Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

30 paired normal and tumor colorectal samples

ABSTRACT: Analysis of differentially regulated genes in patients normal and colorectal tumor samples. The aim of this study was to identify genes that were differentially up- or down-regulated in the tumor samples as compared to the normal colon tissue

ORGANISM(S): Homo sapiens

PROVIDER: GSE74602 | GEO | 2016/11/02

SECONDARY ACCESSION(S): PRJNA300952

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Global proteome analysis of paired colorectal cancer sample using LC-MS/MS

Project description:To find differentially expressed protein in colorectal cancer compared with normal colon tissue, we performed global proteome analysis using LC-MS.

2020-09-30 | PXD019504 | Pride

Decoding differentially regulated epithelial and stromal pathways in colorectal cancer

Project description:Analysis of differentially expressed genes from dissected whole tissue and laser capture microdissected colorectal cancer tissue samples The analysis, in colorectal cancer tissues, of compartmental and whole tissue expression profiles as well as the significantly active pathways that were differentially deregulated between the epithelial and stromal compartments when compared alongside that of whole tissue dissection Comparison of tumor epithelium vs normal epithelium; tumor stroma vs normal stroma and tumor whole tissue vs normal whole tissue

2011-08-09 | E-GEOD-31279 | biostudies-arrayexpress

Analysis of copy number changes primary and metastatic colorectal cancer samples

Project description:Structural rearrangements form a major class of somatic variation in cancer genomes. Local chromosome shattering, termed chromothripsis, is a mechanism proposed to be the cause of clustered chromosomal rearrangements and was recently described to occur in a small percentage of tumors. The significance of these clusters for tumor development or metastatic spread is largely unclear. We used genome-wide long mate-pair sequencing and SNP array profiling to reveal that chromothripsis is a widespread phenomenon in primary colorectal cancer and metastases. We find large and small chromothripsis events in nearly every colorectal tumor sample and show that several breakpoints of chromothripsis clusters and isolated rearrangements affect cancer genes, including NOTCH2, EXO1 and MLL3. We complemented the structural variation studies by sequencing the coding regions of a cancer exome in all colorectal tumor samples and found somatic mutations in 24 genes, including APC, KRAS, SMAD4 and PIK3CA. A pairwise comparison of somatic variations in primary and metastatic samples indicated that in many chromothripsis clusters, isolated rearrangements and point mutations are exclusively present in either the primary tumor or the metastasis and may affect cancer genes in a lesion-specific manner. We conclude that chromothripsis is a prevalent mechanism driving structural rearrangements in colorectal cancer and show that a complex interplay between point mutations, simple copy number changes and chromothripsis events drive colorectal tumor development and metastasis. We analyzed 16 tissue samples from four patients. For each patient we analyzed the DNA of a primary colon tumor sample, a normal colon tissue sample, a metastatic liver tumor sample and a normal liver tissue sample. The normal colon and normal liver samples serve as a control for the primary and metastatic tumor samples.

2011-10-11 | E-GEOD-32711 | biostudies-arrayexpress

Expression of immune-related genes in the normal colorectal mucosa and colorectal carcinoma samples from Lynch syndrome individuals

Project description:Colorectal carcinomas arising in the context of Lynch syndrome, the most common inherited cancer syndrome, typically show deficiency of the DNA MMR (mismatch repair) system. Lack of functional MMR leads to accumulation of frameshift mutations at micosatellites (microsatellite instability, MSI). High load of highly immunogenic tumor-specific frameshift neoantigens results in strong immune response against Lynch syndrome MSI cancers. Previous studies have shown systemic immune responses against frameshift neoantigens in Lynch syndrome carriers long before tumor manifestation. In the present study, we analyzed the immune profile of normal colorectal mucosa in Lynch syndrome carriers without current or previous cancer history and in Lynch syndrome colorectal cancer patients, as well as of Lynch syndrome colorectal carcinomas. The unsupervised cluster analysis of gene expression data revealed a sharp differentiation between normal mucosa from Lynch syndrome individuals with and without manifest cancer as well as between normal mucosa in general and Lynch syndrome cancer tissue. Deconvolution analysis for predicting the prevalence of immune cell population among the three groups revealed 10 out of 14 investigated populations to be significantly different between the three tissue types (FDR=10%). In contrast to normal mucosa samples, tumor tissue showed overrepresentation of immune-suppressive cell populations, such as regulatory T cells and neutrophils. Taken together with the quantitative T cell density analysis on the basis of immunohistochemical T cell stainings, our data show strong immune infiltration of the normal colorectal mucosa in Lynch syndrome individuals even in the absence of a manifest cancer.

