CELLector
Select Cell Lines
BEM builder
Genomics Guided Selection of Cancer
in vitro
Models
v1.0.3
Tutorial
Code
CELLector R Package
CELLector R Package interactive vignette
User Defined Binary genomic Event Matrices (BEMs)
Select Primary Tumour BEMs file:
Browse...
Select Cell Line BEMs file:
Browse...
Validate and update BEMs
Cancer Type:
BLCA
BRCA
COREAD
HNSC
KIRC
LAML
LGG
LUAD
LUSC
OV
PRAD
SKCM
STAD
THCA
UCEC
Underlying data available at the
GDSC1000 data portal.
Build Search Space
Download Search Space
Representative Cell Line Selection
N. of Cell Lines to Select:
CELLect Cell Lines
Score cell lines
Cell lines SubTypes Map
Signature Length weight (= 1 - n. Patients score weight)
Please cite:
Najgebauer et al. 2018 - CELLector: Genomics Guided Selection of Cancer in vitro Models
Primary Tumours: Subtyping Criteria
Cancer Functional Events (CFEs) to consider:
Mutations in high confidence cancer genes
Recurrently CN altered chromosomal segments
Both
Include Methylation data
Alteration set size:
Global support (%):
Supervised Search Space Construction
1. Define subcohort based on the status of an individual CFE:
ABCB1
ABL2
ACACA
ACAD8
ACO1
ACSL3
ACSL6
ACTB
ACTG1
ACTG2
ACVR1B
ACVR2A
ADAM10
ADCY1
AFF4
AHCTF1
AHNAK
AHR
AKAP9
AKT1
ALK
AMOT
ANK3
APAF1
APC
AQR
ARAP3
ARFGAP1
ARFGAP3
ARFGEF1
ARFGEF2
ARHGAP26
ARHGAP29
ARHGAP35
ARHGEF2
ARHGEF6
ARID1A
ARID1B
ARID2
ARID4A
ARID4B
ARID5B
ARNTL
ASH1L
ASPM
ASXL1
ASXL2
ATF1
ATIC
ATM
ATP6AP2
ATR
ATRX
AXIN1
AXIN2
B2M
BAP1
BAZ2B
BCL11A
BCLAF1
BCOR
BLM
BMPR2
BNC2
BPTF
BRAF
BRCA1
BRCA2
BRWD1
C15orf55
CAD
CAPN7
CARM1
CASP1
CASP8
CAST
CAT
CBFB
CCAR1
CCND1
CCT5
CDC27
CDC73
CDH1
CDK12
CDK4
CDKN1A
CDKN1B
CDKN2A
CEBPA
CEP290
CHD1L
CHD3
CHD4
CHD6
CHD8
CHD9
CHEK2
CIC
CIITA
CLASP2
CLCC1
CLOCK
CLSPN
CLTC
cna1
cna10
cna100
cna101
cna102
cna103
cna104
cna105
cna106
cna107
cna108
cna109
cna11
cna110
cna111
cna112
cna113
cna114
cna115
cna116
cna117
cna118
cna119
cna12
cna120
cna121
cna122
cna123
cna124
cna125
cna126
cna127
cna128
cna129
cna13
cna130
cna131
cna132
cna133
cna134
cna135
cna136
cna137
cna14
cna15
cna16
cna17
cna18
cna19
cna2
cna20
cna21
cna22
cna23
cna24
cna25
cna26
cna27
cna28
cna29
cna3
cna30
cna31
cna32
cna33
cna34
cna35
cna36
cna37
cna38
cna39
cna4
cna40
cna41
cna42
cna43
cna44
cna45
cna46
cna47
cna48
cna49
cna5
cna50
cna51
cna52
cna53
cna54
cna55
cna56
cna57
cna58
cna59
cna6
cna60
cna61
cna62
cna63
cna64
cna65
cna66
cna67
cna68
cna69
cna7
cna70
cna71
cna72
cna73
cna74
cna75
cna76
cna77
cna78
cna79
cna8
cna80
cna81
cna82
cna83
cna84
cna85
cna86
cna87
cna88
cna89
cna9
cna90
cna91
