Investigation Title	Transcription profiling of human normal prostate tissue free of any pathological alteration	
Comment[Submitted Name]	Expression data from Normal Prostate Tissue free of any pathological alteration	
Experimental Design	unknown_experiment_design_type	transcription profiling by array	
Experimental Design Term Source REF		EFO	
Comment[ArrayExpressReleaseDate]	2008-06-15	
Comment[SecondaryAccession]	GSE6604	
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressAccession]	E-GEOD-6604	
Comment[MAGETAB TimeStamp_Version]	2011-01-23 00:45:58 Last Changed Rev: 14857	
Experimental Factor Name	
Experimental Factor Type	
Experimental Factor Term Source REF	
Person Last Name	Monzon	
Person First Name	Federico Alberto	
Person Mid Initials	
Person Email	monzonfa@upmc.edu	
Person Phone	
Person Fax	
Person Address	Clinical Genomics Facility,Pathology,University of Pittsburgh,5230 Centre Ave., WG22,Pittsburgh,15232,USA	
Person Affiliation	University of Pittsburgh	
Person Roles	submitter	
Person Roles Term Source REF		
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2008-06-15	
PubMed ID	17430594	
Publication DOI	17430594	
Publication Author List	Uma R Chandran, Changqing Ma, Rajiv Dhir, Michelle Bisceglia, Maureen Lyons-Weiler, Wenjing Liang, George Michalopoulos, Michael Becich, Federico A Monzon	
Publication Title	Gene expression profiles of prostate cancer reveal involvement of multiple molecular pathways in the metastatic process.	
Publication Status	journal_article	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	Prostate cancer is characterized by heterogeneity in the clinical course that often does not to correlate with morphologic features of the tumor. Metastasis reflects the most adverse outcome of prostate cancer, and to date there are no reliable morphologic features or serum biomarkers that can reliably predict which patients are at higher risk of developing metastatic disease. Understanding the differences in the biology of metastatic and organ confined primary tumors is essential for developing new prognostic markers and therapeutic targets. Using Affymetrix oligonucleotide arrays, we analyzed gene expression profiles of 24 androgen-ablation resistant metastatic samples obtained from 4 patients and a previously published dataset of 64 primary prostate tumor samples. Differential gene expression was analyzed after removing potentially uninformative stromal genes, addressing the differences in cellular content between primary and metastatic tumors. The metastatic samples are highly heterogeneous in expression; however, differential expression analysis shows that 415 genes are upregulated and 364 genes are downregulated at least 2 fold in every patient with metastasis. The expression profile of metastatic samples reveals changes in expression of a unique set of genes representing both the androgen ablation related pathways and other metastasis related gene networks such as cell adhesion, bone remodeling and cell cycle. The differentially expressed genes include metabolic enzymes, transcription factors such as Forkhead Box M1 (FoxM1) and cell adhesion molecules such as Osteopontin (SPP1). We hypothesize that these genes have a role in the biology of metastatic disease and that they represent potential therapeutic targets for prostate cancer. Experiment Overall Design: Using Affymetrix oligonucleotide arrays, we analyzed gene expression profiles of 24 androgen-ablation resistant metastatic samples obtained from 4 patients and a previously published dataset of 64 primary prostate tumor samples. Differential gene expression was analyzed after removing potentially uninformative stromal genes, addressing the differences in cellular content between primary and metastatic tumors.	
Protocol Name	P-G6604-1	P-G6604-3	P-G6604-2	Affymetrix:Protocol:Hybridization-Unknown	P-AFFY-6	
Protocol Type	specified_biomaterial_action	nucleic_acid_extraction	labeling	hybridization	feature_extraction	
Protocol Description	Donor prostate tissues were obtained at the time of organ donation in brain-dead men. Samples were collected from peripheral zone of the prostate gland with at least 60% glandular components and free of any pathological alteration.	Total RNA was extracted with Qiagen Rneasy kit according to the manufacturer's instructions.	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).	Title: Affymetrix Generic Hybridization. Description: 	Title: Affymetrix CEL analysis. Description: 	
Protocol Parameters	
Protocol Hardware	
Protocol Software				MicroArraySuite 5.0	MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF				mo	
SDRF File	E-GEOD-6604.sdrf.txt	
Term Source Name	mo	The MGED Ontology	ArrayExpress	EFO	The MGED Ontology	mo	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version