Adam Margolin & Nicole DeFlaux Science Online London 2011-09-01

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Adam Margolin & Nicole DeFlaux, Sept 1, 2011. Science Online London 2011 London, UK

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Adam Margolin & Nicole DeFlaux Science Online London 2011-09-01

  1. 1. Nicole  Deflaux,  Adam  Margolin   Sage  Bionetworks   1  
  2. 2. Getting started: While Adam talks:1.  Go to http://scienceonline.sagebase.org2.  Install the Sage R packages and dependencies by following instructions on the home page.3.  Create a Synapse account by following the How-To Guide: “How to Create a Synapse Account”. 2  
  3. 3. Sage Bionetworks Mission Sage Bionetworks is a non-profit organization with a vision to create a commonswhere integrative bionetworks are evolved by contributor scientists with a shared vision to accelerate the elimination of human disease Building Disease Maps Data Repository Commons Pilots Discovery Platform
  4. 4. Synapse Platform and Repository Roadmap Synapse Platform Functionality Publicly Hosted Datasets Social Networking & Attribution Projects and Datasets Tool / Workflow Support Networks and Models Demo System Internal Alpha Invited External Beta Public Beta Full ProductionQ1-2011 Q2-2011 Q3-2011 Q4-2011 Q1-2012 Q2-2012 Q3-2012 Q4-2012 Curation Pipeline Statistical QC Pipeline Crowd-sourcing web tools Bioconductor Analysis Packages Coexpression Networks Data Analysis Capabilities
  5. 5. Predictive model
  6. 6. Sage Repository: reduce, reuse, recycle A Repository of Data, Tools, and Models  
  7. 7. Synapse workflows: reproducible research 1. Load feature data and phenotype data into R objects. 2. Create matrix aggregating feature data 3.  Write  custom  predicBve  modeling  funcBon.   •  Includes  parameter  selecBon  procedure.   •  Will  also  do  first  example  with  a  modeling  funcBon   4.  Wrap  predicBve  model  in  cross-­‐ that  we  provide  (i.e.  elasBc  net).   validaBon  procedure  for  performance   evaluaBon.   5.  Output  final  predicBve  model  (e.g.   biomarkers).   7  
  8. 8. 1. Load feature data and phenotype data into R objects. (Synapse workflow) 1. Load feature data and phenotype data into R objects. 2. Create matrix aggregating feature data 3.  Write  custom  predicBve  modeling  funcBon.   •  Includes  parameter  selecBon  procedure.   •  Will  also  do  first  example  with  a  modeling  funcBon   4.  Wrap  predicBve  model  in  cross-­‐ that  we  provide  (i.e.  elasBc  net).   validaBon  procedure  for  performance   evaluaBon.   5.  Output  final  predicBve  model  (e.g.   biomarkers).   8  
