STANDARD_NAME	LIU_BREAST_CANCER
SYSTEMATIC_NAME	M16584
COLLECTION	C2:CGP
MSIGDB_URL	https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/LIU_BREAST_CANCER
NAMESPACE	AFFY_HG_U133
DESCRIPTION_BRIEF	Low abundance transcripts specific for breast cancer.
DESCRIPTION_FULL	Most human cancers are characterized by genetic aberrations accompanied by altered expression and function of numerous genes. Applying genome-wide, microarray gene expression analysis to identify deregulated genes in different tumour types can provide potential gene candidates as diagnostic and prognostic tools and promising targets for drug development. However, the detection of deregulated genes with low levels of expression remains a major challenge. In this study, we have designed a strategy, termed modified suppression subtractive hybridization (mSSH), to identify genes encoding rare transcripts. The strategy entails incorporating the T(7)-promoter sequence at the 5' end of the noncoding cDNA strand during first strand cDNA synthesis to generate unidirectional antisense RNA from the resultant cDNA following conventional SSH. These transcripts are subsequently analysed by Affymetrix oligonucleotide gene arrays. Here, we have used five hepatocellular carcinoma (HCC), five breast carcinoma and four nasopharyngeal carcinoma (NPC) biopsies separately as testers and their corresponding normal biopsies as drivers to enrich for low abundance tumour type-specific transcripts. The total detectable number of probe sets following mSSH was reduced almost 10-fold in comparison to those detected for the same resected tumour tissues without undergoing subtraction, thus yielding a subtraction efficacy of over 90%. Using this experimental approach, we have identified 48 HCC-specific, 45 breast carcinoma-specific, and 83 NPC-specific genes. In addition, 115 genes were upregulated in all the three cancer types. When compared to gene-profiling data obtained without mSSH, the majority of these identified transcripts were of low abundance in the original cancer tissues. mSSH can therefore serve as a comprehensive molecular strategy for pursuing functional genomic studies of human cancers.
PMID	18332864
GEOID	
AUTHORS	Liu BH,Goh CH,Ooi LL,Hui KM
CONTRIBUTOR	Jessica Robertson
CONTRIBUTOR_ORG	MSigDB Team
EXACT_SOURCE	Supplementary Data 2B
FILTERED_BY_SIMILARITY	
EXTERNAL_NAMES_FOR_SIMILAR_TERMS	
EXTERNAL_DETAILS_URL	
SOURCE_MEMBERS	200019_s_at,200838_at,200855_at,203694_s_at,208439_s_at,208974_x_at,209191_at,211416_x_at,211600_at,211628_x_at,211921_x_at,211945_s_at,211956_s_at,213356_x_at,218211_s_at,218625_at,221505_at,221717_at,224549_x_at,225069_at,225558_at,225841_at,226097_at,227330_x_at,229083_at,229586_at,229748_x_at,231595_at,232016_at,233008_at,233912_x_at,234496_x_at,234921_at,235399_at,236479_at,236699_at,240950_s_at,241735_at,242131_at,242240_at,242819_at,244481_at,244618_at,44673_at
GENE_SYMBOLS	FAU,,NCOR1,DHX16,,KPNB1,TUBB6,GGTLC1,MT-ND5,FTH1P5,PTMA,ITGB1,EIF1,HNRNPA1,MLPH,NRN1,ANP32E,,,PCYT1A,GIT2,HENMT1,FNDC5,,HNRNPA0,CHD9,,IRAG1-AS1,FAN1,FAM242E,,NYX,ZNF470,ERCC2,SCN8A,,KASH5,RASSF8,,,,,,SIGLEC1
FOUNDER_NAMES