STANDARD_NAME	IVANOV_MUTATED_IN_COLON_CANCER
SYSTEMATIC_NAME	M5989
COLLECTION	C2:CGP
MSIGDB_URL	https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/IVANOV_MUTATED_IN_COLON_CANCER
NAMESPACE	HUMAN_GENE_SYMBOL
DESCRIPTION_BRIEF	Genes mutated in colon cancer cell lines, identified using the GINI method described in the paper.
DESCRIPTION_FULL	Inhibition of the nonsense-mediated decay (NMD) mechanism in cells results in stabilization of transcripts carrying premature translation termination codons. A strategy referred to as gene identification by NMD inhibition (GINI) has been proposed to identify genes carrying nonsense mutations. Genes containing frameshift mutations in colon cancer cell line have been identified using a modified version of GINI. To increase the efficiency of identifying mutant genes using GINI, we have now further improved the strategy. In this approach, inhibition of NMD with emetine is complemented with inhibiting NMD by blocking the phosphorylation of the hUpf1 protein with caffeine. In addition, to enhance the GINI strategy, comparing mRNA level alterations produced by inhibiting transcription alone or inhibiting transcription together with NMD following caffeine pretreatment were used for the efficient identification of false positives produced as a result of stress response to NMD inhibition. To demonstrate the improved efficiency of this approach, we analysed colon cancer cell lines showing microsatellite instability. Bi-allelic inactivating mutations were found in the FXR1, SEC31L1, NCOR1, BAT3, PHF14, ZNF294, C19ORF5 genes as well as genes coding for proteins with yet unknown functions.
PMID	17086209
GEOID	GSE5486
AUTHORS	Ivanov I,Lo KC,Hawthorn L,Cowell JK,Ionov Y
CONTRIBUTOR	Leona Saunders
CONTRIBUTOR_ORG	MSigDB Team
EXACT_SOURCE	Table 2
FILTERED_BY_SIMILARITY	
EXTERNAL_NAMES_FOR_SIMILAR_TERMS	
EXTERNAL_DETAILS_URL	
SOURCE_MEMBERS	B2M,BAT3,BPY2IP1,CTNND1,FXR1,MARCKS,MSH3,NCOR1,PHF14,RBM35A,RHAMM,RNF43,ZNF294
GENE_SYMBOLS	B2M,BAG6,MAP1S,CTNND1,FXR1,MARCKS,MSH3,NCOR1,PHF14,ESRP1,HMMR,RNF43,LTN1
FOUNDER_NAMES