adam margolin & nicole deflaux science online london 2011-09-01
DESCRIPTION
Adam Margolin & Nicole DeFlaux, Sept 1, 2011. Science Online London 2011 London, UKTRANSCRIPT
Nicole Deflaux, Adam Margolin Sage Bionetworks
1
Getting started: While Adam talks:
1. Go to http://scienceonline.sagebase.org 2. 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
Sage Bionetworks Mission Sage Bionetworks is a non-profit organization with a vision to create a “commons”
where integrative bionetworks are evolved by contributor scientists with a shared vision to accelerate the elimination of human disease
Data Repository
Discovery Platform
Building Disease Maps
Commons Pilots
Synapse Platform and Repository Roadmap
Q1-2011 Q2-2011 Q3-2011 Q4-2011 Q1-2012 Q2-2012
Projects and Datasets
Publicly Hosted Datasets
Synapse Platform Functionality
Data Analysis Capabilities
Tool / Workflow Support
Social Networking & Attribution
Q3-2012 Q4-2012
Demo System Internal Alpha Invited External Beta Public Beta Full Production
Networks and Models
Curation Pipeline
Statistical QC Pipeline
Bioconductor Analysis Packages
Coexpression Networks
Crowd-sourcing web tools
Predictive model
Sage Repository: reduce, reuse, recycle
A Repository of Data, Tools, and Models
Synapse workflows: reproducible research
7
1. Load feature data and phenotype data into R objects.
3. Write custom predicBve modeling funcBon. • Includes parameter selecBon procedure. • Will also do first example with a modeling funcBon
that we provide (i.e. elasBc net).
4. Wrap predicBve model in cross-‐validaBon procedure for performance evaluaBon. 5. Output final predicBve model (e.g. biomarkers).
2. Create matrix aggregating feature data
1. Load feature data and phenotype data into R objects. (Synapse workflow)
8
3. Write custom predicBve modeling funcBon. • Includes parameter selecBon procedure. • Will also do first example with a modeling funcBon
that we provide (i.e. elasBc net).
4. Wrap predicBve model in cross-‐validaBon procedure for performance evaluaBon. 5. Output final predicBve model (e.g. biomarkers).
1. Load feature data and phenotype data into R objects.
2. Create matrix aggregating feature data
SIGM
5_HA
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OIET
IC_AND
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PHOID_
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IC_AND
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PHOID_
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IC_AND
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PHOID_
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2_HA
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IC_AND
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L22_HA
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IC_AND
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1_HA
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OIET
IC_AND
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L_HA
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OIET
IC_AND
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PHOID_
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UEMHH
ES1_BO
NEJVM3_HA
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OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH2286_LUN
G697_HA
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OIET
IC_AND
_LYM
PHOID_
TISS
UEOC
IAML5_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEIM95_STO
MAC
HNU
GC4_STOM
ACH
SW48_LAR
GE_INT
ESTINE
HDQP
1_BR
EAST
TE617T_SOF
T_TISS
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4_UR
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OIET
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UEWM88_SKIN
MALME3M_SKIN
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INWM2664_SKIN
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201_LARG
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S11_HA
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OIET
IC_AND
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DHL6_H
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OIET
IC_AND
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PHOID_
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HH2_HA
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OIET
IC_AND
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PHOID_
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OIET
IC_AND
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PHOID_
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OIET
IC_AND
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DHL4_H
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OIET
IC_AND
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PHOID_
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OIET
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A_HA
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OIET
IC_AND
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PHOID_
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UEKM
S34_HA
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OIET
IC_AND
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PHOID_
TISS
UERP
MI8402_HA
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OIET
IC_AND
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PHOID_
TISS
UEKM
S26_HA
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OIET
IC_AND
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PHOID_
TISS
UEGR
ANTA519_HA
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OIET
IC_AND
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PHOID_
TISS
UESU
DHL8_H
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OIET
IC_AND
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PHOID_
TISS
UEKA
SUMI2_H
AEMATOP
OIET
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PHOID_
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UEG4
01_SOF
T_TISS
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1_HA
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OIET
IC_AND
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PHOID_
TISS
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TONO
MIC_G
ANGL
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521_STOM
ACH
MB157_BRE
AST
DV90_LUN
GES
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RIUM
KYM1_SO
FT_TISSU
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GBA_CE
NTRA
L_NE
RVOU
S_SY
STEM
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MAC
HNC
IH2170_LUN
GAU
565_BR
EAST
SKMES
1_LU
NGTE
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HAGU