cna92
cna93
cna94
cna95
cna96
cna97
cna98
cna99
CNOT1
CNOT3
CNOT4
CNTNAP1
COL1A1
COPS2
CREBBP
CRNKL1
CRTC3
CSDA
CSDE1
CSNK1G3
CSNK2A1
CTCF
CTNNB1
CTNND1
CTTN
CUL1
CUL2
CUL3
CUX1
CYLD
CYTH4
DDX3X
DDX5
DEPDC1B
DHX15
DHX35
DHX9
DICER1
DIS3
DLG1
DNMT3A
EEF1A1
EEF1B2
EFTUD2
EGFR
EIF1AX
EIF2AK3
EIF2C3
EIF4A2
EIF4G1
EIF4G3
ELF1
ELF3
ELF4
EP300
EPC1
EPHA1
EPHA2
EPHA4
EPHB2
ERBB2
ERBB2IP
ERBB3
ERCC2
EZH2
F8
FAF1
FAM123B
FAM46C
FANCI
FAS
FAT1
FAT2
FBXO11
FBXW7
FCRL4
FGFR1
FGFR2
FGFR3
FIP1L1
FKBP5
FLT3
FMR1
FN1
FOXA1
FOXA2
FOXP1
FRG1
FRG1B
FTSJD1
FUBP1
FUS
FXR1
G3BP1
G3BP2
GATA3
GNA11
GNAI1
GNAS
GNG2
GOLGA5
GPS2
GPSM2
HCFC1
HDAC3
HDAC9
HGF
HLA-A
HLA-B
HLF
HNF1A
HNRPDL
HRAS
HSP90AA1
HSP90AB1
HSPA8
IDH1
IDH2
ING1
INPP4A
INPPL1
IREB2
IRF2
IRF6
IRF7
IRS2
ITGA9
ITSN1
JMY
KALRN
KAT6B
KDM5C
KDM6A
KDR
KEAP1
KIT
KLF4
KLF6
KRAS
LAMA2
LARP4B
LCP1
LDHA
LIMA1
LNPEP
LPHN2
LRP6
LRPPRC
MACF1
MAGI2
MAP2K1
MAP2K4
MAP3K11
MAP3K4
MAP4K1
MAP4K3
MAT2A
MAX
MBD2
MCM3
MCM8
MECOM
MED12
MED17
MED23
MED24
MEF2C
MEN1
MET
MFNG
MGA
MGMT
MKL1
MLH1
MLH3
MLL
MLL2
MLL3
MLLT4
MMP2
MNDA
MSR1
MTOR
MUC20
MYB
MYC
MYCN
MYD88
MYH10
MYH11
MYH14
MYH9
NAP1L1
NCF2
NCK1
NCKAP1
NCOR1
NCOR2
NDRG1
NEDD4L
NF1
NF2
NFATC4
NFE2L2
NKX3-1
NOTCH1
NOTCH2
NPM1
NR2F2
NR4A2
NRAS
NSD1
NTN4
NTRK2
NUP107
NUP93
NUP98
PABPC1
PABPC3
PAX5
PBRM1
PCBP1
PCDH18
PCSK5
PCSK6
PER1
PGR
PHF6
PHLPP1
PIK3C2B
PIK3CA
PIK3CB
PIK3R1
PIK3R3
PIP5K1A
PLCB1
PLCG1
PLXNA1
PLXNB2
POLR2B
POM121
PPM1D
PPP2R1A
PPP2R5A
PPP2R5C
PPP6C
PRKAR1A
PRKCZ
PRPF8
PRRX1
PSIP1
PSMA6
PSMD11
PSME3
PTCH1
PTEN
PTGS1
PTPN11
PTPRF
PTPRU
RAC1
RAD21
RAD23B
RASA1
RASA2
RASGRP1
RB1
RBBP7
RBM10
RBM5
RFC4
RGS3
RHEB
RHOA
RHOT1
RNF43
ROBO2
RPGR
RPL22
RPL5
RPSAP58
RTN4
RUNX1
SACS
SCAI
SEC24D
SEC31A
SETD2
SETDB1
SF3A3
SF3B1
SFPQ
SHMT1
SIN3A
SMAD2
SMAD4
SMARCA1
SMARCA4
SMARCB1
SMC1A
SMO
SMURF2
SOS1
SOS2
SOX17
SOX9
SPOP
SPRR3
SPTAN1
SRGAP1
SRGAP3
STAG1
STAG2
STARD13
STIP1
STK11
STK4
SUZ12
SVEP1
SYK
SYNCRIP
TAF1
TAOK1
TAOK2
TBL1XR1
TBX3
TCF12
TCF4
TCF7L2
TET2
TFDP1
TFDP2
TGFBR2
THRAP3
TJP1
TJP2
TNPO1
TNPO2
TOM1
TP53
TP53BP1
TRERF1
TRIO
TRIP10
TSC1
TXNIP
U2AF1
UPF3B
USP6
VHL
VIM
WASF3
WHSC1
WHSC1L1
WIPF1
WNK1
WNT5A
WT1
XPO1
XRN1
YBX1
ZC3H11A
ZFHX3
ZFP36L1
ZFP36L2
ZMYM2
ZNF292
ZNF638
ZNF750
ZNF814
ZNRF3
wild-type
2. Focus on CFEs in cancer pathways (max 3):
Cell Cycle
DNA Damage Response
Histone Modifier
Other growth / proliferation signaling
PI3K-AKT-MTOR signaling
RAS-RAF-MEK-ERK / JNK signaling
Regulation of ribosomal protein synthesis
RTK signaling family
Survival / cell death regulation signaling
Telomere maintenance
TGF-beta signalling
