ONTOLOGY SOURCE REFERENCE
Term Source Name	"mo"	"The MGED Ontology"	"ArrayExpress"	"EFO"	"CHEBI"	"NCBITaxon"	"BTO"	"NCIt"	"DOID"	"XCO"	
Term Source File	"http://mged.sourceforge.net/ontologies/MGEDontology.php"	"http://www.ebi.ac.uk/arrayexpress"	"http://www.ebi.ac.uk/efo/"	""	"http://bioportal.bioontology.org/ontologies/50526"	"http://bioportal.bioontology.org/ontologies/47845"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO"	"http://bioportal.bioontology.org/ontologies/50586"	"http://bioportal.bioontology.org/ontologies/50310"	"http://bioportal.bioontology.org/ontologies/50514"	
Term Source Version	""	""	""	""	"50526"	"47845"	"Jun 2010"	"50586"	"50310"	"50514"	
Term Source Description	""	""	""	""	"Chemical Entities of Biological Interest Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"BRENDA tissue / enzyme source"	"National Cancer Institute Thesaurus"	"Human Disease Ontology"	"Experimental Conditions Ontology"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-11237"
Study Title	"Transcription profiling of human colorectal adenocarcinoma patients after Celecoxib pre-treatment"
Study Description	"23 patients. 11 received 400 mg celecoxib 2x/day for 7d prior to surgical resection of colorectal adenocarcinoma, followed by transcriptional profiling of resected tumors. (12 no-drug controls.) [original description: Pharmacological inhibition of cyclooxygenase-2 (COX-2) is being explored as a chemotherapeutic option because COX-2 protein expression is often elevated in many cancers. Cancer cells treated with COX-2 inhibitors, such as the selective COX-2 inhibitor celecoxib, show growth inhibition and the induction of apoptosis, through alterations in inflammatory processes, angiogenesis, cell adhesion and transforming growth factor beta (TGF-beta) signaling. This study was conducted to determine if the same processes are relevant to celecoxib's effects on human colorectal adenocarcinomas treated in vivo. A cohort of 23 patients with primary colorectal adenocarcinomas was randomized to receive a 7-day course of celecoxib (400 mg b.i.d.) or no drug prior to surgical resection. Gene expression profiling was performed on resected adenocarcinomas from patients with and without celecoxib pre-treatment. Using fold change (>1.5) and p-value (<0.05) cut-offs, 190 genes were differentially expressed between adenocarcinomas from patients receiving celecoxib and those that did not. Of the differentially expressed genes, multiple genes involved in cellular lipid and glutathione metabolism showed decreased expression levels in celecoxib pre-treated samples; changes associated with diminished cellular proliferation. Other observed gene expression changes consistent with reduced proliferation include: altered expression of genes involved in cell adhesion (including collagen, laminin, von Willebrand factor and tenascin C), increased expression of inflammatory modulators (including interleukin-6, S100 calcium binding protein A8, and several chemokines) and decreased expression of the pro-angiogenic gene, angiogenin. Celecoxib pre-treatment for 7 days in vivo is associated with alterations in colorectal adenocarcinoma gene expression which are suggestive of diminished cellular proliferation. Experiment Overall Design: Patients undergoing surgical resection of histologically proven primary colorectal adenocarcinomas were consented for participation in the study. The patients enrolled in this study were randomized to receive either 400 mg celecoxib two times per day (n=11) or no COX-2 inhibitor (n=12) for 7 days prior to surgical resection. Total RNA (5 ug) from each sample was converted to double stranded cDNA using a dT-T7 promoter primer. The double stranded cDNA was then used as a template to synthesize biotinylated RNA, which was fragmented and hybridized to the Affymetrix HG_U95av2 microarray chip using Affymetrix's labeling and hybridization protocol. Experiment Overall Design: The array data was imported into GeneSpring GX 7.3 using the GC-RMA file preprocessor. The data was normalized by: (1) setting all expression measurements <0.01 to 0.01, (2) a per chip normalization to the 50th percentile, and (3) a per gene normalization to the median value across all chips.]"
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
Study Submission Date	""
Study Public Release Date	"2008-10-25"
Study File Name	"s_E-GEOD-11237_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"unknown_experiment_design_type"	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"18653328"
Study Publication DOI	"18653328"
Study Publication Author List	"James Todd Auman, Robert Church, Soo-Youn Lee, Mark A Watson, James W Fleshman, Howard L McLeod"
Study Publication Title	"Celecoxib pre-treatment in human colorectal adenocarcinoma patients is associated with gene expression alterations suggestive of diminished cellular proliferation."
Study Publication Status	"journal_article"
Study Publication Status Term Accession Number	""
Study Publication Status Term Source REF	"The MGED Ontology"
STUDY FACTORS
Study Factor Name	"tumor site"	"NSAID treatment"	"tumor type"	"NSAID dosage"
Study Factor Type	"organ"	"treatment"	"tumor type"	"dosage"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-11237_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-G11237-1"	"P-G11237-3"	"P-G11237-2"	"hyb"
Study Protocol Type	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"	"hybridization protocol"
Study Protocol Type Term Accession Number	""	""	""	"efo:EFO_0003790"
Study Protocol Type Term Source REF	""	""	""	"EFO"
Study Protocol Description	"Patients undergoing surgical resection of histologically proven primary colorectal adenocarcinomas were consented for participation in the study.  The patients enrolled in this study were randomized to receive either 400 mg celecoxib two times per day (n=11) or no COX-2 inhibitor (n=12) for 7 days prior to surgical resection."	"Total RNA was isolated from surgically resected, histologically confirmed colorectal primary adenocarcinomas using a TRIzol RNA isolation kit (Invitrogen, Carlsbad, CA) according to the manufacturer's recommended protocol at the Siteman Cancer Center Tissue Procurement Core (St. Louis, MO)."	"standard Affymetrix protocol"	"***INSERT HYBRIDIZATION PROTOCOL HERE***"
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STUDY CONTACTS
Study Person Last Name	"Auman"
Study Person First Name	"James Todd"
Study Person Mid Initials	""
Study Person Email	"auman@niehs.nih.gov"
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Study Person Address	"National Center for Toxicogenomics, National Institute of Environmental Health Sciences, 111 T.W. Alexander Dr., Research Triangle Park, 27709, USA"
Study Person Affiliation	"National Institute of Environmental Health Sciences"
Study Person Roles	"submitter"
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