  9. 9. compounds   Muta6on   Copy  number   Data   Data   SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MHHES1_BONE NCIH2286_LUNG 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE IM95_STOMACH NUGC4_STOMACH SW48_LARGE_INTESTINE HDQP1_BREAST TE617T_SOFT_TISSUE RT4_URINARY_TRACT WM983B_SKIN COLO205_LARGE_INTESTINE CHP212_AUTONOMIC_GANGLIA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE WM88_SKIN MALME3M_SKIN SKMEL5_SKIN MELHO_SKIN A375_SKIN COLO201_LARGE_INTESTINEIGR37_SKIN WM2664_SKIN UACC62_SKIN LS411N_LARGE_INTESTINE HT29_LARGE_INTESTINE HEPG2_LIVER SW620_LARGE_INTESTINE OCUM1_STOMACH OV90_OVARY L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE IPC298_SKIN HT144_SKIN COLO679_SKIN SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KPNSI9S_AUTONOMIC_GANGLIA AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE CMK86_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEP12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE G401_SOFT_TISSUE MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SIMA_AUTONOMIC_GANGLIA AZ521_STOMACH MB157_BREAST DV90_LUNG ESS1_ENDOMETRIUM KYM1_SOFT_TISSUE 8MGBA_CENTRAL_NERVOUS_SYSTEM NCIN87_STOMACH NCIH2170_LUNG AU565_BREAST SKMES1_LUNG TE15_OESOPHAGUS CAL12T_LUNG JHH7_LIVER KYSE70_OESOPHAGUS PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUESNU16_STOMACH TE11_OESOPHAGUS KYSE180_OESOPHAGUS ISHIKAWAHERAKLIO02ER_ENDOMETRIUM 42MGBA_CENTRAL_NERVOUS_SYSTEM NCIH1703_LUNG SCC25_UPPER_AERODIGESTIVE_TRACT CAL27_UPPER_AERODIGESTIVE_TRACT SCC9_UPPER_AERODIGESTIVE_TRACT NCIH2030_LUNG FADU_UPPER_AERODIGESTIVE_TRACT JHH5_LIVER HCC1806_BREAST A253_SALIVARY_GLAND LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE LUDLU1_LUNG L33_PANCREAS HEC6_ENDOMETRIUM KURAMOCHI_OVARY F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCIH1693_LUNG NCIH1666_LUNG CAL851_BREAST OE21_OESOPHAGUS SCABER_URINARY_TRACT HUPT4_PANCREAS LS513_LARGE_INTESTINE SW403_LARGE_INTESTINE HEC151_ENDOMETRIUM TT2609C02_THYROID KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCIH2122_LUNG MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MDAMB435S_BREAST DBTRG05MG_CENTRAL_NERVOUS_SYSTEMBCPAP_THYROID 8305C_THYROID HDMYZ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE WM1799_SKIN G361_SKIN K029AX_SKIN LOXIMVI_SKIN SKNAS_AUTONOMIC_GANGLIA ES2_OVARY PSN1_PANCREAS SNU1_STOMACH SW1990_PANCREAS SW1417_LARGE_INTESTINE SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCIH1299_LUNG NCIH2087_LUNG EBC1_LUNG MKN45_STOMACH MIAPACA2_PANCREAS 22RV1_PROSTATE WM793_SKIN LU99_LUNG A2780_OVARY GCT_SOFT_TISSUE HS944T_SKIN OE33_OESOPHAGUS HPAC_PANCREAS SKNBE2_AUTONOMIC_GANGLIA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SKLU1_LUNG RT112_URINARY_TRACT JMSU1_URINARY_TRACT MDAMB468_BREAST NUGC3_STOMACH T24_URINARY_TRACT 639V_URINARY_TRACT ISTMES2_PLEURA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KE97_STOMACH CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SKES1_BONE KMS12BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUENCIH1048_LUNG OVCAR8_OVARY IMR32_AUTONOMIC_GANGLIA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE JHUEM2_ENDOMETRIUM A673_BONE NCIH1155_LUNG KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCIH2228_LUNG SKNSH_AUTONOMIC_GANGLIA DMS114_LUNG