SCA
L12T_LUN
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KYSE
70_O
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HAGU
SSN
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ACH
PFEIFFER
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MATOP
OIET
IC_AND
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PHOID_
TISS
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SE180_OE
SOPH
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WAH
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LIO0
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ENDO
MET
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NTRA
L_NE
RVOU
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STEM
NCIH1703_LUN
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AERO
DIGE
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ACT
CAL27_UP
PER_
AERO
DIGE
STIVE_TR
ACT
SCC9
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IH2030_LUN
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AND
LUDL
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GL33_PANC
REAS
LP1_HA
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OIET
IC_AND
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PHOID_
TISS
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IC_AND
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620_HA
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OIET
IC_AND
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TISS
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GCA
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AST
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ESOP
HAGU
SSC
ABER
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RY_TRA
CTHU
PT4_PANC
REAS
LS513_LARG
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STINE
SW403_LARG
E_INTE
STINE
HEC1
51_END
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RIUM
TT2609C0
2_TH
YROID
NCIH2122_LUN
GKU
812_HA
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OIET
IC_AND
_LYM
PHOID_
TISS
UEMEG
01_H
AEMATOP
OIET
IC_AND
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PHOID_
TISS
UEMDA
MB435S_BR
EAST
BCPAP_TH
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DBTR
G05M
G_CE
NTRA
L_NE
RVOU
S_SY
STEM
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THYR
OID
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G361_SKIN
K029AX
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HDMYZ
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MATOP
OIET
IC_AND
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PHOID_
TISS
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XIMVI_SKIN
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ARY
SKNA
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TONO
MIC_G
ANGL
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SSN
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MAC
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1990_PAN
CREA
SSW
1417_LAR
GE_INT
ESTINE
NCIH1299_LUN
GNC
IH2087_LUN
GSU
PM2_HA
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OIET
IC_AND
_LYM
PHOID_
TISS
UEEB
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GMKN
45_STO
MAC
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2_PANC
REAS
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OSTATE
WM793_SK
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99_LUN
GA2780_OV
ARY
GCT_SO
FT_TISSU
EHS
944T_SKIN
OE33_O
ESOP
HAGU
SHP
AC_PAN
CREA
SSK
LU1_LU
NGSK
NBE2_AUT
ONOM
IC_G
ANGL
IASU
DHL10_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UERT
112_UR
INAR
Y_TR
ACT
JMSU
1_UR
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Y_TR
ACT
MDA
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AST
NUGC
3_STOM
ACH
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INAR
Y_TR
ACT
639V_U
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RY_TRA
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97_STO
MAC
HSK
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NEMINO_
HAEM
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OIET
IC_AND
_LYM
PHOID_
TISS
UECI1_HA
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OIET
IC_AND
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PHOID_
TISS
UEBL70_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1048_LUN
GOV
CAR8
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KMS12BM_H
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OIET
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MATOP
OIET
IC_AND
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TISS
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H_HA
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OIET
IC_AND
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DOMET
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GKA
RPAS
299_HA
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OIET
IC_AND
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NSH_
AUTO
NOMIC_G
ANGL
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NDZ_AU
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ANGL
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30_SOF
T_TISS
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STEM
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ENTR
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TEM
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STEM
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ENC
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STEM
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CENT
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S_SY
STEM
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ENTR
AL_N
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TEM
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MATOP
OIET
IC_AND
_LYM
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TISS
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MI7951_SK
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37_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMJ_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMES
SA_SOF
T_TISS
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314_OV
ARY
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_LUN
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5_OE
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AGUS
MFE
296_EN
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RIUM
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ERVO
US_SYS
TEM
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T_TISS
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SE510_OE
