Comment[ArrayExpressAccession]	E-GEOD-45114
MAGE-TAB Version	1.1													
Public Release Date	2013-03-14
Investigation Title	Transcriptional profiling of HCC vs. Normal liver and Pericancer vs. Normal liver.													
Comment[Submitted Name]	Transcriptional profiling of HCC vs. Normal liver and Pericancer vs. Normal liver.
Experiment Description	Hepatocellular carcinoma (HCC) is one of the most malignant and lethal cancers in the world. Its complex process of molecular pathogenesis indicates that HCC is caused by multiple etiological factors and involves multiple types of genes during its development and progression. In the current study, we performed a microarray analysis on the mRNA transcriptome of HCC (C), peri-cancerous liver (P) and normal liver (N) tissues. After integrating these results with information from the Gene Ontology and KEGG Pathway databases, we analyzed the potential interactions between different genes and constructed an interaction network, and identified the regulator, mediator and effector genes in this interaction network. Three types of tissues: 49 pairs of homogenous human primary hepatocellular carcinoma (Cancer, C) and pericancer liver tissues (Pericancer, P), 10 normal liver tissues (Normal, N). Three-condition experiment, HCC vs. Normal and Pericancer vs. Normal.													
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl												
Person Last Name	Wei	Wei	Lian	Zhang	Li	Gu	Xie	He						
Person First Name	Lin	Lin	Baofeng	Yuannv	Wei	Jianren	Lu	Xianghuo						
Person Email	kylin9wei@gmail.com													
Person Affiliation	Shanghai Cancer Institute													
Person Address	Shanghai Cancer Institute, No.25/Ln.2200, Xie Tu Road, Shanghai, China													
Person Roles	submitter													
Protocol Name	P-GSE45114-1	P-GSE45114-5	P-GSE45114-4	P-GSE45114-2	P-GSE45114-3	P-GSE45114-6								
Protocol Description	ID_REF =  VALUE = Normalized log2 ratio representing Cancer/Normal or Pericancer/Normal	Scanned with a confocal LuxScan scanner and the images obtained were then analyzed using LuxScan 3.0 software (Both from CapitalBio).	Labeled controls and test samples labeled with Cy5-dCTP and Cy3-dCTP were dissolved in 80 M-5L hybridization solution containing 3M-CM-^WSSC, 0.2% SDS, 5M-CM-^WDenhardtM-bM-^@M-^Ys solution and 25% formamide. DNA in hybridization solution was denatured at 95M-bM-^DM-^C for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a CapitalBio BioMixer II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42M-bM-^DM-^C and washed with two consecutive solutions (0.2% SDS, 2M-CM-^W SSC at 42M-bM-^DM-^C for 5 min, and 0.2M-CM-^W SSC for 5 min at room temperature).	Total RNA was extracted using TRIzol reagent (Invitrogen, CA, USA).	EberwineM-bM-^@M-^Ys linear RNA amplification method and subsequent enzymatic reaction	Faint spots (intensity < 400) removed, background subtracted data were normalized by LOWESS program.								
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	labeling	feature_extraction								
Experimental Factor Name	CIRRHOSIS	EDMONSON	MONTH	AGE	ID	SURVIVAL	ENVELOP	400	SEX	RECURRENCE	METASTASIS	TYPE	INVASION	POSITIVE
Experimental Factor Type	cirrhosis	edmonson	month	age	id	survival	envelop	400	sex	recurrence	metastasis	type	invasion	positive
Comment[SecondaryAccession]	GSE45114													
Comment[GEOReleaseDate]	2013-03-14													
Comment[ArrayExpressSubmissionDate]	2013-03-12													
Comment[GEOLastUpdateDate]	2013-03-15													
Comment[AEExperimentType]	transcription profiling by array													
SDRF File	E-GEOD-45114.sdrf.txt