SKNDZ_AUTONOMIC_GANGLIA SJRH30_SOFT_TISSUE VMRCLCD_LUNG HGC27_STOMACH GI1_CENTRAL_NERVOUS_SYSTEM H4_CENTRAL_NERVOUS_SYSTEM BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE TC71_BONE MG63_BONE LOUNH91_LUNG TOV112D_OVARY SAOS2_BONE GLC82_LUNG BGC823_STOMACH HS683_CENTRAL_NERVOUS_SYSTEM TCCSUP_URINARY_TRACT DAOY_CENTRAL_NERVOUS_SYSTEM HOS_BONE SBC5_LUNG OC315_OVARY OC316_OVARY KP1N_PANCREAS UMUC3_URINARY_TRACT KNS42_CENTRAL_NERVOUS_SYSTEMNCIH520_LUNG LCLC103H_LUNG MPP89_PLEURA SF295_CENTRAL_NERVOUS_SYSTEMSW1353_BONE NCIH522_LUNG HUH1_LIVER U118MG_CENTRAL_NERVOUS_SYSTEM A172_CENTRAL_NERVOUS_SYSTEM BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE HLE_LIVER RPMI7951_SKIN U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MESSA_SOFT_TISSUE OC314_OVARY HARA_LUNG TE5_OESOPHAGUS MFE296_ENDOMETRIUM 1321N1_CENTRAL_NERVOUS_SYSTEM G402_SOFT_TISSUE KYSE510_OESOPHAGUS MDAMB453_BREAST BT549_BREAST HEC265_ENDOMETRIUM SW579_THYROID NCIH1341_LUNG LN18_CENTRAL_NERVOUS_SYSTEM CAL78_BONE NCIH211_LUNG NCIH1339_LUNG NCIH2452_PLEURA HLF_LIVER TYKNU_OVARY 5637_URINARY_TRACT ONCODG1_OVARY TE9_OESOPHAGUS HMCB_SKIN DU145_PROSTATE NIHOVCAR3_OVARY CHL1_SKIN TOV21G_OVARY SKMM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SNGM_ENDOMETRIUM HEC251_ENDOMETRIUM NCIH1915_LUNG RKO_LARGE_INTESTINE HCT116_LARGE_INTESTINE KNS60_CENTRAL_NERVOUS_SYSTEM A2058_SKIN KP4_PANCREAS RERFLCAI_LUNG PANC0327_PANCREAS KALS1_CENTRAL_NERVOUS_SYSTEM PK1_PANCREAS HEYA8_OVARY 8505C_THYROID PANC1005_PANCREAS PL45_PANCREAS MCAS_OVARY HCC70_BREAST NCIH3255_LUNG PC14_LUNG HCC4006_LUNG HCC827_LUNG VMRCRCW_KIDNEY HCC2935_LUNG HT1376_URINARY_TRACT NCIH1650_LUNG 769P_KIDNEY KYSE140_OESOPHAGUS CALU3_LUNG CCK81_LARGE_INTESTINE C2BBE1_LARGE_INTESTINE NCIH28_PLEURA NCIH727_LUNG HT1197_URINARY_TRACT MDAMB175VII_BREAST NCIH1869_LUNG KLE_ENDOMETRIUM CORL105_LUNG SNU449_LIVER EFE184_ENDOMETRIUM OVSAHO_OVARY T98G_CENTRAL_NERVOUS_SYSTEM HS895T_SKIN VMRCRCZ_KIDNEY FUOV1_OVARY CAKI2_KIDNEY HEP3B217_LIVER SKNFI_AUTONOMIC_GANGLIA T84_LARGE_INTESTINE PATU8902_PANCREAS SNUC2A_LARGE_INTESTINE SNU182_LIVER LS123_LARGE_INTESTINE NCIH1793_LUNG MCF7_BREAST NCIH2172_LUNG BT474_BREAST ZR7530_BREAST T47D_BREAST NCIH661_LUNG NCIH1563_LUNG HCC1569_BREAST JHH6_LIVER MDAMB415_BREAST MEWO_SKIN HS229T_LUNG UACC812_BREAST NCIH1373_LUNG SHP77_LUNG EN_ENDOMETRIUM Cell  Lines   WM115_SKIN T3M10_LUNG NCIH1944_LUNG NCIH647_LUNG AN3CA_ENDOMETRIUM RERFLCMS_LUNG HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEBFTC909_KIDNEY NCIH1651_LUNG MKN74_STOMACH J82_URINARY_TRACT Cell  Lines   SU8686_PANCREAS DKMG_CENTRAL_NERVOUS_SYSTEM SKHEP1_LIVER LC1SQSF_LUNG NCIH226_LUNG JHOS2_OVARY EFO21_OVARY MDAMB436_BREAST SNU387_LIVER NCIH2085_LUNG Feature  Matrix   SKMEL31_SKIN KYSE410_OESOPHAGUS KE39_STOMACH GCIY_STOMACH PC3_PROSTATE CAS1_CENTRAL_NERVOUS_SYSTEM COV504_OVARY KP1NL_PANCREAS SW1088_CENTRAL_NERVOUS_SYSTEM SW900_LUNG MOGGCCM_CENTRAL_NERVOUS_SYSTEM SNU423_LIVER KP3_PANCREAS