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CaArray_EXP-576: TCGA (LUAD): Gene Expression Analysis of TCGA samples using Agilent Expression 244K microarrays (UNC)

ABSTRACT: Gene Expression Analysis of TCGA samples using Agilent Expression 244K microarrays. EXP-576 Assay Type: Gene Expression Provider: Agilent Array Designs: AgilentG4502A_07_3 Organism: Homo sapiens (ncbitax) Tissue Sites: Lung Material Types: Control Analyte, organism_part, Primary solid_tumor, genomic_DNA Disease States: Lung Adenocarcinoma, NOT SPECIFIED

ORGANISM(S): Homo sapiens

SUBMITTER: Mervi Heiskanen

PROVIDER: E-GEOD-68787 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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caArray_EXP-574: TCGA(Kirc): Gene Expression Analysis of TCGA samples using Agilent Expression 244K microarrays (UNC)

Project description:Gene Expression Analysis of TCGA samples using Agilent Expression 244K microarrays. EXP-574 Assay Type: Gene Expression Provider: Agilent Array Designs: AgilentG4502A_07_3 Organism: Homo sapiens (ncbitax) Tissue Sites: Kidney Material Types: Control Analyte, organism_part, Primary solid_tumor, genomic_DNA Disease States: Kidney Clear Cell Renal Carcinoma, NOT SPECIFIED

2015-05-13 | E-GEOD-68784 | biostudies-arrayexpress

caArray_gabri-00003: TCGA Analysis of RNA Expression for Glioblastoma Multiforme

Project description:TCGA Analysis of RNA Expression for Glioblastoma Multiforme Using Affymetrix HT_HG-U133A gabri-00003 Assay Type: Gene Expression Provider: Affymetrix Array Designs: HT_HG-U133A Organism: Homo sapiens (ncbitax) Tissue Sites: Brain Material Types: synthetic_RNA, organism_part, solid_tumor, total_RNA, cell Disease States: GLIOBLASTOMA MULTIFORME, NOT SPECIFIED

2015-05-14 | E-GEOD-68850 | biostudies-arrayexpress

caArray_EXP-620: TCGA (Coad): Analysis of DNA Methylation for COAD using Illumina Infinium HumanMethylation450 platform (Jhu-usc)

Project description:TCGA Analysis of DNA Methylation for COAD using Illumina Infinium HumanMethylation450 platform EXP-620 Assay Type: Methylation Provider: Illumina Array Designs: jhu-usc.edu_TCGA_HumanMethylation450 Organism: Homo sapiens (ncbitax) Tissue Sites: Colon Material Types: Control Analyte, Solid normal_tissue, organism_part, Primary solid_tumor

2015-05-14 | E-GEOD-68838 | biostudies-arrayexpress

caArray_EXP-598: TCGA (LUSC): Analysis of DNA Methylation for LUSC using Illumina Infinium HumanMethylation450 platform (jhu-usc)

Project description:TCGA Analysis of DNA Methylation for LUSC using Illumina Infinium HumanMethylation450 platform EXP-598 Assay Type: Methylation Provider: Illumina Array Designs: jhu-usc.edu_TCGA_HumanMethylation450 Organism: Homo sapiens (ncbitax) Tissue Sites: Lung Material Types: Control Analyte, Solid normal_tissue, organism_part, Primary solid_tumor Disease States: Lung Squamous Cell Carcinoma, NOT SPECIFIED

2015-05-14 | E-GEOD-68825 | biostudies-arrayexpress

caArray_laird-00224: TCGA Ovarian: Analysis of DNA Methylation for Ovarian Using Illumina Infinium Human DNA Methylation 27 platform (HumanMethylation27) (USC)

Project description:TCGA Analysis of DNA Methylation Using Illumina Infinium Human DNA Methylation 27 platform laird-00224 Assay Type: Methylation Provider: Illumina Array Designs: jhu-usc.edu_OV.HumanMethylation27.1.adf, jhu-usc.edu_OV.HumanMethylation27.v2 Organism: Homo sapiens (ncbitax) Tissue Sites: Ovary, Ovary, NOT SPECIFIED, PERITONEUM (OVARY), OMENTUM Material Types: Control Cell Line, Solid normal_tissue, organism_part, Primary solid_tumor, whole_organism, Recurrent Solid Tumor Disease States: Serous Cystadenocarcinoma, Serous cystadenocarcinoma, NOT SPECIFIED

2015-11-21 | E-GEOD-75268 | biostudies-arrayexpress

caArray_EXP-592: TCGA (LUSC): Analysis of Gene Expression for Non Small Cell Lung Cancer, Squamous Cell Carcinoma Using Affymetrix HT_HG-U133A (Broad)

Project description:TCGA Analysis of RNA Expression for Non Small Cell Lung Cancer, Squamous Cell Carcinoma Using Affymetrix HT_HG-U133A EXP-592 Assay Type: Gene Expression Provider: Affymetrix Array Designs: HT_HG-U133A Organism: Homo sapiens (ncbitax) Tissue Sites: Lung Material Types: organism_part, Primary solid_tumor Disease States: Lung Squamous Cell Carcinoma, NOT SPECIFIED

2015-05-13 | E-GEOD-68793 | biostudies-arrayexpress

caArray_EXP-550: TCGA (READ): Analysis of DNA Methylation for rectal adenocarcinoma (READ) Using Illumina Infinium Human DNA Methylation 27 platform (HumanMethylation27)(jhu-usc)