TP53 signaling
Transcription Factor/Regulation
WNT signaling
3. Consider only cell lines that are:
Microsatellite stable
Microsatellite instable
All
Show CNA id decoding table
Id decoding for recurrently CN altered chromosomal segments (values in Id column can be used in box 1)
Full decoding table available at the
GDSC1000 data portal
Show HyperMeth. id decoding table
Id decoding for informative CpG island hyper-methylations (values in Id column can be used in box 1)
Full decoding table available at the
GDSC1000 data portal
Use Different Color Scheme
Legend
Genomic Binary Event Matrix (BEM) builder
v1.0.1
Tutorial
Code
CELLector R Package
CELLector R Package interactive vignette
Primary tumours
Variant catalogue to consider:
Use curated TCGA data from Iorio et al. 2016
Upload Variants
Cancer Type:
ALL
BLCA
BRCA
CLL
COAD/READ
DLBCL
ESCA
GBM
HNSC
KIRC
LAML
LGG
LIHC
LUAD
LUSC
MB
MM
NB
OV
PA
PAAD
PRAD
SCLC
SKCM
STAD
THCA
UCEC
Genes to consider:
All
Iorio et al. 2016 drivers
CMPs drivers
User defined list
Upload a plain .txt file with Gene identifiers (one per line):
Browse...
Variants to consider:
All
Iorio et al. 2016 variants (COSMIC filtered)
User defined list
Upload a plain .txt file with tab separated [Gene identifier - variant] (one pair per line):
Browse...
Upload the variant catalogue as a plain tab separated .txt file:
Browse...
Make new BEM
BEM file format:
R object
.tsv
Save BEM
in-vitro models
Variant catalogue to consider:
Use Variants Catalogue from Cell Model Passports (CMPs)
Upload Variants
Exclude organoids
Human derived only
Filter based on age at sampling
Gender:
Male
Female
All (including Unknown)
Filter based on etnicity
MSI status:
MSS
MSI
All (including NA)
Filter based on mutation burden
Filter based on ploidy
Tissue:
Adrenal Gland
Biliary Tract
Bladder
Bone
Breast
Central Nervous System
Cervix
Endometrium
Esophagus
Eye
Haematopoietic and Lymphoid
Head and Neck
Kidney
Large Intestine
Liver
Lung
Ovary
Pancreas
Peripheral Nervous System
Placenta
Prostate
Skin
Small Intestine
Soft Tissue
Stomach
Testis
Thyroid
Unknown
Uterus
Vulva
Genes to consider:
All
Iorio et al. 2016 drivers
CMPs drivers
User defined list
Upload a plain .txt file with Gene identifiers (one per line):
Browse...
Variants to consider:
All
Iorio et al. 2016 variants (COSMIC filtered)
User defined list
Upload a plain .txt file with tab separated [Gene identifier - variant] (one pair per line):
Browse...
Upload the variant catalogue as a plain tab separated .txt file:
Browse...
Make new BEM
BEM file format:
R object
.tsv
Save BEM