NCIH1975_LUNG YKG1_CENTRAL_NERVOUS_SYSTEM Sensi.vity  Matrix   SH10TC_STOMACH NCIH2023_LUNG KYSE150_OESOPHAGUS GAMG_CENTRAL_NERVOUS_SYSTEM U87MG_CENTRAL_NERVOUS_SYSTEM GMS10_CENTRAL_NERVOUS_SYSTEM ONS76_CENTRAL_NERVOUS_SYSTEM NCIH650_LUNG SUIT2_PANCREAS SW480_LARGE_INTESTINE SKMEL2_SKIN HCC56_LARGE_INTESTINE SKMEL30_SKIN C32_SKIN RVH421_SKIN UACC257_SKIN NCIH747_LARGE_INTESTINE QGP1_PANCREAS HS939T_SKIN HS936T_SKIN RL952_ENDOMETRIUM NCIH358_LUNG NCIH1573_LUNG NCIH1355_LUNG NCIH322_LUNG PANC0203_PANCREAS PK45H_PANCREAS HS766T_PANCREAS CAPAN2_PANCREAS SKCO1_LARGE_INTESTINE COLO678_LARGE_INTESTINE KYSE30_OESOPHAGUS RKN_OVARY SW780_URINARY_TRACTA549_LUNG HMC18_BREAST KP2_PANCREAS NCIH2009_LUNG KMBC2_URINARY_TRACT NCIH2444_LUNG ASPC1_PANCREAS SKMEL24_SKIN HS695T_SKIN PK59_PANCREAS PANC0403_PANCREAS HUPT3_PANCREAS HUCCT1_BILIARY_TRACT CALU1_LUNG IALM_LUNG NCIH1092_LUNG TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE HCC78_LUNG OVTOKO_OVARY IGROV1_OVARY EFO27_OVARY KARPAS422_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE JHH4_LIVER JHH2_LIVER BT20_BREAST SKBR3_BREAST NCIH1184_LUNG NCIH1694_LUNG NCIH810_LUNG CAMA1_BREAST EFM19_BREAST SKOV3_OVARY OVCAR4_OVARY TEN_ENDOMETRIUM OVMANA_OVARY COV318_OVARY COLO699_LUNG COLO320_LARGE_INTESTINE ISTMES1_PLEURA MKN7_STOMACH L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE A204_SOFT_TISSUE HSC2_UPPER_AERODIGESTIVE_TRACT 786O_KIDNEY HEC59_ENDOMETRIUM DOV13_OVARY CORL23_LUNG GB1_CENTRAL_NERVOUS_SYSTEM SF126_CENTRAL_NERVOUS_SYSTEM HCT15_LARGE_INTESTINE HS739T_BREAST KNS81_CENTRAL_NERVOUS_SYSTEM KMRC1_KIDNEY SW1271_LUNG NCIH441_LUNG HS294T_SKIN IGR39_SKIN HCC1187_BREAST MORCPR_LUNG HS578T_BREAST OCILY10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCIH1581_LUNG HEC1A_ENDOMETRIUM JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE EB2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUENCIH1648_LUNG EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE JHOS4_OVARY HCC1395_BREAST MFE319_ENDOMETRIUM KYSE450_OESOPHAGUS DETROIT562_UPPER_AERODIGESTIVE_TRACT ACHN_KIDNEY MFE280_ENDOMETRIUM KMRC2_KIDNEY RERFGC1B_STOMACH NCIH1568_LUNG SJSA1_BONE NCIH2052_PLEURA MDAMB157_BREAST SW1573_LUNG KELLY_AUTONOMIC_GANGLIA HS746T_STOMACH HPAFII_PANCREAS KCIMOH1_PANCREAS SKLMS1_SOFT_TISSUE BXPC3_PANCREAS COLO741_SKIN CALU6_LUNG SNU398_LIVER RD_SOFT_TISSUE HT1080_SOFT_TISSUE NCIH23_LUNG MSTO211H_PLEURA HCC15_LUNG SQ1_LUNG C3A_LIVER HCC44_LUNG SNU475_LIVER HS729_SOFT_TISSUE ZR751_BREAST TE1_OESOPHAGUS NCIH460_LUNG KNS62_LUNG PLCPRF5_LIVER U2OS_BONE FU97_STOMACH HS840T_UPPER_AERODIGESTIVE_TRACT HCC1954_BREAST KYSE520_OESOPHAGUS HS852T_SKIN LN229_CENTRAL_NERVOUS_SYSTEM NCIH1792_LUNG T T TKI258 AE684 Nilotinib LBH589 Erlotinib RAF265 Nutlin!3 17!AAG LBW242 AEW541 Lapatinib PLX4720 ZD!6474 Paclitaxel AZD6244 AZD0530 Sorafenib Irinotecan L!685458 opotecan PF2341066 PD!0325901 PD!0332991 PHA!665752 (conceptual) 1. Load feature data and phenotype data into matrix objects.
