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Copy pathHistologyCellMap
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HistologyCellMap
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//each matching keyword and its reference cell lines must be defined in CellNamesDict
Biliary-AdenoCA=Biliary
Bladder-TCC=Bladder
Bone-Osteosarc=Bone
Bone-Epith=Bone
Bone-Cart=Bone
Breast-AdenoCa=Breast
Breast-LobularCa=Breast
Breast-DCIS=Breast
Cervix-SCC=Cervix
Cervix-AdenoCA=Cervix
Lymph-CLL=Lymphocyte
Lymph-BNHL=Lymphnode
Lymph-NOS=Lymphnode
Myeloid-MPN=Lymphoblast
Myeloid-MDS=Lymphoblast
Myeloid-AML=Myeloid
Eso-AdenoCa=Esophagus
Stomach-AdenoCA=Gastric
CNS-GBM=CNS-glial
CNS-Oligo=CNS-oligo
//Ca9-22,HO-1-u-1,HSC-3,SAS: oral squamous cell carcinoma cell line
Kidney-ChRCC=Kidney
Kidney-RCC=Kidney
Liver-HCC=Liver
Lung-AdenoCA=Lung-epithelial
Lung-SCC=Lung-squamous
Skin-Melanoma=Skin
Head-SCC=Head-squamous
Ovary-AdenoCA=Ovary
Panc-AdenoCA=Pancreas
Panc-Endocrine=Pancreas
CNS-Medullo=Brain
CNS-PiloAstro=Brain
Prost-AdenoCA=Prostate
ColoRect-AdenoCA=Colon
Bone-Leiomyo=Bone-epithelial
Thy-AdenoCA=Thyroid
Uterus-AdenoCA=Uterus
###Old values are below
Biliary-AdenoCA=TGBC14TKB,TGBC2TKB
Bladder-TCC=UT189,TGBC14TKB,TGBC2TKB
Bone-Osteosarc=osteoblast,U2OS,HS-Os-1,Hs
Bone-Epith=osteoblast,U2OS,HS-Os-1,Hs
Bone-Cart=osteoblast,U2OS,HS-Os-1,Hs
Breast-AdenoCa=MCF-7,T47D,MCF 10A,HMEC,MCF7,MDA-MB-453,Mcf7
Breast-LobularCa=MCF-7,T47D,MCF 10A,HMEC,MCF7,MDA-MB-453,Mcf7
Breast-DCIS=MCF-7,T47D,MCF 10A,HMEC,MCF7,MDA-MB-453,Mcf7
//some LIRI-JP have been classified as Biliary-AdenoCA
Cervix-SCC=HeLa-S3,HeLa,ME-180,D98-AH2,HCSC-1,Helas3
Cervix-AdenoCA=HeLa-S3,HeLa,ME-180,D98-AH2,HCSC-1,Helas3
Lymph-CLL=GM12878,SKW-3,Gm12878
Lymph-BNHL=GM12878,Gm12878,CTB-1,MLMA
Lymph-NOS=GM12878,Gm12878,CTB-1,MLMA
Myeloid-MPN=K562,KBM7
Myeloid-MDS=K562,KBM7
Myeloid-AML=K562,KG-1,Kasumi-1,Kasumi-3,Kasumi-6,M-MOK,MKPL-1,NKM-1,NOMO-1,THP-1,U-937,EEB,EoL-1,EoL-3,F-36E,F-36P,FKH-1,HL60,HYT-1
Eso-AdenoCa=epithelial cell of esophagus,FHs
Stomach-AdenoCA=Gastric,GSS,AZ521,MKN1,MKN45
CNS-GBM=astrocyte,T98G,A172
//Ca9-22,HO-1-u-1,HSC-3,SAS: oral squamous cell carcinoma cell line
Kidney-ChRCC=HEK293,HEK293/SLAM,Kidney_curated
Kidney-RCC=HEK293,OS-RC-2,TUHR10TKB,Kidney_curated
CNS-Oligo=astrocyte,GI-1
Liver-HCC=HepG2,Hepg2
Lung-AdenoCA=A549,IMR-90,IMR90,Imr90,NCI-H441,PC-14
Lung-SCC=A549,IMR-90,IMR90,Imr90,LC-1F,EBC-1
Skin-Melanoma=keratinocyte,NHEK,Nhek,G-361
Head-SCC=SalivaryCell,ThyroidCell,Ca9-22,HO-1-u-1,HSC-3,SAS
Ovary-AdenoCA=Ovary,SK-OV-3-R
Panc-AdenoCA=Panc1,NOR-P1,Pancreas_curated
Panc-Endocrine=Panc1,NOR-P1,Pancreas_curated
CNS-Medullo=SK-N-SH,Sknsh
CNS-PiloAstro=SK-N-SH,Sknsh
Prost-AdenoCA=LNCaP clone FGC,DU145,PC-3,Prostate_curated
ColoRect-AdenoCA=HCT116,COLO-320,CACO-2,TT1TKB
//HS-ES-1: epithelioid sarcoma cell line
Bone-Leiomyo=HS-ES-1
Thy-AdenoCA=SalivaryCell,ThyroidCell,TCO-1,KHM-5M
Uterus-AdenoCA=Ishikawa,urothelium cell line,OMC-2
//LAML-US=K562,KG-1,Kasumi-1,Kasumi-3,Kasumi-6,M-MOK,MKPL-1,NKM-1,NOMO-1,THP-1,U-937,EEB,EoL-1,EoL-3,F-36E,F-36P,FKH-1,HL60,HYT-1