Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

32 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Type II Enteropathy-associated T-cell lymphoma

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Sanjanaa Nagarajan

PROVIDER: E-GEOD-70654 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Affymetrix Genome-Wide Human SNP Array 6.0 data for Type II Enteropathy-associated T-cell lymphoma

Project description:Type II Enteropathy-associated T-cell lymphoma (Type II EATL) is an aggressive intestinal T-cell lymphoma with poor prognosis and has not been molecularly profiled. Through targeted amplicon sequencing, we identified a large portion of Type II EATL samples that harbor mutations in the STAT5B, JAK3 and GNAI2 genes. Genome-wide DNA copy number profiling of Type II EATL tumors and matched normal samples was performed to determine copy-number changes in this disease. Affymetrix SNP6 arrays were performed according to the manufacturer's directions on gDNA extracted from 4 tumors and 4 matched whole blood samples.

2016-03-03 | E-GEOD-70653 | biostudies-arrayexpress

Distinct Mutational Patterns of Infection and Non-Infection-Related Bile Duct Cancers Revealed by Exome Sequencing

Project description:The impact of different carcinogenic exposures on the specific patterns of somatic mutations in human tumors remains unclear. To clarify this issue, we profiled 209 cholangiocarcinomas (CCAs) from Asia and Europe, including 108 cases caused by liver fluke Opisthorchis viverrini (OV)-infection and 101 cases due to non-OV etiologies. Whole-exome (N = 15) and prevalence screening (N = 194) revealed recurrent somatic mutations in BAP1 and ARID1A, neither of which has been previously reported to be mutated in CCA. Comparisons between intrahepatic OV and non-OV CCAs demonstrated statistically significant different mutation patterns: BAP1 and IDH1/2 were more frequently mutated in non-OV CCAs, while TP53 displayed the reciprocal pattern. Functional studies demonstrated tumor suppressive roles of BAP1 and ARID1A, establishing the role of chromatin modulators in CCA pathogenesis. These findings indicate that different causative etiologies may induce distinct somatic alterations even within the same tumor type. Affymetrix SNP6 arrays were performed according to the manufacturer's directions on DNA extracted from the 15 tumors and the 15 matched normal discovery samples.

2013-11-03 | E-GEOD-49666 | biostudies-arrayexpress

Expression data from gastroesphageal cancers and adjascent normal tissue

Project description:The primary objective of this study was to determine the effectiveness of bortezomib alone or in combination with irinotecan in patients with advanced gastric and gastroesphageal cancer. A secondary objecitve was to determine whether treatment was associated with changes in gene expression in the tumor and normal adjascent tissue. Tumor biopsies and biopsies of normal adjascent tissue were obtained before therapy and 24 hours after therapy. Differences in gene expression were evaluated between tumor and normal tissue (N=8 patients), and between post-treatment and pretreatment specimens for bortezomib alone (N=2 patients) and bortezomib plus irinotecan (N=10 patients).

2013-11-07 | E-GEOD-52138 | biostudies-arrayexpress

Copy number variation data in malignant mouse mammary cell lines

Project description:Many preclinical therapy studies have focused on a small number of well-described mouse allograft or human xenograft models that poorly represent the heterogeneity of human disease. Here we have assembled a panel of mouse mammary cell lines derived from spontaneously-arising mouse mammary tumors or from mammary tumors arising in genetically engineered mouse models. We used the Affymetrix Mouse Diversity Genotyping Array to address DNA copy number variation in the genomes of the cell lines of this panel. The resulting information about regions of amplification and deletion should help inform biological analyses as well as provide a reference for cell line authentication/identification. Affymetrix Mouse Diversity Genotyping arrays were used according to manufacturer's directions to analyze gDNA extracted from 27 mouse mammary cell lines of varying malignancy.

2016-06-15 | E-GEOD-69902 | biostudies-arrayexpress

Amplification of 1q32.1 refines the molecular classification of endometrial carcinoma: SNP array

Project description:The experiment aimed at refining the classification of endometrial cancer by profiling somatic copy number aberrations (SCNAs). SCNAs affecting chromosome 1q32.1 significantly correlated with worse survival and functional validation of a plausible oncogene showed MDM4 as an oncogenic driver in 1q32.1 and a putative therapeutic target for NSMP ECs.

2019-07-27 | E-MTAB-5908 | biostudies-arrayexpress

Methylation in breast cancer vs. normal tissue

Project description:We applied a combination of Methyl-CpG Immunoprecipitation (MCIp) and Human CpG Island microarrays to identify aberrant DNA methylation in eight low-grade breast invasive carcinomas and two pre-invasive breast tumors against ten normal breast tissues. 10 breast tumor samples (8 invasive, 2 pre-invasive) and 10 normal breast tissues, paired randomly (except Array 10: matched pair)

2012-09-14 | E-GEOD-35263 | biostudies-arrayexpress

Integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell carcinoma

Project description:Genomic instability plays an important role in human cancers. We previously characterized genomic instability in esophageal squamous cell carcinomas (ESCC) in terms of loss of heterozygosity (LOH) and copy number (CN) changes in tumors. In the current study we focus on biallelic loss and its relation to expression of mRNA and miRNA in ESCC using results from 500K SNP, mRNA, and miRNA arrays in 30 cases from a high-risk region of China. 30 matched tumors and normal tissue

2016-02-29 | E-GEOD-66274 | biostudies-arrayexpress

Affymetrix SNP6.0 array for comparison of lung tumor and adjacent normal to high-throughput sequencing data

Project description:One lung tumor and its adjacent normal were profiled for copy-number alterations with the high-resolution Affymetrix SNP6.0 Array. The SRA ID for the high throughput sequencing project will accompany our study is SRP002045. One lung tumor sample and an adjacent normal sample were assayed on the Affymetrix SNP6.0 array.

2010-06-09 | E-GEOD-20584 | biostudies-arrayexpress

Profiling of pancreatic adenocarcinoma using artificial intelligence-based integration of multi-omic and computational pathology features

Project description:Contemporary analyses focused on a limited number of clinical and molecular features have been unable to accurately predict clinical outcomes in pancreatic ductal adenocarcinoma (PDAC). Here we describe a novel, conceptual approach and use it to analyze clinical, computational pathology, and molecular (DNA, RNA, protein, and lipid) analyte data from 74 patients with resectable PDAC. Multiple, independent, machine learning models were developed and tested on curated singleand multi-omic feature/analyte panels to determine their ability to predict clinical outcomes in patients. The multi-omic models predicted recurrence with an accuracy and positive predictive value (PPV) of 0.90, 0.91, and survival of 0.85, 0.87, respectively, outperforming every singleomic model. In predicting survival, we defined a parsimonious model with only 589 multi-omic analytes that had an accuracy and PPV of 0.85. Our approach enables discovery of parsimonious biomarker panels with similar predictive performance to that of larger and resource consuming panels and thereby has a significant potential to democratize precision cancer medicine worldwide.

2024-01-23 | PXD037038 | Pride

Segment files from SNP array analysis of 145 myxofibrosarcoma and undifferentiated pleomorphic sarcoma

Project description:Genomic profiling of myxofibrosarcoma and undifferentiated pleomorphic sarcomas was done to correlate genomic profiles and signatures with outcome and transcriptomic features.

2024-09-30 | E-MTAB-13948 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data