  10. 10. 2. Create matrix aggregating feature data (Synapse workflow) 1. Load feature data and phenotype data into R objects. 2. Create matrix aggregating feature data3.  Write  custom  predicBve  modeling  funcBon.  •  Includes  parameter  selecBon  procedure.  •  Will  also  do  first  example  with  a  modeling  funcBon   4.  Wrap  predicBve  model  in  cross-­‐ that  we  provide  (i.e.  elasBc  net).   validaBon  procedure  for  performance   evaluaBon.   5.  Output  final  predicBve  model  (e.g.   biomarkers).   10  
  11. 11. compounds   20,000  gene  features   SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MHHES1_BONE NCIH2286_LUNG 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE IM95_STOMACH NUGC4_STOMACH SW48_LARGE_INTESTINE HDQP1_BREAST TE617T_SOFT_TISSUE RT4_URINARY_TRACT WM983B_SKIN COLO205_LARGE_INTESTINE CHP212_AUTONOMIC_GANGLIA HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE WM88_SKIN MALME3M_SKIN SKMEL5_SKIN MELHO_SKIN A375_SKIN COLO201_LARGE_INTESTINEIGR37_SKIN WM2664_SKIN UACC62_SKIN LS411N_LARGE_INTESTINE HT29_LARGE_INTESTINE HEPG2_LIVER SW620_LARGE_INTESTINE OCUM1_STOMACH OV90_OVARY L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE IPC298_SKIN HT144_SKIN COLO679_SKIN SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KPNSI9S_AUTONOMIC_GANGLIA AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE CMK86_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEP12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE G401_SOFT_TISSUE MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SIMA_AUTONOMIC_GANGLIA AZ521_STOMACH MB157_BREAST DV90_LUNG ESS1_ENDOMETRIUM KYM1_SOFT_TISSUE 8MGBA_CENTRAL_NERVOUS_SYSTEM NCIN87_STOMACH NCIH2170_LUNG AU565_BREAST SKMES1_LUNG TE15_OESOPHAGUS CAL12T_LUNG JHH7_LIVER KYSE70_OESOPHAGUS PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUESNU16_STOMACH TE11_OESOPHAGUS KYSE180_OESOPHAGUS ISHIKAWAHERAKLIO02ER_ENDOMETRIUM 42MGBA_CENTRAL_NERVOUS_SYSTEM NCIH1703_LUNG SCC25_UPPER_AERODIGESTIVE_TRACT CAL27_UPPER_AERODIGESTIVE_TRACT SCC9_UPPER_AERODIGESTIVE_TRACT NCIH2030_LUNG FADU_UPPER_AERODIGESTIVE_TRACT JHH5_LIVER HCC1806_BREAST A253_SALIVARY_GLAND LP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE LUDLU1_LUNG L33_PANCREAS HEC6_ENDOMETRIUM KURAMOCHI_OVARY F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCIH1693_LUNG NCIH1666_LUNG CAL851_BREAST OE21_OESOPHAGUS SCABER_URINARY_TRACT HUPT4_PANCREAS LS513_LARGE_INTESTINE SW403_LARGE_INTESTINE HEC151_ENDOMETRIUM TT2609C02_THYROID KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCIH2122_LUNG MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MDAMB435S_BREAST DBTRG05MG_CENTRAL_NERVOUS_SYSTEMBCPAP_THYROID 8305C_THYROID HDMYZ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE WM1799_SKIN G361_SKIN K029AX_SKIN LOXIMVI_SKIN SKNAS_AUTONOMIC_GANGLIA ES2_OVARY PSN1_PANCREAS SNU1_STOMACH SW1990_PANCREAS SW1417_LARGE_INTESTINE SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCIH1299_LUNG NCIH2087_LUNG EBC1_LUNG MKN45_STOMACH MIAPACA2_PANCREAS 22RV1_PROSTATE WM793_SKIN LU99_LUNG A2780_OVARY GCT_SOFT_TISSUE HS944T_SKIN OE33_OESOPHAGUS HPAC_PANCREAS SKNBE2_AUTONOMIC_GANGLIA SUDHL10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SKLU1_LUNG RT112_URINARY_TRACT JMSU1_URINARY_TRACT MDAMB468_BREAST NUGC3_STOMACH T24_URINARY_TRACT 639V_URINARY_TRACT ISTMES2_PLEURA MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE KE97_STOMACH CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SKES1_BONE KMS12BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUENCIH1048_LUNG OVCAR8_OVARY IMR32_AUTONOMIC_GANGLIA REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE JHUEM2_ENDOMETRIUM A673_BONE NCIH1155_LUNG KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCIH2228_LUNG SKNSH_AUTONOMIC_GANGLIA DMS114_LUNG SKNDZ_AUTONOMIC_GANGLIA SJRH30_SOFT_TISSUE VMRCLCD_LUNG HGC27_STOMACH GI1_CENTRAL_NERVOUS_SYSTEM H4_CENTRAL_NERVOUS_SYSTEM BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE TC71_BONE MG63_BONE LOUNH91_LUNG TOV112D_OVARY SAOS2_BONE GLC82_LUNG BGC823_STOMACH HS683_CENTRAL_NERVOUS_SYSTEM TCCSUP_URINARY_TRACT DAOY_CENTRAL_NERVOUS_SYSTEM HOS_BONE SBC5_LUNG OC315_OVARY OC316_OVARY KP1N_PANCREAS UMUC3_URINARY_TRACT KNS42_CENTRAL_NERVOUS_SYSTEMNCIH520_LUNG LCLC103H_LUNG MPP89_PLEURA SF295_CENTRAL_NERVOUS_SYSTEMSW1353_BONE NCIH522_LUNG HUH1_LIVER U118MG_CENTRAL_NERVOUS_SYSTEM A172_CENTRAL_NERVOUS_SYSTEM BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE HLE_LIVER RPMI7951_SKIN U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MESSA_SOFT_TISSUE OC314_OVARY HARA_LUNG TE5_OESOPHAGUS MFE296_ENDOMETRIUM 1321N1_CENTRAL_NERVOUS_SYSTEM G402_SOFT_TISSUE KYSE510_OESOPHAGUS MDAMB453_BREAST BT549_BREAST HEC265_ENDOMETRIUM SW579_THYROID NCIH1341_LUNG LN18_CENTRAL_NERVOUS_SYSTEM CAL78_BONE NCIH211_LUNG NCIH1339_LUNG NCIH2452_PLEURA HLF_LIVER TYKNU_OVARY 5637_URINARY_TRACT ONCODG1_OVARY TE9_OESOPHAGUS HMCB_SKIN DU145_PROSTATE NIHOVCAR3_OVARY CHL1_SKIN TOV21G_OVARY SKMM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SNGM_ENDOMETRIUM HEC251_ENDOMETRIUM NCIH1915_LUNG RKO_LARGE_INTESTINE HCT116_LARGE_INTESTINE KNS60_CENTRAL_NERVOUS_SYSTEM