status: Curated disease: Cancer species: Homo sapiens citation: Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression. Carvalho B, Postma C, Mongera S, Hopmans E, Diskin S, van de Wiel MA, van Criekinge W, Thas O, Matthai A, Cuesta MA, Terhaar Sive Droste JS, Craanen M, Schrock E, Ylstra B, Meijer GA. Gut. 2009 Jan;58(1):79-89. SampleType: Tumor Tissue numSamples: 68 tissueType: Colorectal Institution: Vumc Investigator: Cavalho curationNotes: Curation notes: Expression was performed on the VUMC MACF human 30K oligo v30 spotted array for all samples. CNV analysis was done on one of 4 versions of the VUMC MACF human BAC spotted array. The version number for each sample is noted in the individuals.txt file. Also, it is important to note that there are three instances in which a pair of tumors come from one individual, so that the tumor samples are not all independent of each other. The matched tumor pairs are: F23A1 & F23A2 F38A1 & F38A2 F58A1 & F58A2 Genome builds: Expression- NCBI35 version of the human genome CNV- UCSC July 2003 Freeze of the Human Golden Path (NCBI build 34) ***************** FILE DESCRIPTIONS ***************** files under each directory individuals.txt individuals description file ** individuals with cnv data only added in release_02_2011-07 ** ******** cnv data ******** platforms: VUMC MACF human 6K BAC v45 (GPL2843) VUMC MACF human 5K BAC v12 (GPL3441) VUMC MACF human 5K BAC v16 (GPL3442) VUMC MACF human 5K BAC v21 (GPL3443) files under ~/cnv/*/ cnv_bad_p.txt A flag to highlight spots that suffer from poor printing and other experimental artifacts (0 acceptable; 1-4 not acceptable) cnv_bkgrd_g_intensity.txt background signal of channel 1 (Cy3) cnv_bkgrd_r_intensity.txt background signal of channel 1 (Cy5) cnv_g_intensity.txt spot signal channel 1 (Cy3) cnv_log2rat.txt log base 2 ratio cnv_norm_log2rat.txt Normalized value of the log2ratio. cnv_norm_nobad_log2rat.txt Normalized value of the log2ratio. Flagged features are excluded. Values where also deleted if the each triplicate had a Standard Deviation higher than 0.2. cnv_r_intensity.txt spot signal channel 2 (Cy5) features.txt probe description files with the following descriptors: probe_id ROW (Coordinate for row number of block of features) COL (Coordinate for column number of block of features) SUBGRIDROW (Coordinate for row number of feature within a block) SUBGRIDCOL (Coordinate for column number of feature within a block) INT_CLONE_NAME (International name to identify BAC or PAC clone) CLONE_ID SPOT_ID SANGER_PLATE_ID (name of the 96-well plate from the Sanger 1 Mb BAC clone set) WELL_NR (Well number within the 96-well plate of the Sanger 1 Mb BAC clone set) BIOSEQUENCE_TYPE (Type of biosequence spotted on the arra) REPORTER_USAGE (Role of the reporter (experimental, control or empty)) ORGANISM (organism source of the feature) CHROMOSOME_NR (Number of the chromosome to which the clone has been mapped) START (Start position of the clone on the chromosome to which it has been mapped) END (End position of the clone on the chromosome to which it has been mapped) *************** expression data *************** platform: VUMC MACF human 30K oligo v30 (GPL3055) files under ./expression/ expression_bad_p.txt A flag to highlight spots that suffer from poor printing and other experimental artifacts (0 acceptable; 1-4 not acceptable) expression_bkgrd_g_intensity.txt background signal of channel 1 (Cy3) expression_bkgrd_r_intensity.txt background signal of channel 1 (Cy5) expression_g_intensity.txt spot signal channel 1 (Cy3) expression_log2rat.txt log base 2 ratio expression_norm_log2rat.txt Normalized value of the log2ratio. expression_norm_nobad_log2rat.txt Normalized value of the log2ratio. Flagged features are excluded. Values where also deleted if the each triplicate had a Standard Deviation higher than 0.2. expression_r_intensity.txt spot signal channel 2 (Cy5) features.txt probe description file with the following descriptors: probe_id ROW (Coordinate for row number of block of features) COL (Coordinate for column number of block of features) SUBGRIDROW (Coordinate for row number of feature within a block) SUBGRIDCOL (Coordinate for column number of feature within a block) GB_ACC (GeneBank accession number as supplied by Compugen LINK_PRE: "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&term=") SPOT_ID UNIGENE (UniGene accession number as supplied by Compugen LINK_PRE: "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=") COMPUGEN_SERIAL_NR (Serial number of the oligonucleotide as supplied by Compugen) GENE_DESCRIPTION (Description of the gene from which the oligo has been designed as supplied by Compugen) GENE_ONTOLOGY (Ontology of the gene from which the oligo has been designed as assigned by Compugen) PLATE_NR (Number of the 384-well plate in which the oligo was supplied) WELL_NR (Well number within the 384-well plate in which the oligo was supplied) BIOSEQUENCE_TYPE (Type of biosequence spotted on the array) REPORTER_USAGE (Role of the reporter (control or experimental)) CHROMOSOME_NR (Number of the chromosome to which the oligonucleotide has been mapped) START (Start position of the oligonucleotide on the chromosome to which it has been mapped) END (End position of the oligonucleotide on the chromosome to which it has been mapped) ************** phenotype data ************** files under ./phenotype/ phenotype.txt phenotype trait values for each individual ** phenotypes for patients with cnv data only added in release_02_2011-07 ** ** row names are changed to omit any spaces that were previously included ** features.txt description of each phenotype trait ** row names are changed to omit any spaces that were previously included ** syn47231 syn88641 syn47230
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