ONTOLOGY SOURCE REFERENCE Term Source Name "CHEBI" "BTO" "CLO" "EFO" "PATO" "XCO" "MESH" "UO" Term Source File "http://data.bioontology.org/ontologies/CHEBI" "http://data.bioontology.org/ontologies/BTO" "http://data.bioontology.org/ontologies/CLO" "http://data.bioontology.org/ontologies/EFO" "http://data.bioontology.org/ontologies/PATO" "http://data.bioontology.org/ontologies/XCO" "http://data.bioontology.org/ontologies/MESH" "http://data.bioontology.org/ontologies/UO" Term Source Version "78" "20" "39" "111" "160" "33" "5" "42" Term Source Description "Chemical Entities of Biological Interest Ontology" "BRENDA Tissue and Enzyme Source Ontology" "Cell Line Ontology" "Experimental Factor Ontology" "Phenotypic Quality Ontology" "Experimental Conditions Ontology" "Medical Subject Headings" "Units of Measurement Ontology" INVESTIGATION Investigation Identifier "" Investigation Title "" Investigation Description "" Investigation Submission Date "" Investigation Public Release Date "" Comment [Created with configuration] "" Comment [Last Opened With Configuration] "" Comment[Created With Configuration] "" Comment[Last Opened With Configuration] "" INVESTIGATION PUBLICATIONS Investigation PubMed ID "" Investigation Publication DOI "" Investigation Publication Author List "" Investigation Publication Title "" Investigation Publication Status "" Investigation Publication Status Term Accession Number "" Investigation Publication Status Term Source REF "" INVESTIGATION CONTACTS Investigation Person Last Name "" Investigation Person First Name "" Investigation Person Mid Initials "" Investigation Person Email "" Investigation Person Phone "" Investigation Person Fax "" Investigation Person Address "" Investigation Person Affiliation "" Investigation Person Roles "" Investigation Person Roles Term Accession Number "" Investigation Person Roles Term Source REF "" STUDY Study Identifier "E-GEOD-18232" Study Title "RAS signaling in colon carcinoma: Target gene deregulation and growth control through Y-box-binding protein 1" Study Description "3 colon cancer cell lines treated with sulindac sulfide, sulindac sulfone, or other chemicals. [original description: The perturbation of the genetic program due to mutational activation of KRAS- or BRAF-mediated signal transduction is a prerequisite for the expression of neoplastic phenotypes; however, the mechanisms of cancer cell-specific transcriptional deregulation are poorly understood. We have analyzed the human colorectal cancer cell lines HCT116, HT29 and SW480 using an integrated approach combining transcriptional profiling, small molecule inhibitors targeting signaling pathway effectors, and computational prediction of regulatory elements in promoters of co-expressed genes with chromatin-based and cellular assays. We identified groups of coexpressed genes involved in similar biological processes, demonstrating a link between biological function and transcriptional organization. Among them we found groups of proliferation associated genes which responded to MEK/MAPK inhibition in all three cell lines. We predicted by computational analysis of the promoter regions of these genes, that NFY binding sites might be important regulatory elements for the MEK/MAPK-dependent transcriptional control. We validated this prediction in reporter gene assays by using a fragment of the CCNB1 promoter as a model. We discovered YBX1 to be associated with the endogenous CCNB1 promoter and the promoters of 62 additional genes within the proliferation associated gene groups by a ChIP-on-chip assay. Silencing of YBX1 expression by siRNA prevents CCNB1 expression and partially inhibits proliferation of HCT116 cells. In view of multiple known YBX1 functions in stress response, chromatin remodeling, transcriptional and translational regulation, our results indicate that this factor may also contribute to RAS-induced pleiotropic effects in cancer. The cells were treated with certain inhibitors for 48 hours. We used one sample per cell line treated with DMSO as a control, and one sample for each of the treatments.]" Comment[Study Grant Number] "" Comment[Study