A2058_SKIN KP4_PANCREAS RERFLCAI_LUNG PANC0327_PANCREAS KALS1_CENTRAL_NERVOUS_SYSTEM PK1_PANCREAS HEYA8_OVARY 8505C_THYROID PANC1005_PANCREAS PL45_PANCREAS MCAS_OVARY HCC70_BREAST NCIH3255_LUNG PC14_LUNG HCC4006_LUNG HCC827_LUNG VMRCRCW_KIDNEY HCC2935_LUNG HT1376_URINARY_TRACT NCIH1650_LUNG 769P_KIDNEY KYSE140_OESOPHAGUS CALU3_LUNG CCK81_LARGE_INTESTINE C2BBE1_LARGE_INTESTINE NCIH28_PLEURA NCIH727_LUNG HT1197_URINARY_TRACT MDAMB175VII_BREAST NCIH1869_LUNG KLE_ENDOMETRIUM CORL105_LUNG SNU449_LIVER EFE184_ENDOMETRIUM OVSAHO_OVARY T98G_CENTRAL_NERVOUS_SYSTEM HS895T_SKIN VMRCRCZ_KIDNEY FUOV1_OVARY CAKI2_KIDNEY HEP3B217_LIVER SKNFI_AUTONOMIC_GANGLIA T84_LARGE_INTESTINE PATU8902_PANCREAS SNUC2A_LARGE_INTESTINE SNU182_LIVER LS123_LARGE_INTESTINE NCIH1793_LUNG MCF7_BREAST NCIH2172_LUNG BT474_BREAST ZR7530_BREAST T47D_BREAST NCIH661_LUNG NCIH1563_LUNG HCC1569_BREAST JHH6_LIVER MDAMB415_BREAST MEWO_SKIN HS229T_LUNG UACC812_BREAST NCIH1373_LUNG SHP77_LUNG EN_ENDOMETRIUM Cell  Lines   WM115_SKIN T3M10_LUNG NCIH1944_LUNG NCIH647_LUNG AN3CA_ENDOMETRIUM RERFLCMS_LUNG HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUEBFTC909_KIDNEY NCIH1651_LUNG MKN74_STOMACH J82_URINARY_TRACT Cell  Lines   SU8686_PANCREAS DKMG_CENTRAL_NERVOUS_SYSTEM SKHEP1_LIVER LC1SQSF_LUNG NCIH226_LUNG JHOS2_OVARY EFO21_OVARY MDAMB436_BREAST SNU387_LIVER NCIH2085_LUNG Feature  Matrix   SKMEL31_SKIN KYSE410_OESOPHAGUS KE39_STOMACH GCIY_STOMACH PC3_PROSTATE CAS1_CENTRAL_NERVOUS_SYSTEM COV504_OVARY KP1NL_PANCREAS SW1088_CENTRAL_NERVOUS_SYSTEM SW900_LUNG MOGGCCM_CENTRAL_NERVOUS_SYSTEM SNU423_LIVER KP3_PANCREAS NCIH1975_LUNG YKG1_CENTRAL_NERVOUS_SYSTEM Sensi.vity  Matrix   SH10TC_STOMACH NCIH2023_LUNG KYSE150_OESOPHAGUS GAMG_CENTRAL_NERVOUS_SYSTEM U87MG_CENTRAL_NERVOUS_SYSTEM GMS10_CENTRAL_NERVOUS_SYSTEM ONS76_CENTRAL_NERVOUS_SYSTEM NCIH650_LUNG SUIT2_PANCREAS SW480_LARGE_INTESTINE SKMEL2_SKIN HCC56_LARGE_INTESTINE SKMEL30_SKIN C32_SKIN RVH421_SKIN UACC257_SKIN NCIH747_LARGE_INTESTINE QGP1_PANCREAS HS939T_SKIN HS936T_SKIN RL952_ENDOMETRIUM NCIH358_LUNG NCIH1573_LUNG NCIH1355_LUNG NCIH322_LUNG PANC0203_PANCREAS PK45H_PANCREAS HS766T_PANCREAS CAPAN2_PANCREAS SKCO1_LARGE_INTESTINE COLO678_LARGE_INTESTINE KYSE30_OESOPHAGUS RKN_OVARY SW780_URINARY_TRACTA549_LUNG HMC18_BREAST KP2_PANCREAS NCIH2009_LUNG KMBC2_URINARY_TRACT NCIH2444_LUNG ASPC1_PANCREAS SKMEL24_SKIN HS695T_SKIN PK59_PANCREAS PANC0403_PANCREAS HUPT3_PANCREAS HUCCT1_BILIARY_TRACT CALU1_LUNG IALM_LUNG NCIH1092_LUNG TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE HCC78_LUNG OVTOKO_OVARY IGROV1_OVARY EFO27_OVARY