SOPH
AGUS
MDA
MB453_BRE
AST
BT549_BR
EAST
HEC2
65_END
OMET
RIUM
SW579_TH
YROID
NCIH1341_LUN
GLN
18_C
ENTR
AL_N
ERVO
US_SYS
TEM
CAL78_BO
NENC
IH211_LU
NGNC
IH1339_LUN
GNC
IH2452_PLEUR
AHL
F_LIVE
RTY
KNU_
OVAR
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RINA
RY_TRA
CTON
CODG
1_OV
ARY
TE9_OE
SOPH
AGUS
HMCB
_SKIN
DU145_PR
OSTATE
NIHO
VCAR
3_OV
ARY
CHL1_SKIN
TOV21G
_OVARY
SKMM2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESN
GM_END
OMET
RIUM
HEC2
51_END
OMET
RIUM
NCIH1915_LUN
GRK
O_LARG
E_INTE
STINE
HCT116_LAR
GE_INT
ESTINE
A2058_SK
INKN
S60_CE
NTRA
L_NE
RVOU
S_SY
STEM
KP4_PANC
REAS
RERF
LCAI_LUN
GPANC
0327_PAN
CREA
SKA
LS1_CE
NTRA
L_NE
RVOU
S_SY
STEM
PK1_PANC
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ARY
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THYR
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1005_PAN
CREA
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CREA
SMCA
S_OV
ARY
HCC7
0_BR
EAST
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GPC
14_LUN
GHC
C4006_LU
NGHC
C827_LUN
GVM
RCRC
W_KIDNE
YHC
C2935_LU
NGHT
1376_U
RINA
RY_TRA
CTNC
IH1650_LUN
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CALU
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E_INTE
STINE
C2BB
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GE_INT
ESTINE
NCIH28_PLEUR
ANC
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NGHT
1197_U
RINA
RY_TRA
CTMDA
MB175VII_BR
EAST
NCIH1869_LUN
GKLE_EN
DOMET
RIUM
CORL
105_LU
NGSN
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EFE184_END
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RIUM
OVSA
HO_O
VARY
HS895T_SKIN
T98G
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TRAL_N
ERVO
US_SYS
TEM
VMRC
RCZ_KIDN
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OV1_OV
ARY
CAKI2_KIDN
EYHE
P3B217_LIVER
SKNF
I_AU
TONO
MIC_G
ANGL
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E_INTE
STINE
PATU
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SSN
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GE_INT
ESTINE
SNU1
82_LIVER
LS123_LARG
E_INTE
STINE
NCIH1793_LUN
GMCF
7_BR
EAST
NCIH2172_LUN
GBT
474_BR
EAST
ZR7530_BRE
AST
T47D
_BRE
AST
NCIH661_LU
NGNC
IH1563_LUN
GHC
C1569_BR
EAST
JHH6
_LIVER
MDA
MB415_BRE
AST
MEW
O_SK
INHS
229T_LUN
GUA
CC812_BR
EAST
NCIH1373_LUN
GSH
P77_LU
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_END
OMET
RIUM
WM115_SK
INT3M10_LUN
GNC
IH1944_LUN
GNC
IH647_LU
NGAN
3CA_EN
DOMET
RIUM
RERF
LCMS_LU
NGBF
TC909_KIDN
EYHE
L9217_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1651_LUN
GMKN
74_STO
MAC
HJ82_UR
INAR
Y_TR
ACT
SU8686_PAN
CREA
SSK
HEP1_LIVER
DKMG_
CENT
RAL_NE
RVOU
S_SY
STEM
LC1SQS
F_LU
NGNC
IH226_LU
NGJHOS
2_OV
ARY
EFO2
1_OV
ARY
MDA
MB436_BRE
AST
SNU3
87_LIVER
NCIH2085_LUN
GSK
MEL31_SKIN
KYSE
410_OE
SOPH
AGUS
KE39_STO
MAC
HGC
IY_STO
MAC
HPC
3_PR
OSTATE
CAS1_C
ENTR
AL_N
ERVO
US_SYS
TEM
COV504_O
VARY
KP1N
L_PANC
REAS
SW900_LU
NGSW
1088_C
ENTR
AL_N
ERVO
US_SYS
TEM
SNU4
23_LIVER
MOG
GCCM
_CEN
TRAL_N
ERVO
US_SYS
TEM
KP3_PANC
REAS
NCIH1975_LUN
GYK
G1_C
ENTR
AL_N
ERVO
US_SYS
TEM
SH10TC
_STO
MAC
HNC
IH2023_LUN
GKY
SE150_OE
SOPH
AGUS
GAMG_
CENT
RAL_NE
RVOU
S_SY
STEM
U87M
G_CE
NTRA
L_NE
RVOU
S_SY
STEM
GMS10_CE
NTRA
L_NE
RVOU
S_SY
STEM
NCIH650_LU
NGON
S76_CE
NTRA
L_NE
RVOU
S_SY
STEM
SUIT2_PANC
REAS
SW480_LARG
E_INTE
STINE
SKMEL2_SK
INHC
C56_LARG
E_INTE
STINE
SKMEL30_SKIN
C32_SK
INRV
H421_SKIN
UACC
257_SK
INNC
IH747_LARG
E_INTE
STINE
QGP1_PAN
CREA
SHS
939T_SKIN
HS936T_SKIN
RL952_EN
DOMET
RIUM
NCIH358_LU
NGNC
IH1573_LUN
GNC
IH1355_LUN
GNC
IH322_LU
NGPANC
0203_PAN
CREA
SPK
45H_
PANC
REAS
HS766T_PAN
CREA
SCA
PAN2
_PAN
CREA
SSK
CO1_LARG
E_INTE
STINE
COLO
678_LARG
E_INTE
STINE
KYSE
30_O
ESOP
HAGU
SRK
N_OV
ARY
A549_LUN
GSW
780_UR
INAR
Y_TR
ACT
HMC1
8_BR
EAST
KP2_PANC
REAS
NCIH2009_LUN
GKM
BC2_UR
INAR
Y_TR
ACT
NCIH2444_LUN
GAS
PC1_PANC
REAS
SKMEL24_SKIN
HS695T_SKIN
PK59_PAN
CREA
SPANC
0403_PAN
CREA
SHU
PT3_PANC
REAS
HUCC
T1_BILIARY
_TRA
CTCA
LU1_LU
NGIALM
_LUN
GNC
IH1092_LUN
GHC
C78_LU
NGTO
LEDO
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEOV
TOKO
_OVARY
IGRO
V1_O
VARY
EFO2
7_OV
ARY
JHH4
_LIVER
JHH2
_LIVER
BT20_BRE
AST
KARP
AS422_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEOP
M2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESK
BR3_BR
EAST
NCIH1184_LUN
GNC
IH1694_LUN
GNC
IH810_LU
NGCA
MA1_BRE
AST
EFM19_BRE
AST
SKOV
3_OV
ARY
OVCA
R4_O
VARY
TEN_
ENDO
MET
RIUM
OVMAN
A_OV
ARY
COV318_O
VARY
COLO
699_LU
NGCO
LO320_LARG
E_INTE
STINE
ISTM
ES1_PLEU
RAMKN
7_STOM
ACH
L428_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEA204_SOF
T_TISS
UE786O
_KIDNE
YHS
C2_U
PPER
_AER
ODIGES
TIVE
_TRA
CTHE
C59_EN
DOMET
RIUM
DOV13_OV
ARY
CORL
23_LUN
GGB
1_CE
NTRA
L_NE
RVOU
S_SY
STEM
SF126_CE
NTRA
L_NE
RVOU
S_SY
STEM
HCT15_LARG
E_INTE
STINE
HS739T_BRE
AST
KNS81_CE
NTRA
L_NE
RVOU
S_SY
STEM
KMRC
1_KIDN
EYSW
1271_LUN
GNC
IH441_LU
NGHS
294T_SKIN
IGR3
9_SK
INHC
C1187_BR
EAST
MOR
CPR_
LUNG
HS578T_BRE
AST
OCILY
10_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1581_LUN
GHE
C1A_EN
DOMET
RIUM
JM1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UERA
JI_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMC1
16_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEP3HR
1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESU
PT1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEEB
2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1648_LUN
GJHOS
4_OV
ARY
EB1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEHC
C1395_BR
EAST
MFE
319_EN
DOMET
RIUM
KYSE
450_OE
SOPH
AGUS
DETR
OIT562_U
PPER
_AER
ODIGES
TIVE
_TRA
CTAC
HN_KIDNE
YMFE
280_EN
DOMET
RIUM
KMRC
2_KIDN
EYRE
RFGC
1B_STO
MAC
HNC
IH1568_LUN
GSJSA
1_BO
NENC
IH2052_PLEUR
AMDA
MB157_BRE
AST
SW1573_LUN
GKE
LLY_AU
TONO
MIC_G
ANGL
IAHS
746T_STO
MAC
HHP
AFII_PANC
REAS
KCIMOH
1_PANC
REAS
SKLM
S1_SOF
T_TISS
UEBX
PC3_PANC
REAS
COLO
741_SK
INCA
LU6_LU
NGSN
U398_LIVER
RD_SOF
T_TISS
UEHT
1080_SOF
T_TISS
UENC
IH23_LUN
GMSTO2
11H_
PLEU
RAHC
C15_LU
NGSQ
1_LU
NGC3
A_LIVE
RHC
C44_LU
NGSN
U475_LIVER
HS729_SO
FT_TISSU
EZR
751_BR
EAST
TE1_OE
SOPH
AGUS
NCIH460_LU
NGKN
S62_LU
NGPLCP
RF5_LIVE
RU2
OS_BON
EFU
97_STO
MAC
HHS
840T_U
PPER
_AER
ODIGES
TIVE
_TRA
CTHC
C1954_BR
EAST
KYSE
520_OE
SOPH
AGUS
HS852T_SKIN
LN229_CE
NTRA
L_NE
RVOU
S_SY
STEM
NCIH1792_LUN
G
Paclitaxel
LBH589
17!AAG
Topotecan
Irinotecan
PD!0325901
AZD6244
RAF265
TAE684
AEW541
TKI258
ZD!6474
AZD0530
Lapatinib
Erlotinib
LBW242
PLX4720
Nilotinib
PF2341066
Sorafenib
Nutlin!3
PD!0332991
PHA!665752
L!685458
1. Load feature data and phenotype data into matrix objects. (conceptual)
Cell Lines
Feature Matrix
Cell Lines Sensi.vity Matrix
