STANDARD_NAME	LIN_MELANOMA_COPY_NUMBER_UP
SYSTEMATIC_NAME	M346
COLLECTION	C2:CGP
MSIGDB_URL	https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/LIN_MELANOMA_COPY_NUMBER_UP
NAMESPACE	HUMAN_GENE_SYMBOL
DESCRIPTION_BRIEF	Candidate genes in significant regions of chromosomal copy number gains in a panel of melanoma samples.
DESCRIPTION_FULL	The classification of human tumors based on molecular criteria offers tremendous clinical potential; however, discerning critical and druggable effectors on a large scale will also require robust experimental models reflective of tumor genomic diversity. Here, we describe a comprehensive genomic analysis of 101 melanoma short-term cultures and cell lines. Using an analytic approach designed to enrich for putative driver events, we show that cultured melanoma cells encompass the spectrum of significant genomic alterations present in primary tumors. When annotated according to these lesions, melanomas cluster into subgroups suggestive of distinct oncogenic mechanisms. Integrating gene expression data suggests novel candidate effector genes linked to recurrent copy gains and losses, including both phosphatase and tensin homologue (PTEN)-dependent and PTEN-independent tumor suppressor mechanisms associated with chromosome 10 deletions. Finally, sample-matched pharmacologic data show that FGFR1 mutations and extracellular signal-regulated kinase (ERK) activation may modulate sensitivity to mitogen-activated protein kinase/ERK kinase inhibitors. Genetically defined cell culture collections therefore offer a rich framework for systematic functional studies in melanoma and other tumors.
PMID	18245465
GEOID	GSE2631
AUTHORS	Lin WM,Baker AC,Beroukhim R,Winckler W,Feng W,Marmion JM,Laine E,Greulich H,Tseng H,Gates C,Hodi FS,Dranoff G,Sellers WR,Thomas RK,Meyerson M,Golub TR,Dummer R,Herlyn M,Getz G,Garraway LA
CONTRIBUTOR	Jessica Robertson
CONTRIBUTOR_ORG	MSigDB Team
EXACT_SOURCE	Table 1
FILTERED_BY_SIMILARITY	
EXTERNAL_NAMES_FOR_SIMILAR_TERMS	
EXTERNAL_DETAILS_URL	
SOURCE_MEMBERS	AP3S2,ARL4A,ARNT,ATP9A,BRAF,C6orf146,C6orf201,C8orf32,CCND1,CDC42SE1,CDYL,COPG2,CPA1,CTNND2,DDX11,DERL1,DNAH5,DNM1L,ECM1,ENSA,EP300,FADD,FAM60A,FAM63A,FARS2,FGF19,FGF3,FGF4,FLJ42258,IDH2,IQGAP1,KIAA1618,KLF14,KRAS,KU-MEL-3,LASS2,LYRM4,MEST,MGC15523,MITF,MKRN1,MLLT11,MRPL9,MRPS35,MYC,NAGA,NDUFB2,NFATC2,ORAOV1,PECI,PIK4CB,PIP5K1A,PMM1,POGZ,POLG,PRPF4B,PRUNE,PSMB4,PSMD4,RFX5,RNF139,RPP40,SALL4,SCIN,SETDB1,TARSL1,TBC1D16,TMEM16A,TRIO,TSGA14,WDR67,YARS2,ZFP64
GENE_SYMBOLS	AP3S2,ARL4A,ARNT,ATP9A,BRAF,FAM217A,TEX56P,NTAQ1,CCND1,CDC42SE1,CDYL,COPG2,CPA1,CTNND2,DDX11,DERL1,DNAH5,DNM1L,ECM1,ENSA,EP300,FADD,SINHCAF,MINDY1,FARS2,FGF19,FGF3,FGF4,,IDH2,IQGAP1,RNF213,KLF14,KRAS,KU-MEL-3,CERS2,LYRM4,MEST,SLC38A10,MITF,MKRN1,MLLT11,MRPL9,MRPS35,MYC,NAGA,NDUFB2,NFATC2,LTO1,ECI2,PI4KB,PIP5K1A,PMM1,POGZ,POLG,PRP4K,PRUNE1,PSMB4,PSMD4,RFX5,RNF139,RPP40,SALL4,SCIN,SETDB1,TARS2,TBC1D16,ANO1,TRIO,CEP41,TBC1D31,YARS2,ZFP64
FOUNDER_NAMES