Funding Agency] "" Study Submission Date "" Study Public Release Date "2010-10-09" Study File Name "s_E-GEOD-18232_study_samples.txt" STUDY DESIGN DESCRIPTORS Study Design Type "transcription profiling by array" Study Design Type Term Accession Number "" Study Design Type Term Source REF "" STUDY PUBLICATIONS Study PubMed ID "21170361" Study Publication DOI "" Study Publication Author List "" Study Publication Title "" Study Publication Status "" Study Publication Status Term Accession Number "" Study Publication Status Term Source REF "" STUDY FACTORS Study Factor Name "cell line" "genotype" Study Factor Type "cell line" "genotype" Study Factor Type Term Accession Number "" "" Study Factor Type Term Source REF "" "" STUDY ASSAYS Study Assay File Name "a_E-GEOD-18232_GeneChip_assay.txt" Study Assay Measurement Type "transcription profiling" Study Assay Measurement Type Term Accession Number "" Study Assay Measurement Type Term Source REF "" Study Assay Technology Type "DNA microarray" Study Assay Technology Type Term Accession Number "" Study Assay Technology Type Term Source REF "" Study Assay Technology Platform "" STUDY PROTOCOLS Study Protocol Name "P-GSE18232-3" "P-GSE18232-2" "P-GSE18232-4" "P-GSE18232-5" "P-GSE18232-6" "P-GSE18232-7" "P-GSE18232-1" Study Protocol Type "growth protocol" "sample treatment protocol" "nucleic acid extraction protocol" "labeling protocol" "hybridization protocol" "array scanning protocol" "normalization data transformation protocol" Study Protocol Type Term Accession Number "" "" "" "" "" "" "" Study Protocol Type Term Source REF "" "" "" "" "" "" "" Study Protocol Description "SW480, HT29 and HCT116 cells were cultured in complete L-15 medium at 37¡C and 5% CO2 in a humidified incubator." "After 24 hours, the cells were treated once with the indicated inhibitors for 48 hours." "Trizol extraction of total RNA was performed according to the manufacturer's instructions." "Labeling of RNA targets were performed according to protocols provided by Affymetrix." "Hybridization and post-hybridization procedures were performed according to protocols provided by Affymetrix." "Arrays were scanned twice at 3 µm resolution using a confocal argon laser scanner (Hewlett-Packard, Santa Clara, CA), controlled by Microarray Suite 5.0 software (Affymetrix). Photoemission was detected by a photomultiplier tube through a 570-nm long-pass filter." "Computer-generated array images were overlaid with a virtual grid, controlled by Microarray Suite 5.0 software. About 40 pixels within each feature were averaged after discarding outliers and pixels close to feature boundaries. ID_REF = VALUE = Gene expression levels were calculated according to the average hybridization intensities of perfectly matched versus mismatched oligonucleotide probes. Arrays were scaled by Microarray Suite 5.0 software to an average hybridization intensity of 2,500 per gene and analyzed independently. ABS_CALL = DETECTION P-VALUE = " Study Protocol URI "" "" "" "" "" "" "" Study Protocol Version "" "" "" "" "" "" "" Study Protocol Parameters Name "" "" "" "" "" "" "" Study Protocol Parameters Name Term Accession Number "" "" "" "" "" "" "" Study Protocol Parameters Name Term Source REF "" "" "" "" "" "" "" Study Protocol Components Name "" "" "" "" "" "" "" Study Protocol Components Type "" "" "" "" "" "" "" Study Protocol Components Type Term Accession Number "" "" "" "" "" "" "" Study Protocol Components Type Term Source REF "" "" "" "" "" "" "" STUDY CONTACTS Study Person Last Name "J�rchott" "J�rchott" "Sch�fer" Study Person First Name "Karsten" "Karsten" "Reinhold" Study Person Mid Initials "" "" "" Study Person Email "karsten.juerchott@charite.de" "" "" Study Person Phone "" "" "" Study Person Fax "" "" "" Study Person Address "Institute of Theoretical Biology, Charit� - Universit�tsmedizin Berlin, Invalidenstr. 43, Berlin, Germany" "" "" Study Person Affiliation "Charit� - Universit�tsmedizin Berlin" "" "" Study Person Roles "submitter" "" "" Study Person Roles Term Accession Number "" "" "" Study Person Roles Term Source REF "" "" "" Comment[Study Person REF] "" "" ""