Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Methylation profiling of human colon cancer specimens with or without methylation of the MLH1 promoter.

ABSTRACT: Expression profile was obtained for GeneChip probe sets among colon cancer specimens with or without the methylation of MLH1 promoter.

ORGANISM(S): Homo sapiens

SUBMITTER: Hiroyuki Mano

PROVIDER: E-GEOD-2138 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Epigenetic silencing of AXIN2 in colorectal carcinoma with microsatellite instability.

Koinuma K K Yamashita Y Y Liu W W Hatanaka H H Kurashina K K Wada T T Takada S S Kaneda R R Choi Y L YL Fujiwara S-I SI Miyakura Y Y Nagai H H Mano H H

Oncogene 20060101 1

Mutation or epigenetic silencing of mismatch repair genes, such as MLH1 and MSH2, results in microsatellite instability (MSI) in the genome of a subset of colorectal carcinomas (CRCs). However, little is yet known of genes that directly contribute to tumor formation in such cancers. To characterize MSI-dependent changes in gene expression, we have now compared transcriptomes between fresh CRC specimens positive or negative for MSI (n=10 for each) with the use of high-density oligonucleotide micr ...[more]

PMID: 16247484

Similar Datasets

Colon cancer profiling

Project description:Expression profile was obtained for GeneChip probe sets among colon cancer specimens with or without the methylation of MLH1 promoter. Keywords: other

2005-08-26 | GSE2138 | GEO

Systematic Evaluation and Optimization of Protein Extraction Parameters in Diagnostic FFPE Specimens

Project description:Objectives: Formalin-fixed paraffin-embedded (FFPE) tissue is the standard material for di-agnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction pro-tocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservation of membrane proteins (MP) as key subgroup of func-tionally relevant proteins. Methods: Using the example of urothelial carcinoma, FFPE tissue sections were subjected to various deparaffinization, protein extraction and antigen retrieval protocols and buffers as well as different extraction techniques. Performance was meas-ured by protein concentration and western blot analysis of cellular compart-ment markers as well as liquid chromatography-coupled mass spectrometry (LC-MS). Results: Commercially available extraction buffers showed reduced extraction of MPs and came at considerably increased costs. On-slide extraction did not improve PE whereas several other preanalytical steps could be simplified. Systematic variation of temperature and exposure duration demonstrated a quantitatively relevant corridor of optimal antigen retrieval. Conclusions: Preanalytical protein extraction can be optimized at various levels to improve unbiased protein extraction and to reduce time and costs.

2022-05-19 | PXD029133 | Pride

Data independent MS phenotyping of melanoma tissue specimens

Project description:Phenotyping of Stage III BRAF or NRAS mutant melanoma tissue specimens to predict drug response and patient survival

2018-10-11 | PXD007083 | Pride

Quantitative proteomic analysis of primary prostate cancer tissue specimens

Project description:Currently, comprehensive and quantitative proteomic analysis of human prostate cancer tissue specimens remains scarce, hindering the identification of protein complexes and pathways deregulated in prostate cancer. In this study, we applied TMT-SPS-MS3-based quantitative proteomics to analzye 9 normal controls, 9 low-grade prostate cancer, and 9 high-grade prostate cancer. About 3,600 proteins were quantified across all the 27 prostate specimens. Statistical analysis identified 651 proteins that are differentially expressed in high-grade prostate cancer and normal prostate. Pathway enrichment analysis revealed that the LXR/RXR activation and integrin signaling pathways are substantially downregulated in high-grade prostate cancer, compared with normal prostate cancer. In addition, protein complex analysis suggested that mitochondrial ribosomes and ribosome-biogenesis complexes are significnatly overexpressed, whereas the cholesterol effluex and focal adhesion comlexes are significantly downregulated in high-grade prostate cancer, compared with normal controls. Furthermore, differential correlation analysis indicated that the spliceosome machinery might be more active in low-grade prostate cancer, compared with normal controls. The results are expected to shed light on the molecular mechnanisms underlying the development and progression of primary prostate cancer in human patients.

