A community challenge for a pancancer drug mechanism of action inference from perturbational profile data

. 2022 Jan 18;3(1):100492. doi: 10.1016/j.xcrm.2021.100492

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins

AEE788	SelleckChem	S1486
Afatinib	SelleckChem	S1011
AZD5363	SelleckChem	S8019
Bafetinib	SelleckChem	S1369
Bosutinib	SelleckChem	S1014
Cabozantinib	SelleckChem	S1119
Cediranib	SelleckChem	S1017
Crenolanib	SelleckChem	S2730
Crizotinib	SelleckChem	S1068
Dacomitinib	SelleckChem	S2727
Dasatinib	SelleckChem	S1021
Dovitinib	SelleckChem	S1018
Foretinib	SelleckChem	S1111
Gefitinib	SelleckChem	S1025
Icotinib	SelleckChem	S2922
Imatinib	SelleckChem	S2475
KW2449	SelleckChem	S2158
Lapatinib	SelleckChem	S2111
Linifanib	SelleckChem	S1003
MGCD365	SelleckChem	S1361
MK2206	SelleckChem	S1078
Neratinib	SelleckChem	S2150
Nilotinib	SelleckChem	S1033
Osimertinib	SelleckChem	S7297
Ponatinib	SelleckChem	S1490
Quizartinib	SelleckChem	S1526
Regorafenib	SelleckChem	S1178
Sorafenib	SelleckChem	S1040
Sunitinib	SelleckChem	S1042
Tivantinib	SelleckChem	S2753
Vandetanib	SelleckChem	S1046
Varlitinib	SelleckChem	S2755

Critical commercial assays

CellTiter-Glo Luminescent Viability Assay	Promega	G7570

Deposited data

PANACEA gene expression profiles.	This paper	GEO: GSE186341

Experimental models: Cell lines

AsPC-1	ATCC	ATCC Cat# CRL-1682; RRID:CVCL_0152
DU 145	ATCC	ATCC Cat# HTB-81; RRID:CVCL_0105
EFO-21	DSMZ	DSMZ Cat# ACC-235; RRID:CVCL_0029
HCC1143	ATCC	ATCC Cat# CRL-2321; RRID:CVCL_1245
HF2597	Henry Ford	N/A
HSTS	Broad	RRID:CVCL_L296
KRJ1	Califano Lab	RRID:CVCL_8886
LNCaP	ATCC	ATCC Cat# CRL-1740; RRID:CVCL_1379
NCI-H1793	ATCC	ATCC Cat# CRL-5896; RRID:CVCL_1496
PANC-1	ATCC	ATCC Cat# CRL-1469; RRID:CVCL_0480
U-87 MG	ATCC	ATCC Cat# HTB-14; RRID:CVCL_0022

Software and algorithms

STAR aligner, 2.5.2b	Dobin et al.⁵⁷	https://github.com/alexdobin/STAR
Limma 3.48.1	Ritchie et al.⁵⁸	https://bioconductor.org/packages/release/bioc/html/limma.html
DESeq2	Love et al.⁵⁹	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
ComBat	Johnson et al.⁶⁰	https://bioconductor.org/packages/release/bioc/html/sva.html
Analysis code	This paper	https://github.com/Sage-Bionetworks-Challenges/CTD2-Panacea-Challenge