compo
unds
Copy num
ber
Data
Muta6
on
Data
2. Create matrix aggregating feature data (Synapse workflow)
10
3. Write custom predicBve modeling funcBon. • Includes parameter selecBon procedure. • Will also do first example with a modeling funcBon
that we provide (i.e. elasBc net). 4. Wrap predicBve model in cross-‐validaBon procedure for performance evaluaBon. 5. Output final predicBve model (e.g. biomarkers).
1. Load feature data and phenotype data into R objects.
2. Create matrix aggregating feature data
SIGM
5_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEALLSIL_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
O2_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEEM
2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKC
L22_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMON
OMAC
1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEDE
L_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMHH
ES1_BO
NEJVM3_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH2286_LUN
G697_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEOC
IAML5_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEIM95_STO
MAC
HNU
GC4_STOM
ACH
SW48_LAR
GE_INT
ESTINE
HDQP
1_BR
EAST
TE617T_SOF
T_TISS
UERT
4_UR
INAR
Y_TR
ACT
WM983B_SKIN
COLO
205_LARG
E_INTE
STINE
CHP212_AUT
ONOM
IC_G
ANGL
IAHU
T78_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEOC
IAML2_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKO
52_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEP31FUJ_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEWM88_SKIN
MALME3M_SKIN
SKMEL5_SK
INMELHO
_SKIN
A375_SKIN
IGR3
7_SK
INWM2664_SKIN
COLO
201_LARG
E_INTE
STINE
UACC
62_SKIN
LS411N
_LAR
GE_INT
ESTINE
HT29_LAR
GE_INT
ESTINE
HEPG
2_LIVE
RSW
620_LARG
E_INTE
STINE
OCUM
1_STOM
ACH
OV90_O
VARY
IPC2
98_SKIN
HT144_SK
INCO
LO679_SK
INL363_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKM
S11_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESU
DHL6_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEDO
HH2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEJURK
AT_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMOLT16_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESU
DHL4_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMOL
P8_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKM
M1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKH
M1B_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKP
NSI9S_AU
TONO
MIC_G
ANGL
IAAM
O1_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UECM
K86_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEP12ICH
IKAW
A_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKM
S34_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UERP
MI8402_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKM
S26_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEGR
ANTA519_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESU
DHL8_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKA
SUMI2_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEG4
01_SOF
T_TISS
UEMEC
1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESIMA_AU
TONO
MIC_G
ANGL
IAAZ
521_STOM
ACH
MB157_BRE
AST
DV90_LUN
GES
S1_END
OMET
RIUM
KYM1_SO
FT_TISSU
E8M
GBA_CE
NTRA
L_NE
RVOU
S_SY
STEM
NCIN87_STO
MAC
HNC
IH2170_LUN
GAU
565_BR
EAST
SKMES
1_LU
NGTE
15_O
ESOP
HAGU
SCA
L12T_LUN
GJHH7
_LIVER
KYSE
70_O
ESOP
HAGU
SSN
U16_STOM
ACH
PFEIFFER
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UETE
11_O
ESOP
HAGU
SKY
SE180_OE
SOPH
AGUS
ISHIKA
WAH
ERAK
LIO0
2ER_
ENDO
MET
RIUM
42MGB
A_CE
NTRA
L_NE
RVOU
S_SY
STEM
NCIH1703_LUN
GSC
C25_UP
PER_
AERO
DIGE
STIVE_TR
ACT
CAL27_UP
PER_
AERO
DIGE
STIVE_TR
ACT
SCC9
_UPP
ER_AER
ODIGES
TIVE
_TRA
CTNC
IH2030_LUN
GFADU
_UPP
ER_AER
ODIGES
TIVE
_TRA
CTJHH5
_LIVER
HCC1
806_BR
EAST
A253_SALIVAR
Y_GL
AND
LUDL
U1_LUN
GL33_PANC
REAS
LP1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKG
1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEHE
C6_END
OMET
RIUM
KURA
MOC
HI_O
VARY
NCIH1693_LUN
GF36P_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKA
RPAS
620_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1666_LUN
GCA
L851_BRE
AST
OE21_O
ESOP
HAGU
SSC
ABER
_URINA
RY_TRA
CTHU
PT4_PANC
REAS
LS513_LARG
E_INTE
STINE
SW403_LARG
E_INTE
STINE
HEC1
51_END
OMET
RIUM
TT2609C0
2_TH
YROID
NCIH2122_LUN
GKU
812_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMEG
01_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMDA
MB435S_BR
EAST
BCPAP_TH
YROID
DBTR
G05M
G_CE
NTRA
L_NE
RVOU
S_SY
STEM
8305C_
THYR
OID
WM1799_SKIN
G361_SKIN
K029AX
_SKIN
HDMYZ
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UELO
XIMVI_SKIN
ES2_OV
ARY
SKNA
S_AU
TONO
MIC_G
ANGL
IAPS
N1_PAN
CREA
SSN
U1_STO
MAC
HSW
1990_PAN
CREA
SSW
1417_LAR
GE_INT
ESTINE
NCIH1299_LUN
GNC
IH2087_LUN
GSU
PM2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEEB
C1_LUN
GMKN
45_STO
MAC
HMIAPACA
2_PANC
REAS
22RV
1_PR
OSTATE
WM793_SK
INLU
99_LUN
GA2780_OV
ARY
GCT_SO
FT_TISSU
EHS
944T_SKIN
OE33_O
ESOP
HAGU
SHP
AC_PAN
CREA
SSK
LU1_LU
NGSK
NBE2_AUT
ONOM
IC_G
ANGL
IASU
DHL10_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UERT
112_UR
INAR
Y_TR
ACT
JMSU
1_UR
INAR
Y_TR
ACT
MDA
MB468_BRE
AST
NUGC
3_STOM
ACH
T24_UR
INAR
Y_TR
ACT
639V_U
RINA
RY_TRA
CTISTM
ES2_PLEU
RAKE
97_STO
MAC
HSK
ES1_BO
NEMINO_
HAEM
ATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UECI1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEBL70_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1048_LUN
GOV
CAR8
_OVARY
KMS12BM_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEHT
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEHH
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEIMR3
2_AU
TONO
MIC_G
ANGL
IAA673_BON
ERE
H_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEJHUE
M2_EN
DOMET
RIUM
NCIH1155_LUN
GNC
IH2228_LUN
GKA
RPAS
299_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESK
NSH_
AUTO
NOMIC_G
ANGL
IADM
S114_LUN
GSK
NDZ_AU
TONO
MIC_G
ANGL
IASJRH
30_SOF
T_TISS
UEVM
RCLC
D_LU
NGHG
C27_STOM
ACH
GI1_CE
NTRA
L_NE
RVOU
S_SY
STEM
H4_C
ENTR
AL_N
ERVO
US_SYS
TEM
BL41_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UETC
71_BON
EMG6
3_BO
NELO
UNH9
1_LU
NGTO
V112D_
OVAR
YSA
OS2_BO
NEGL
C82_LU
NGBG
C823_STO
MAC
HHS
683_CE
NTRA
L_NE
RVOU
S_SY
STEM
TCCS
UP_U
RINA
RY_TRA
CTHO
S_BO
NESB
C5_LUN
GDA
OY_C
ENTR
AL_N
ERVO
US_SYS
TEM
OC315_OV
ARY
OC316_OV
ARY
KP1N
_PAN
CREA
SUM
UC3_UR
INAR
Y_TR
ACT
NCIH520_LU
NGKN
S42_CE
NTRA
L_NE
RVOU
S_SY
STEM
LCLC
103H
_LUN
GMPP
89_PLEUR
ASW
1353_BON
ENC
IH522_LU
NGSF
295_CE
NTRA
L_NE
RVOU
S_SY
STEM
HUH1
_LIVER
U118MG_
CENT
RAL_NE
RVOU
S_SY