2019-04-23 | PXD010744 | Pride

miRNA expression profile in leprosy skin biopsy specimens

Project description:Skin biopsy specimens of skin lesions were profiled for miRNA expression. In this study, we indentified miRNA species that were differentially expressed in the skin lesions of either the lepromatous or tuberculoid forms of leprosy. One miRNA species, hsa-mir-21, found in the lepromatous lesions was capable of downregulating the vitamin D-dependent antimicrobial pathway. Scalpel or punch skin biopsy specimens were obtained after informed consent from patients with tuberculoid leprosy and patients with lepromatous leprosy at the time of diagnosis. Specimens were embedded in OCT medium, snap-frozen in liquid nitrogen and stored at 80°C until sectioning.

2011-12-31 | E-GEOD-33192 | biostudies-arrayexpress

Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

Project description:This SuperSeries is composed of the following subset Series: GSE23384: Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FFPE samples) GSE23385: Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FNA samples) Refer to individual Series

2011-06-22 | E-GEOD-23386 | biostudies-arrayexpress

ZNF350 promoter methylation accelerates colon cancer cell migration.

Project description: Not available

| S-EPMC6298409 | biostudies-literature

High throughput bisulfite sequencing of the MLH1 promoter in human hematiopoietic progenitor cell clones

Project description:Using single molecule ultra-deep bisulfite sequencing we characterized the CpG methylation landscape from –938 to –337 bp upstream of the MLH1 transcriptional start site position 0, from 30 hematopoietic colony forming cell clones (CFC) either expressing or not expressing MLH1. We identify a correlation between MLH1 promoter methylation and loss of MLH1 expression. Additionally, using the CpG site methylation frequencies obtained in this study we are able to generate a classification algorithm capable of sorting the expressing and non-expressing CFC. Thus, as previously described for many tumor cell types, MLH1 promoter methylation in hematopoietic stem cell clones correlates with the loss of MLH1 expression, a critically important gene in the mismatch repair pathway.

2017-02-09 | GSE73868 | GEO

Chip-chip from Hepatocellular carcinoma (HCC) specimens with H3K4me3

Project description:Epigenetic changes commonly occur in hepatocellular carcinoma (HCC) and are associated with aberrant gene expression. Recently, we demonstrated the pivotal role of abnormal H3K4me3 methylation, which is catalyzed by the menin/MLL, a TrxG family, in HCC development. Meanwhile, there is clear evidence that increasing global levels of H3K27me3 are activated in human primary HCC. To further elucidate the functional relatedness of the active H3K4me3 and repressive H3K27me3 histone remodeling in HCC, we performed H3K4me3 and H3K27me3 ChIP-on-chip screen using three HCC specimens and their adjacent tissues. Comparison of ChIP-on-chip results between tumor(C) and adjacent tissues(N) from three HCC specimens with H3K4me3

2013-11-08 | E-GEOD-52190 | biostudies-arrayexpress

Chip-chip from Hepatocellular carcinoma (HCC) specimens with H3K27me3

Project description:Epigenetic changes commonly occur in hepatocellular carcinoma (HCC) and are associated with aberrant gene expression. Recently, we demonstrated the pivotal role of abnormal H3K4me3 methylation, which is catalyzed by the menin/MLL, a TrxG family, in HCC development. Meanwhile, there is clear evidence that increasing global levels of H3K27me3 are activated in human primary HCC. To further elucidate the functional relatedness of the repressive H3K27me3 and active H3K4me3 histone remodeling in HCC, we performed H3K27me3 and H3K4me3 ChIP-on-chip screen using three HCC specimens and their adjacent tissues. Comparison of ChIP-on-chip results between tumor(C) and adjacent tissues(N) from three HCC specimens with H3K27me3

2013-11-13 | E-GEOD-52301 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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