Project description:TCGA Analysis of DNA Methylation for rectal adenocarcinoma (READ) Using Illumina Infinium Human DNA Methylation 27 platform EXP-550 Assay Type: Methylation Provider: Illumina Array Designs: jhu-usc.edu_OV.HumanMethylation27.v2 Organism: home sapiens (ncbitax) Tissue Sites: rectal Material Types: Primary solid_tumor, Control Cell Line, organism_part, Solid normal_tissue Disease States: Rectal Adenocarcinoma, NOT SPECIFIED, [Not Available], Rectal Mucinous Adenocarcinoma

2015-05-12 | E-GEOD-68751 | biostudies-arrayexpress

caArray_becic-00229: Gene expression analysis of prostate cancers

Project description:Prostate cancer is a biologically heterogeneous disease with considerable variation in clinical aggressiveness. The behavior of prostate cancer can be considered a direct or indirect result of aberrant alterations of gene expression in prostate epithelial cells. Identification of the patterns of gene-expression alterations that are related to the aggressiveness of prostate cancers will greatly assist the development of tools for early detection of prostate cancers with poor clinical outcome and identification of targets for future therapeutic intervention. To detect the patterns of gene-expression alterations of prostate cancers, we performed a comprehensive gene-expression analysis on 30 prostate tissues of various levels of invasiveness (ranging from those confined to the organ to distant metastases) and Gleason grades (combined scores 4-9), using the Affymetrix chip set Hu35k (A-D) and U95a. Following three sequential selection screens, we identified 84 largely novel genes and expressed sequence tag (EST) sequences whose expression levels were altered significantly in prostate cancer samples compared with control normal tissues. In addition, the expression levels of a group of 12 genes and EST sequences was found to be altered significantly in aggressive type of prostate cancers but not in organ-confined prostate cancers. Cluster analysis using the 84-gene list showed that the highly aggressive prostate cancers contained gene-expression patterns that were distinct from organ-confined prostate cancers ( Molecular Carcinogenesis 33:25-35, 2002). becic-00229 Assay Type: Gene Expression Provider: Affymetrix Array Designs: Hu35KsubA Organism: Homo sapiens (ncbitax) Tissue Sites: Prostate Material Types: synthetic_DNA, synthetic_RNA, organism_part Disease States: Normal, Prostate_Adenocarcinoma

2015-05-06 | E-GEOD-68545 | biostudies-arrayexpress

caArray_becic-00235: Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy

Project description:The incidence of prostate cancer is frequent, occurring in almost one-third of men older than 45 years. Only a fraction of the cases reach the stages displaying clinical significance. Despite the advances in our understanding of prostate carcinogenesis and disease progression, our knowledge of this disease is still fragmented. Identification of the genes and patterns of gene expression will provide a more cohesive picture of prostate cancer biology. PATIENTS AND METHODS: In this study, we performed a comprehensive gene expression analysis on 152 human samples including prostate cancer tissues, prostate tissues adjacent to tumor, and organ donor prostate tissues, obtained from men of various ages, using the Affymetrix (Santa Clara, CA) U95a, U95b, and U95c chip sets (37,777 genes and expression sequence tags). RESULTS: Our results confirm an alteration of gene expression in prostate cancer when comparing with nontumor adjacent prostate tissues. However, our study also indicates that the gene expression pattern in tissues adjacent to cancer is so substantially altered that it resembles a cancer field effect. CONCLUSION: We also found that gene expression patterns can be used to predict the aggressiveness of prostate cancer using a novel model. becic-00235 Assay Type: Gene Expression Provider: Affymetrix Array Designs: HG_U95A, HG_U95Av2, HG_U95B, HG_U95C Organism: Homo sapiens (ncbitax) Material Types: synthetic_RNA, organism_part, whole_organism, total_RNA Disease States: Normal, Prostate_Adenocarcinoma

2015-05-06 | E-GEOD-68555 | biostudies-arrayexpress

caArray_EXP-520: Gene Expression Profiles Predictive of Outcome and Age in Infant Acute Lymphoblastic Leukemia: a Children's Oncology Group Study

Project description:Gene expression profiling was performed on 97 cases of infant ALL from Children's Oncology Group Trial P9407. Statistical modeling of an outcome predictor revealed 3 genes highly predictive of event-free survival (EFS), beyond age and MLL status: FLT3, IRX2, and TACC2. Low FLT3 expression was found in a group of infants with excellent outcome (n = 11; 5-year EFS of 100%), whereas differential expression of IRX2 and TACC2 partitioned the remaining infants into 2 groups with significantly different survivals (5-year EFS of 16% vs 64%; P < .001). When infants with MLL-AFF1 were analyzed separately, a 7-gene classifier was developed that split them into 2 distinct groups with significantly different outcomes (5-year EFS of 20% vs 65%; P < .001). In this classifier, elevated expression of NEGR1 was associated with better EFS, whereas IRX2, EPS8, and TPD52 expression were correlated with worse outcome. This classifier also predicted EFS in an independent infant ALL cohort from the Interfant-99 trial. When evaluating expression profiles as a continuous variable relative to patient age, we further identified striking differences in profiles in infants less than or equal to 90 days of age and those more than 90 days of age. These age-related patterns suggest different mechanisms of leukemogenesis and may underlie the differential outcomes historically seen in these age groups. EXP-520 Assay Type: Gene Expression Provider: Affymetrix Array Designs: HG-U133_Plus_2 Organism: Homo sapiens (ncbitax)

2015-05-12 | E-GEOD-68720 | biostudies-arrayexpress

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