STEM
HLE_LIVE
RA172_C
ENTR
AL_N
ERVO
US_SYS
TEM
BDCM
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UERP
MI7951_SK
INU9
37_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMJ_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMES
SA_SOF
T_TISS
UEOC
314_OV
ARY
HARA
_LUN
GTE
5_OE
SOPH
AGUS
MFE
296_EN
DOMET
RIUM
1321N1
_CEN
TRAL_N
ERVO
US_SYS
TEM
G402_SOF
T_TISS
UEKY
SE510_OE
SOPH
AGUS
MDA
MB453_BRE
AST
BT549_BR
EAST
HEC2
65_END
OMET
RIUM
SW579_TH
YROID
NCIH1341_LUN
GLN
18_C
ENTR
AL_N
ERVO
US_SYS
TEM
CAL78_BO
NENC
IH211_LU
NGNC
IH1339_LUN
GNC
IH2452_PLEUR
AHL
F_LIVE
RTY
KNU_
OVAR
Y5637_U
RINA
RY_TRA
CTON
CODG
1_OV
ARY
TE9_OE
SOPH
AGUS
HMCB
_SKIN
DU145_PR
OSTATE
NIHO
VCAR
3_OV
ARY
CHL1_SKIN
TOV21G
_OVARY
SKMM2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESN
GM_END
OMET
RIUM
HEC2
51_END
OMET
RIUM
NCIH1915_LUN
GRK
O_LARG
E_INTE
STINE
HCT116_LAR
GE_INT
ESTINE
A2058_SK
INKN
S60_CE
NTRA
L_NE
RVOU
S_SY
STEM
KP4_PANC
REAS
RERF
LCAI_LUN
GPANC
0327_PAN
CREA
SKA
LS1_CE
NTRA
L_NE
RVOU
S_SY
STEM
PK1_PANC
REAS
HEYA8_OV
ARY
8505C_
THYR
OID
PANC
1005_PAN
CREA
SPL45_PAN
CREA
SMCA
S_OV
ARY
HCC7
0_BR
EAST
NCIH3255_LUN
GPC
14_LUN
GHC
C4006_LU
NGHC
C827_LUN
GVM
RCRC
W_KIDNE
YHC
C2935_LU
NGHT
1376_U
RINA
RY_TRA
CTNC
IH1650_LUN
G769P_KIDNE
YKY
SE140_OE
SOPH
AGUS
CALU
3_LU
NGCC
K81_LARG
E_INTE
STINE
C2BB
E1_LAR
GE_INT
ESTINE
NCIH28_PLEUR
ANC
IH727_LU
NGHT
1197_U
RINA
RY_TRA
CTMDA
MB175VII_BR
EAST
NCIH1869_LUN
GKLE_EN
DOMET
RIUM
CORL
105_LU
NGSN
U449_LIVER
EFE184_END
OMET
RIUM
OVSA
HO_O
VARY
HS895T_SKIN
T98G
_CEN
TRAL_N
ERVO
US_SYS
TEM
VMRC
RCZ_KIDN
EYFU
OV1_OV
ARY
CAKI2_KIDN
EYHE
P3B217_LIVER
SKNF
I_AU
TONO
MIC_G
ANGL
IAT84_LARG
E_INTE
STINE
PATU
8902_PAN
CREA
SSN
UC2A_LAR
GE_INT
ESTINE
SNU1
82_LIVER
LS123_LARG
E_INTE
STINE
NCIH1793_LUN
GMCF
7_BR
EAST
NCIH2172_LUN
GBT
474_BR
EAST
ZR7530_BRE
AST
T47D
_BRE
AST
NCIH661_LU
NGNC
IH1563_LUN
GHC
C1569_BR
EAST
JHH6
_LIVER
MDA
MB415_BRE
AST
MEW
O_SK
INHS
229T_LUN
GUA
CC812_BR
EAST
NCIH1373_LUN
GSH
P77_LU
NGEN
_END
OMET
RIUM
WM115_SK
INT3M10_LUN
GNC
IH1944_LUN
GNC
IH647_LU
NGAN
3CA_EN
DOMET
RIUM
RERF
LCMS_LU
NGBF
TC909_KIDN
EYHE
L9217_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1651_LUN
GMKN
74_STO
MAC
HJ82_UR
INAR
Y_TR
ACT
SU8686_PAN
CREA
SSK
HEP1_LIVER
DKMG_
CENT
RAL_NE
RVOU
S_SY
STEM
LC1SQS
F_LU
NGNC
IH226_LU
NGJHOS
2_OV
ARY
EFO2
1_OV
ARY
MDA
MB436_BRE
AST
SNU3
87_LIVER
NCIH2085_LUN
GSK
MEL31_SKIN
KYSE
410_OE
SOPH
AGUS
KE39_STO
MAC
HGC
IY_STO
MAC
HPC
3_PR
OSTATE
CAS1_C
ENTR
AL_N
ERVO
US_SYS
TEM
COV504_O
VARY
KP1N
L_PANC
REAS
SW900_LU
NGSW
1088_C
ENTR
AL_N
ERVO
US_SYS
TEM
SNU4
23_LIVER
MOG
GCCM
_CEN
TRAL_N
ERVO
US_SYS
TEM
KP3_PANC
REAS
NCIH1975_LUN
GYK
G1_C
ENTR
AL_N
ERVO
US_SYS
TEM
SH10TC
_STO
MAC
HNC
IH2023_LUN
GKY
SE150_OE
SOPH
AGUS
GAMG_
CENT
RAL_NE
RVOU
S_SY
STEM
U87M
G_CE
NTRA
L_NE
RVOU
S_SY
STEM
GMS10_CE
NTRA
L_NE
RVOU
S_SY
STEM
NCIH650_LU
NGON
S76_CE
NTRA
L_NE
RVOU
S_SY
STEM
SUIT2_PANC
REAS
SW480_LARG
E_INTE
STINE
SKMEL2_SK
INHC
C56_LARG
E_INTE
STINE
SKMEL30_SKIN
C32_SK
INRV
H421_SKIN
UACC
257_SK
INNC
IH747_LARG
E_INTE
STINE
QGP1_PAN
CREA
SHS
939T_SKIN
HS936T_SKIN
RL952_EN
DOMET
RIUM
NCIH358_LU
NGNC
IH1573_LUN
GNC
IH1355_LUN
GNC
IH322_LU
NGPANC
0203_PAN
CREA
SPK
45H_
PANC
REAS
HS766T_PAN
CREA
SCA
PAN2
_PAN
CREA
SSK
CO1_LARG
E_INTE
STINE
COLO
678_LARG
E_INTE
STINE
KYSE
30_O
ESOP
HAGU
SRK
N_OV
ARY
A549_LUN
GSW
780_UR
INAR
Y_TR
ACT
HMC1
8_BR
EAST
KP2_PANC
REAS
NCIH2009_LUN
GKM
BC2_UR
INAR
Y_TR
ACT
NCIH2444_LUN
GAS
PC1_PANC
REAS
SKMEL24_SKIN
HS695T_SKIN
PK59_PAN
CREA
SPANC
0403_PAN
CREA
SHU
PT3_PANC
REAS
HUCC
T1_BILIARY
_TRA
CTCA
LU1_LU
NGIALM
_LUN
GNC
IH1092_LUN
GHC
C78_LU
NGTO
LEDO
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEOV
TOKO
_OVARY
IGRO
V1_O
VARY
EFO2
7_OV
ARY
JHH4
_LIVER
JHH2
_LIVER
BT20_BRE
AST
KARP
AS422_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEOP
M2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESK
BR3_BR
EAST
NCIH1184_LUN
GNC
IH1694_LUN
GNC
IH810_LU
NGCA
MA1_BRE
AST
EFM19_BRE
AST
SKOV
3_OV
ARY
OVCA
R4_O
VARY
TEN_
ENDO
MET
RIUM
OVMAN
A_OV
ARY
COV318_O
VARY
COLO
699_LU
NGCO
LO320_LARG
E_INTE
STINE
ISTM
ES1_PLEU
RAMKN
7_STOM
ACH
L428_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEA204_SOF
T_TISS
UE786O
_KIDNE
YHS
C2_U
PPER
_AER
ODIGES
TIVE
_TRA
CTHE
C59_EN
DOMET
RIUM
DOV13_OV
ARY
CORL
23_LUN
GGB
1_CE
NTRA
L_NE
RVOU
S_SY
STEM
SF126_CE
NTRA
L_NE
RVOU
S_SY
STEM
HCT15_LARG
E_INTE
STINE
HS739T_BRE
AST
KNS81_CE
NTRA
L_NE
RVOU
S_SY
STEM
KMRC
1_KIDN
EYSW
1271_LUN
GNC
IH441_LU
NGHS
294T_SKIN
IGR3
9_SK
INHC
C1187_BR
EAST
MOR
CPR_
LUNG
HS578T_BRE
AST
OCILY
10_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1581_LUN
GHE
C1A_EN
DOMET
RIUM
JM1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UERA
JI_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMC1
16_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEP3HR
1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESU
PT1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEEB
2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1648_LUN
GJHOS
4_OV
ARY
EB1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEHC
C1395_BR
EAST
MFE
319_EN
DOMET
RIUM
KYSE
450_OE
SOPH
AGUS
DETR
OIT562_U
PPER
_AER
ODIGES
TIVE
_TRA
CTAC
HN_KIDNE
YMFE
280_EN
DOMET
RIUM
KMRC
2_KIDN
EYRE
RFGC
1B_STO
MAC
HNC
IH1568_LUN
GSJSA
1_BO
NENC
IH2052_PLEUR
AMDA
MB157_BRE
AST
SW1573_LUN
GKE
LLY_AU
TONO
MIC_G
ANGL
IAHS
746T_STO
MAC
HHP
AFII_PANC
REAS
KCIMOH
1_PANC
REAS
SKLM
S1_SOF
T_TISS
UEBX
PC3_PANC
REAS
COLO
741_SK
INCA
LU6_LU
NGSN
U398_LIVER
RD_SOF
T_TISS
UEHT
1080_SOF
T_TISS
UENC
IH23_LUN
GMSTO2
11H_
PLEU
RAHC
C15_LU
NGSQ
1_LU
NGC3
A_LIVE
RHC
C44_LU
NGSN
U475_LIVER
HS729_SO
FT_TISSU
EZR
751_BR
EAST
TE1_OE
SOPH
AGUS
NCIH460_LU
NGKN
S62_LU
NGPLCP
RF5_LIVE
RU2
OS_BON
EFU
97_STO
MAC
HHS
840T_U
PPER
_AER
ODIGES
TIVE
_TRA
CTHC
C1954_BR
EAST
KYSE
520_OE
SOPH
AGUS
HS852T_SKIN
LN229_CE
NTRA
L_NE
RVOU
S_SY
STEM
NCIH1792_LUN
G
Paclitaxel
LBH589
17!AAG
Topotecan
Irinotecan
PD!0325901
AZD6244
RAF265
TAE684
AEW541
TKI258
ZD!6474
AZD0530
Lapatinib
Erlotinib
LBW242
PLX4720
Nilotinib
PF2341066
Sorafenib
Nutlin!3
PD!0332991
PHA!665752
L!685458
2. Create matrix aggregating feature data (conceptual)
Cell Lines
Feature Matrix
Cell Lines Sensi.vity Matrix
compo
unds
20,000 gen
e features
3. Predictive modeling functions. (Synapse workflow)
12
3. Write custom predicBve modeling funcBon. • Includes parameter selecBon procedure. • Will also do first example with a modeling funcBon
that we provide (i.e. elasBc net). 4. Wrap predicBve model in cross-‐validaBon procedure for performance evaluaBon. 5. Output final predicBve model (e.g. biomarkers).
