP)-associated factor

Regulation of G1/S and G2/M A_44_P914438 114851 Cdkn1a cyclin-dependent kinase inhibitor 1A 2.46 up 6.58 up Regulation of M phase A_44_P482885 365868 Hormad1 HORMA domain containing 1 2.28 down 1.84 up A_44_P1042372 294286 Kifc1 kinesin family member C1 1.78 down 2.22 down LOC498400 A_44_P667084 498400 similar to HORMA domain containing 2 1.82 down 3.14 down (Hormad2) SPO11 meiotic protein covalently bound A_44_P253175 366261 Spo11 3.50 down 4.19 down to DSB homolog (S. cerevisiae) Regulation of ubiquitin-protein ligase A_44_P168103 287280 Skp1 S-phase kinase-associated protein 1 1.55 down 1.55 down activity proteasome (prosome, macropain) 26S A_42_P507857 161475 Psmd9 1.93 down 1.50 down subunit, non-ATPase, 9 cell growth regulator with EF hand Negative regulation of cell cycle A_44_P398193 245918 Cgref1 6.54 down 6.40 down domain 1 growth arrest and DNA-damage- Unknown A_44_P199219 288916 Gadd45gip1 1.60 down 1.60 down inducible, gamma interacting protein 1 A_44_P1034541 64534 Pim3 pim-3 oncogene 1.63 down 2.06 down Apoptosis regulation Regulation of caspase activity A_43_P14915 24237 C6 complement component 6 5.54 up 5.86 up CASP8 and FADD-like apoptosis A_42_P640923 117279 Cflar 5.04 down 5.97 down regulator A_44_P286107 295357 Hbxip hepatitis B virus x interacting protein 1.58 down 1.91 down A_44_P347250 298298 Dhcr24 24-dehydrocholesterol reductase 2.24 down 2.18 down A_44_P503022 192154 Hip1 huntingtin interacting protein 1 1.53 up 1.85 up mitochondrial ubiquitin ligase activator A_44_P532380 298576 Mul1 2.02 down 1.70 down of NFKB 1 A_44_P554332 25309 Cycs cytochrome c, somatic 1.77 down 1.54 down Positive regulation of anti-apoptotic A_44_P914438 114851 Cdkn1a cyclin-dependent kinase inhibitor 1A 2.46 up 6.58 up responses Positive regulation of apoptosis A_43_P13378 246142 Bmf Bcl2 modifying factor 2.06 down 2.10 down A_44_P107199 113894 Sqstm1 sequestosome 1 1.72 down 2.08 down A_44_P142016 29192 Psen1 presenilin 1 1.83 down 2.21 down A_44_P183488 64026 Casp7 caspase 7 1.77 down 1.50 down A_44_P213133 362100 Endog endonuclease G 2.15 down 1.82 down A_44_P1031421 293024 Akap13 A kinase (PRKA) anchor protein 13 1.64 up 1.80 up Fas (TNF receptor superfamily, member A_42_P652897 246097 Fas 2.98 up 2.41 up 6) NM_001013941 298795 LOC298795 similar to 14-3-3 protein sigma 3.46 up 2.57 up Apoptosis regulation-mediated RGD1310686 similar to chromosome 16 open reading NM_001008360 360480 1.83 down 1.60 down p53 response (C16orf5) frame 5 Mdm2 p53 binding protein homolog A_44_P634946 314856 Mdm2 2.10 up 2.04 up (mouse) Unknown A_42_P685368 300799 Dapk2 death-associated kinase 2 1.73 down 2.07 down A_44_P110445 360662 Sap30bp SAP30 binding protein 1.52 down 1.52 down angiotensinogen (serpin peptidase A_43_P13272 24179 Agt 4.94 down 3.90 down inhibitor, clade A, member 8) A_44_P1034541 64534 Pim3 pim-3 oncogene 1.63 down 2.06 down Function Genbank EntrezGene Gene Gene Name COR OM Accession No. ID Symbol Fold change Regulation Fold change Regulation A_44_P1047992 25268 Proc protein C 2.21 down 2.91 down glutamate-cysteine ligase, catalytic A_44_P228874 25283 Gclc 10.44 down 8.23 down subunit A_44_P487249 81683 Mif macrophage migration inhibitory factor 1.74 down 2.09 down A_43_P12384 78971 Birc3 baculoviral IAP repeat-containing 3 1.88 up 2.33 up gonadotropin-releasing hormone 1 A_44_P206985 25194 Gnrh1 2.56 up 4.37 up (luteinizing-releasing hormone) TAF9 RNA polymerase II, TATA box A_44_P269630 373541 Taf9 2.12 up 1.68 up binding protein (TBP)-associated factor A_44_P323404 25707 Cntf ciliary neurotrophic factor 1.83 up 1.64 up A_44_P461154 116510 Timp1 TIMP metallopeptidase inhibitor 1 1.67 up 3.09 up A_44_P992908 24471 Hspb1 heat shock protein 1 1.69 up 3.06 up A_44_P306639 64322 Dap death-associated protein 1.72 up 1.84 up A_44_P311126 24854 Clu clusterin 1.66 up 2.96 up A_42_P522899 59086 Tgfb1 transforming growth factor, beta 1 1.58 up 1.88 up proteasome (prosome, macropain) 26S A_42_P507857 161475 Psmd9 1.93 down 1.50 down subunit, non-ATPase, 9 A_42_P604033 266787 Eaf2 ELL associated factor 2 4.84 down 4.49 down TAF10 RNA polymerase II, TATA box A_44_P193221 293345 Taf10 2.02 down 1.82 down binding protein (TBP)-associated factor DnaJ (Hsp40) homolog, subfamily A, A_44_P208880 360481 Dnaja3 2.09 down 2.13 down member 3 solute carrier family 5 (sodium/glucose A_44_P292711 252854 Slc5a11 1.73 down 2.25 Down cotransporter), member 11 tumor necrosis factor receptor A_44_P458021 25341 Tnfrsf11b 10.50 down 11.68 Down superfamily, member 11b A_44_P714007 500292 Cidec cell death-inducing DFFA-like effector c 5.27 down 5.61 Down A_44_P807777 399489 E2f1 E2F transcription factor 1 1.89 down 1.56 Down