2022-03-14 | GSE178516 | GEO

Proteomic profiling of paired primary and recurrent GBM patient samples

Project description:Formalin fixed paraffin embedded (FFPE) primary-recurrent Glioblastoma (pGBM-rGBM) matched patient samples and normal tissue adjacent to tumor (NAT) were analyzed by shotgun DDA proteomics. The proteomic profiles of pGBM-rGBM pairs revealed differentially expressed proteins in rGBM samples, which in future could be used for potential therapeutic interventions.

2021-08-06 | MSV000087947 | MassIVE

Gene expression profiling of colorectal cancer tissue samples

Project description:We have compared the gene expression profiles of primary colorectal cancers and colorectal liver metastases within the framework of the consensus molecular subtypes. This series represents a subset of the primary tumor samples.

2021-07-27 | GSE178120 | GEO

RNA-seq of two paired normal and cancer tissues in two stage III colorectal cancer patients

Project description:The RNA from two paired normal and colorectal tumor tissue were sequenced by Illumina genome analyzer. 0.8 to 1.1 million reads were generated. Sequencing data was aligned with human RNA, human mitochondrial DNA and human genomic DNA by BWA. Base calling and Phred-like score was calculated by SAMTools. Whole transcriptome sequence of paired normal and tumor tissues obtained from two colorectal cancer patients

2011-05-28 | E-GEOD-29580 | biostudies-arrayexpress

microRNA expression data of tumor tissues and paired pericarcinomatous tissue of 15 ESCC samples

Project description:We detected the expression of miRNA in 15 ESCC samples' tumor tissues and the corresponding normal esophagus tissue. Then, we identified the differentially expressed miRNAs in ESCC.

2021-10-28 | GSE131453 | GEO

Global lncRNA/mRNA expression analysis of colorectal tumor and non-tumor samples from 6 colorectal cancer patients

Project description:Given the role of lncRNAs and mRNAs in tumor pathogenesis, we set out to identify transcripts that potentially drive colorectal tumorigenesis. To do this, we performed microarray analysis on matched colorectal tumor and non-tumor samples from 6 colorectal cancer patients, and determined their lncRNA and mRNA expression profiles with Agilent microarrays (Arraystar Human LncRNA Array v3.0).

2018-01-20 | GSE109454 | GEO

CPTAC, TCGA Colorectal Cancer Proteome Study Comparison and Reference Samples (CompRef)

Project description:Comparison and Reference (CompRef) Samples, initially characterized in the <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S010">System Suitability Study</a>, were analyzed along with the <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S016">TCGA colorectal cancer tumor samples</a> and with the <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S019">normal colon epithelium samples</a>. These interstitial CompRef experiments are global proteomic profiling of the P6 (luminal) and P5 (basal) human-in-mouse xenograft breast carcinoma pooled samples.One CompRef sample was run after every 5 samples of TCGA colorectal cancer tumor tissue, alternating between the P6 and P5 CompRef samples to generate 20 total data sets (designated as 01CompRef_P6_VU through 20CompRef_P5_VU).Twelve CompRef samples were run with the 30 normal colon epithelium samples to produce 12 data sets (designated as 21CompRef_P6_VU through 32CompRef_P5_VU).These experiments were used to monitor the consistency of laboratory protocols and mass spectrometry instrument performance during the TCGA colorectal cancer analysis.<ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S017" target="_blank">https://cptac-data-portal.georgetown.edu/cptac/s/S017</a> on 08/31/18</li></ul>

2018-08-31 | MSV000082875 | MassIVE

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