1. Load feature data and phenotype data into R objects.
2. Create matrix aggregating feature data
SIGM
5_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEALLSIL_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
O2_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEEM
2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKC
L22_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMON
OMAC
1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEDE
L_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMHH
ES1_BO
NEJVM3_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH2286_LUN
G697_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEOC
IAML5_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEIM95_STO
MAC
HNU
GC4_STOM
ACH
SW48_LAR
GE_INT
ESTINE
HDQP
1_BR
EAST
TE617T_SOF
T_TISS
UERT
4_UR
INAR
Y_TR
ACT
WM983B_SKIN
COLO
205_LARG
E_INTE
STINE
CHP212_AUT
ONOM
IC_G
ANGL
IAHU
T78_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEOC
IAML2_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKO
52_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEP31FUJ_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEWM88_SKIN
MALME3M_SKIN
SKMEL5_SK
INMELHO
_SKIN
A375_SKIN
IGR3
7_SK
INWM2664_SKIN
COLO
201_LARG
E_INTE
STINE
UACC
62_SKIN
LS411N
_LAR
GE_INT
ESTINE
HT29_LAR
GE_INT
ESTINE
HEPG
2_LIVE
RSW
620_LARG
E_INTE
STINE
OCUM
1_STOM
ACH
OV90_O
VARY
IPC2
98_SKIN
HT144_SK
INCO
LO679_SK
INL363_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKM
S11_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESU
DHL6_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEDO
HH2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEJURK
AT_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMOLT16_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESU
DHL4_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMOL
P8_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKM
M1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKH
M1B_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKP
NSI9S_AU
TONO
MIC_G
ANGL
IAAM
O1_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UECM
K86_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEP12ICH
IKAW
A_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKM
S34_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UERP
MI8402_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKM
S26_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEGR
ANTA519_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESU
DHL8_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKA
SUMI2_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEG4
01_SOF
T_TISS
UEMEC
1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESIMA_AU
TONO
MIC_G
ANGL
IAAZ
521_STOM
ACH
MB157_BRE
AST
DV90_LUN
GES
S1_END
OMET
RIUM
KYM1_SO
FT_TISSU
E8M
GBA_CE
NTRA
L_NE
RVOU
S_SY
STEM
NCIN87_STO
MAC
HNC
IH2170_LUN
GAU
565_BR
EAST
SKMES
1_LU
NGTE
15_O
ESOP
HAGU
SCA
L12T_LUN
GJHH7
_LIVER
KYSE
70_O
ESOP
HAGU
SSN
U16_STOM
ACH
PFEIFFER
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UETE
11_O
ESOP
HAGU
SKY
SE180_OE
SOPH
AGUS
ISHIKA
WAH
ERAK
LIO0
2ER_
ENDO
MET
RIUM
42MGB
A_CE
NTRA
L_NE
RVOU
S_SY
STEM
NCIH1703_LUN
GSC
C25_UP
PER_
AERO
DIGE
STIVE_TR
ACT
CAL27_UP
PER_
AERO
DIGE
STIVE_TR
ACT
SCC9
_UPP
ER_AER
ODIGES
TIVE
_TRA
CTNC
IH2030_LUN
GFADU
_UPP
ER_AER
ODIGES
TIVE
_TRA
CTJHH5
_LIVER
HCC1
806_BR
EAST
A253_SALIVAR
Y_GL
AND
LUDL
U1_LUN
GL33_PANC
REAS
LP1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKG
1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEHE
C6_END
OMET
RIUM
KURA
MOC
HI_O
VARY
NCIH1693_LUN
GF36P_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEKA
RPAS
620_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1666_LUN
GCA
L851_BRE
AST
OE21_O
ESOP
HAGU
SSC
ABER
_URINA
RY_TRA
CTHU
PT4_PANC
REAS
LS513_LARG
E_INTE
STINE
SW403_LARG
E_INTE
STINE
HEC1
51_END
OMET
RIUM
TT2609C0
2_TH
YROID
NCIH2122_LUN
GKU
812_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMEG
01_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMDA
MB435S_BR
EAST
BCPAP_TH
YROID
DBTR
G05M
G_CE
NTRA
L_NE
RVOU
S_SY
STEM
8305C_
THYR
OID
WM1799_SKIN
G361_SKIN
K029AX
_SKIN
HDMYZ
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UELO
XIMVI_SKIN
ES2_OV
ARY
SKNA
S_AU
TONO
MIC_G
ANGL
IAPS
N1_PAN
CREA
SSN
U1_STO
MAC
HSW
1990_PAN
CREA
SSW
1417_LAR
GE_INT
ESTINE
NCIH1299_LUN
GNC
IH2087_LUN
GSU