KARPAS422_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE JHH4_LIVER JHH2_LIVER BT20_BREAST SKBR3_BREAST NCIH1184_LUNG NCIH1694_LUNG NCIH810_LUNG CAMA1_BREAST EFM19_BREAST SKOV3_OVARY OVCAR4_OVARY TEN_ENDOMETRIUM OVMANA_OVARY COV318_OVARY COLO699_LUNG COLO320_LARGE_INTESTINE ISTMES1_PLEURA MKN7_STOMACH L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE A204_SOFT_TISSUE HSC2_UPPER_AERODIGESTIVE_TRACT 786O_KIDNEY HEC59_ENDOMETRIUM DOV13_OVARY CORL23_LUNG GB1_CENTRAL_NERVOUS_SYSTEM SF126_CENTRAL_NERVOUS_SYSTEM HCT15_LARGE_INTESTINE HS739T_BREAST KNS81_CENTRAL_NERVOUS_SYSTEM KMRC1_KIDNEY SW1271_LUNG NCIH441_LUNG HS294T_SKIN IGR39_SKIN HCC1187_BREAST MORCPR_LUNG HS578T_BREAST OCILY10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NCIH1581_LUNG HEC1A_ENDOMETRIUM JM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE MC116_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE EB2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUENCIH1648_LUNG EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE JHOS4_OVARY HCC1395_BREAST MFE319_ENDOMETRIUM KYSE450_OESOPHAGUS DETROIT562_UPPER_AERODIGESTIVE_TRACT ACHN_KIDNEY MFE280_ENDOMETRIUM KMRC2_KIDNEY RERFGC1B_STOMACH NCIH1568_LUNG SJSA1_BONE NCIH2052_PLEURA MDAMB157_BREAST SW1573_LUNG KELLY_AUTONOMIC_GANGLIA HS746T_STOMACH HPAFII_PANCREAS KCIMOH1_PANCREAS SKLMS1_SOFT_TISSUE BXPC3_PANCREAS COLO741_SKIN CALU6_LUNG SNU398_LIVER RD_SOFT_TISSUE HT1080_SOFT_TISSUE NCIH23_LUNG MSTO211H_PLEURA HCC15_LUNG SQ1_LUNG C3A_LIVER HCC44_LUNG SNU475_LIVER HS729_SOFT_TISSUE ZR751_BREAST TE1_OESOPHAGUS NCIH460_LUNG KNS62_LUNG PLCPRF5_LIVER U2OS_BONE FU97_STOMACH HS840T_UPPER_AERODIGESTIVE_TRACT HCC1954_BREAST KYSE520_OESOPHAGUS HS852T_SKIN LN229_CENTRAL_NERVOUS_SYSTEM NCIH1792_LUNG T T TKI258 AE684 Nilotinib LBH589 Erlotinib RAF265 Nutlin!3 17!AAG LBW242 AEW541 Lapatinib PLX4720 ZD!6474 Paclitaxel AZD6244 AZD0530 Sorafenib Irinotecan L!685458 opotecan PF2341066 PD!0325901 PD!0332991 PHA!665752 (conceptual) 2. Create matrix aggregating feature data
  12. 12. 3. Predictive modeling functions. (Synapse workflow) 1. Load feature data and phenotype data into R objects. 2. Create matrix aggregating feature data3.  Write  custom  predicBve  modeling  funcBon.  •  Includes  parameter  selecBon  procedure.  •  Will  also  do  first  example  with  a  modeling  funcBon   4.  Wrap  predicBve  model  in  cross-­‐ that  we  provide  (i.e.  elasBc  net).   validaBon  procedure  for  performance   evaluaBon.   5.  Output  final  predicBve  model  (e.g.   biomarkers).   12  
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