PM2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEEB
C1_LUN
GMKN
45_STO
MAC
HMIAPACA
2_PANC
REAS
22RV
1_PR
OSTATE
WM793_SK
INLU
99_LUN
GA2780_OV
ARY
GCT_SO
FT_TISSU
EHS
944T_SKIN
OE33_O
ESOP
HAGU
SHP
AC_PAN
CREA
SSK
LU1_LU
NGSK
NBE2_AUT
ONOM
IC_G
ANGL
IASU
DHL10_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UERT
112_UR
INAR
Y_TR
ACT
JMSU
1_UR
INAR
Y_TR
ACT
MDA
MB468_BRE
AST
NUGC
3_STOM
ACH
T24_UR
INAR
Y_TR
ACT
639V_U
RINA
RY_TRA
CTISTM
ES2_PLEU
RAKE
97_STO
MAC
HSK
ES1_BO
NEMINO_
HAEM
ATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UECI1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEBL70_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1048_LUN
GOV
CAR8
_OVARY
KMS12BM_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEHT
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEHH
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEIMR3
2_AU
TONO
MIC_G
ANGL
IAA673_BON
ERE
H_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEJHUE
M2_EN
DOMET
RIUM
NCIH1155_LUN
GNC
IH2228_LUN
GKA
RPAS
299_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESK
NSH_
AUTO
NOMIC_G
ANGL
IADM
S114_LUN
GSK
NDZ_AU
TONO
MIC_G
ANGL
IASJRH
30_SOF
T_TISS
UEVM
RCLC
D_LU
NGHG
C27_STOM
ACH
GI1_CE
NTRA
L_NE
RVOU
S_SY
STEM
H4_C
ENTR
AL_N
ERVO
US_SYS
TEM
BL41_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UETC
71_BON
EMG6
3_BO
NELO
UNH9
1_LU
NGTO
V112D_
OVAR
YSA
OS2_BO
NEGL
C82_LU
NGBG
C823_STO
MAC
HHS
683_CE
NTRA
L_NE
RVOU
S_SY
STEM
TCCS
UP_U
RINA
RY_TRA
CTHO
S_BO
NESB
C5_LUN
GDA
OY_C
ENTR
AL_N
ERVO
US_SYS
TEM
OC315_OV
ARY
OC316_OV
ARY
KP1N
_PAN
CREA
SUM
UC3_UR
INAR
Y_TR
ACT
NCIH520_LU
NGKN
S42_CE
NTRA
L_NE
RVOU
S_SY
STEM
LCLC
103H
_LUN
GMPP
89_PLEUR
ASW
1353_BON
ENC
IH522_LU
NGSF
295_CE
NTRA
L_NE
RVOU
S_SY
STEM
HUH1
_LIVER
U118MG_
CENT
RAL_NE
RVOU
S_SY
STEM
HLE_LIVE
RA172_C
ENTR
AL_N
ERVO
US_SYS
TEM
BDCM
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UERP
MI7951_SK
INU9
37_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMJ_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMES
SA_SOF
T_TISS
UEOC
314_OV
ARY
HARA
_LUN
GTE
5_OE
SOPH
AGUS
MFE
296_EN
DOMET
RIUM
1321N1
_CEN
TRAL_N
ERVO
US_SYS
TEM
G402_SOF
T_TISS
UEKY
SE510_OE
SOPH
AGUS
MDA
MB453_BRE
AST
BT549_BR
EAST
HEC2
65_END
OMET
RIUM
SW579_TH
YROID
NCIH1341_LUN
GLN
18_C
ENTR
AL_N
ERVO
US_SYS
TEM
CAL78_BO
NENC
IH211_LU
NGNC
IH1339_LUN
GNC
IH2452_PLEUR
AHL
F_LIVE
RTY
KNU_
OVAR
Y5637_U
RINA
RY_TRA
CTON
CODG
1_OV
ARY
TE9_OE
SOPH
AGUS
HMCB
_SKIN
DU145_PR
OSTATE
NIHO
VCAR
3_OV
ARY
CHL1_SKIN
TOV21G
_OVARY
SKMM2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESN
GM_END
OMET
RIUM
HEC2
51_END
OMET
RIUM
NCIH1915_LUN
GRK
O_LARG
E_INTE
STINE
HCT116_LAR
GE_INT
ESTINE
A2058_SK
INKN
S60_CE
NTRA
L_NE
RVOU
S_SY
STEM
KP4_PANC
REAS
RERF
LCAI_LUN
GPANC
0327_PAN
CREA
SKA
LS1_CE
NTRA
L_NE
RVOU
S_SY
STEM
PK1_PANC
REAS
HEYA8_OV
ARY
8505C_
THYR
OID
PANC
1005_PAN
CREA
SPL45_PAN
CREA
SMCA
S_OV
ARY
HCC7
0_BR
EAST
NCIH3255_LUN
GPC
14_LUN
GHC
C4006_LU
NGHC
C827_LUN
GVM
RCRC
W_KIDNE
YHC
C2935_LU
NGHT
1376_U
RINA
RY_TRA
CTNC
IH1650_LUN
G769P_KIDNE
YKY
SE140_OE
SOPH
AGUS
CALU
3_LU
NGCC
K81_LARG
E_INTE
STINE
C2BB
E1_LAR
GE_INT
ESTINE
NCIH28_PLEUR
ANC
IH727_LU
NGHT
1197_U
RINA
RY_TRA
CTMDA
MB175VII_BR
EAST
NCIH1869_LUN
GKLE_EN
DOMET
RIUM
CORL
105_LU
NGSN
U449_LIVER
EFE184_END
OMET
RIUM
OVSA
HO_O
VARY
HS895T_SKIN
T98G
_CEN
TRAL_N
ERVO
US_SYS
TEM
VMRC
RCZ_KIDN
EYFU
OV1_OV
ARY
CAKI2_KIDN
EYHE
P3B217_LIVER
SKNF
I_AU
TONO
MIC_G
ANGL
IAT84_LARG
E_INTE
STINE
PATU
8902_PAN
CREA
SSN
UC2A_LAR
GE_INT
ESTINE
SNU1
82_LIVER
LS123_LARG
E_INTE
STINE
NCIH1793_LUN
GMCF
7_BR
EAST
NCIH2172_LUN
GBT
474_BR
EAST
ZR7530_BRE
AST
T47D
_BRE
AST
NCIH661_LU
NGNC
IH1563_LUN
GHC
C1569_BR
EAST
JHH6
_LIVER
MDA
MB415_BRE
AST
MEW
O_SK
INHS
229T_LUN
GUA
CC812_BR
EAST
NCIH1373_LUN
GSH
P77_LU
NGEN
_END
OMET
RIUM
WM115_SK
INT3M10_LUN
GNC
IH1944_LUN
GNC
IH647_LU
NGAN
3CA_EN
DOMET
RIUM
RERF
LCMS_LU
NGBF
TC909_KIDN
EYHE
L9217_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1651_LUN
GMKN
74_STO
MAC
HJ82_UR
INAR
Y_TR
ACT
SU8686_PAN
CREA
SSK
HEP1_LIVER
DKMG_
CENT
RAL_NE
RVOU
S_SY
STEM
LC1SQS
F_LU
NGNC
IH226_LU
NGJHOS
2_OV
ARY
EFO2
1_OV
ARY
MDA
MB436_BRE
AST
SNU3
87_LIVER
NCIH2085_LUN
GSK
MEL31_SKIN
KYSE
410_OE
SOPH
AGUS
KE39_STO
MAC
HGC
IY_STO
MAC
HPC
3_PR
OSTATE
CAS1_C
ENTR
AL_N
ERVO
US_SYS
TEM
COV504_O
VARY
KP1N
L_PANC
REAS
SW900_LU
NGSW
1088_C
ENTR
AL_N
ERVO
US_SYS
TEM
SNU4
23_LIVER
MOG
GCCM
_CEN
TRAL_N
ERVO
US_SYS
TEM
KP3_PANC
REAS
NCIH1975_LUN
GYK
G1_C
ENTR
AL_N
ERVO
US_SYS
TEM
SH10TC
_STO
MAC
HNC
IH2023_LUN
GKY
SE150_OE
SOPH
AGUS
GAMG_
CENT
RAL_NE
RVOU
S_SY
STEM
U87M
G_CE
NTRA
L_NE
RVOU
S_SY
STEM
GMS10_CE
NTRA
L_NE
RVOU
S_SY
STEM
NCIH650_LU
NGON
S76_CE
NTRA
L_NE
RVOU
S_SY
STEM
SUIT2_PANC
REAS
SW480_LARG
E_INTE
STINE
SKMEL2_SK
INHC
C56_LARG
E_INTE
STINE
SKMEL30_SKIN
C32_SK
INRV
H421_SKIN
UACC
257_SK
INNC
IH747_LARG
E_INTE
STINE
QGP1_PAN
CREA
SHS
939T_SKIN
HS936T_SKIN
RL952_EN
DOMET
RIUM
NCIH358_LU
NGNC
IH1573_LUN
GNC
IH1355_LUN
GNC
IH322_LU
NGPANC
0203_PAN
CREA
SPK
45H_
PANC
REAS
HS766T_PAN
CREA
SCA
PAN2
_PAN
CREA
SSK
CO1_LARG
E_INTE
STINE
COLO
678_LARG
E_INTE
STINE
KYSE
30_O
ESOP
HAGU
SRK
N_OV
ARY
A549_LUN
GSW
780_UR
INAR
Y_TR
ACT
HMC1
8_BR
EAST
KP2_PANC
REAS
NCIH2009_LUN
GKM
BC2_UR
INAR
Y_TR
ACT
NCIH2444_LUN
GAS
PC1_PANC
REAS
SKMEL24_SKIN
HS695T_SKIN
PK59_PAN
CREA
SPANC
0403_PAN
CREA
SHU
PT3_PANC
REAS
HUCC
T1_BILIARY
_TRA
CTCA
LU1_LU
NGIALM
_LUN
GNC
IH1092_LUN
GHC
C78_LU
NGTO
LEDO
_HAE
MATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEOV
TOKO
_OVARY
IGRO
V1_O
VARY
EFO2
7_OV
ARY
JHH4
_LIVER
JHH2
_LIVER
BT20_BRE
AST
KARP
AS422_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEOP
M2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESK
BR3_BR
EAST
NCIH1184_LUN
GNC
IH1694_LUN
GNC
IH810_LU
NGCA
MA1_BRE
AST
EFM19_BRE
AST
SKOV
3_OV
ARY
OVCA
R4_O
VARY
TEN_
ENDO
MET
RIUM
OVMAN
A_OV
ARY
COV318_O
VARY
COLO
699_LU
NGCO
LO320_LARG
E_INTE
STINE
ISTM
ES1_PLEU
RAMKN
7_STOM
ACH
L428_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEA204_SOF
T_TISS
UE786O
_KIDNE
YHS
C2_U
PPER
_AER
ODIGES
TIVE
_TRA
CTHE
C59_EN
DOMET
RIUM
DOV13_OV
ARY
CORL
23_LUN
GGB
1_CE
NTRA
L_NE
RVOU
S_SY
STEM
SF126_CE
NTRA
L_NE
RVOU
S_SY
STEM
HCT15_LARG
E_INTE
STINE
HS739T_BRE
AST
KNS81_CE
NTRA
L_NE
RVOU
S_SY
STEM
KMRC
1_KIDN
EYSW
1271_LUN
GNC
IH441_LU
NGHS
294T_SKIN
IGR3
9_SK
INHC
C1187_BR
EAST
MOR
CPR_
LUNG
HS578T_BRE
AST
OCILY
10_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1581_LUN
GHE
C1A_EN
DOMET
RIUM
JM1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UERA
JI_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEMC1
16_H
AEMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEP3HR
1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UESU
PT1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEEB
2_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UENC
IH1648_LUN
GJHOS
4_OV
ARY
EB1_HA
EMATOP
OIET
IC_AND
_LYM
PHOID_
TISS
UEHC
C1395_BR
EAST
MFE
319_EN
DOMET
RIUM
KYSE
450_OE
SOPH
AGUS
DETR
OIT562_U
PPER
_AER
ODIGES
TIVE
_TRA
CTAC
HN_KIDNE
YMFE
280_EN
DOMET
RIUM
KMRC
2_KIDN
EYRE
RFGC
1B_STO
MAC
HNC
IH1568_LUN
GSJSA
1_BO
NENC
IH2052_PLEUR
AMDA
MB157_BRE
AST
SW1573_LUN
GKE
LLY_AU
TONO
MIC_G
ANGL
IAHS
746T_STO
MAC
HHP
AFII_PANC
REAS
KCIMOH
1_PANC
REAS
SKLM
S1_SOF
T_TISS
UEBX
PC3_PANC
REAS
COLO
741_SK
INCA
LU6_LU
NGSN
U398_LIVER
RD_SOF
T_TISS
UEHT
1080_SOF
T_TISS
UENC
IH23_LUN
GMSTO2
11H_
PLEU
RAHC
C15_LU
NGSQ
1_LU
NGC3
A_LIVE
RHC
C44_LU
NGSN
U475_LIVER
HS729_SO
FT_TISSU
EZR
751_BR
EAST
TE1_OE
SOPH
AGUS
NCIH460_LU
NGKN
S62_LU
NGPLCP
RF5_LIVE
RU2
OS_BON
EFU
97_STO
MAC
HHS
840T_U
PPER
_AER
ODIGES
TIVE
_TRA
CTHC
C1954_BR
EAST
KYSE
520_OE
SOPH
AGUS
HS852T_SKIN
LN229_CE
NTRA
L_NE
RVOU
S_SY
STEM
NCIH1792_LUN
G
Paclitaxel
LBH589
17!AAG
Topotecan
Irinotecan
PD!0325901
AZD6244
RAF265
TAE684
AEW541
TKI258
ZD!6474
AZD0530
Lapatinib
Erlotinib
LBW242
PLX4720
Nilotinib
PF2341066
Sorafenib
Nutlin!3
PD!0332991
PHA!665752
L!685458
3. Predictive modeling functions. (conceptual)
450 Cell Lines
Feature Matrix
450 Cell Lines Sensi.vity Matrix
24 com
poun
ds
Pred
ic.ve Features
40,000 gen
e features
450 Cell Lines Sensi.ve Refractory
Sensi.vity Vector
Parameter es.ma.on (conceptual) 500
Features
100
Features
20
Features
1 Feature
14
4. Wrap predictive model in cross-validation procedure for performance evaluation.
(Synapse workflow)
15
3. Write custom predicBve modeling funcBon. • Includes parameter selecBon procedure. • Will also do first example with a modeling funcBon
that we provide (i.e. elasBc net). 4. Wrap predicBve model in cross-‐validaBon procedure for performance evaluaBon. 5. Output final predicBve model (e.g. biomarkers).
1. Load feature data and phenotype data into R objects.
2. Create matrix aggregating feature data
Now let’s do it! http://scienceonline.sagebase.org/
16