Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer using macrodissected tissues

ABSTRACT: The experiment was to elucidate the association between copy number variation (CNV) and gene expression in colorectal cancer (CRC) samples and their corresponding non-cancerous tissues.

ORGANISM(S): Homo sapiens

SUBMITTER: Norfilza Mokhtar

PROVIDER: E-MEXP-3980 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer tissues.

Ali Hassan Nur Zarina NZ Mokhtar Norfilza Mohd NM Kok Sin Teow T Mohamed Rose Isa I Sagap Ismail I Harun Roslan R Jamal Rahman R

PloS one 20140402 4

Integrative analyses of multiple genomic datasets for selected samples can provide better insight into the overall data and can enhance our knowledge of cancer. The objective of this study was to elucidate the association between copy number variation (CNV) and gene expression in colorectal cancer (CRC) samples and their corresponding non-cancerous tissues. Sixty-four paired CRC samples from the same patients were subjected to CNV profiling using the Illumina HumanOmni1-Quad assay, and validatio ...[more]

PMID: 24694993

Similar Datasets

Comparative genomic hybridization of human colorectal carcinoma samples - chromosome copy number and LOH analysis

Project description:Structural changes of chromosomes play important roles in the carcinogenesis of colorectal carcinoma (CRC). Here, by using SNP-typing arrays, we have tried to screen for recurrent chromosome copy number changes and loss-of-heterozygosity in the genome of colorectal carcinoma. Genomic DNA was isolated from tumor and paired normal tissues of CRC (n=94), and was hybridized to Affymetrix Mapping 50K Xba 240 arrays. Chromosome copy number and LOH likelihood score was inferred at every SNP locus with CNAG2.0 software (http://www.genome.umin.jp). Experiment Overall Design: Tumor samples and paired normal tissues (n=94 for each) were hybridized to the microarrays. Signal intensity data as well as genotype data were compared between a pair of tumor and normal samples with CNAG2.0. The resultant copy number and LOH likelihood score for each sample are thus calculated from two datasets (tumor and normal).

2008-10-26 | E-GEOD-11417 | biostudies-arrayexpress

Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers

Project description:Purpose: Small bowel adenocarcinoma (SBA) is a rare cancer and consequently the number of clinical trials has been very limited due to the small numbers of patients. Chemotherapy regimens are currently rather arbitrarily chosen between either a colorectal (CRC) or a gastric cancer (GC) regimen. Chromosomal copy number aberrations are a hallmark of solid tumours and can be measured by array comparative genomic hybridization (aCGH). The aim of the present study is to investigate whether genome-wide copy number aberrations of SBA are more similar to CRC or GC in order to support treatment of SBA according to either regimen. Experimental Design: A total of 85 GCs, CRCs and SBAs were selected from existing in house aCGH datasets based on array quality and clinical parameters. Differences and similarities in gains and losses of the three tumor types were analyzed using supervised and unsupervised analysis. Results: Hierarchical clustering revealed substantial overlap of chromosomal copy number profiles between SBA and CRC and less overlap between SBA and GC. Chromosome 13q13.2-q31.3 is primarily gained in SBA and CRC and the strongest feature discriminating SBA from GC. Further strong discriminating copy number characteristics are aberrations at chromosomes 1p36.3-p34.3, 4p15.3-q35.2, 9p24.3-p11.1 and 17p13.3-p13.2. Conclusions: SBA is more similar to CRC than to GC, based on genome-wide copy number aberrations. These data provide molecular support for treatment of SBA according to a CRC regimen. 29 gastric adenocarcinomas on 5K or 6K BAC arrays of which 2 samples are also done on 30K oligonucleotide arrays as control samples, 29 colorectal adenocarcinomas on 5K or 6K BAC arrays of which 2 samples are also done on 30K oligonucleotide arrays as control, 27 small bowel adenocarcinomas done on 30K oligonucleotide arrays of which 2 samples are also done on 5K BAC arrays as control.

2011-06-13 | E-GEOD-23418 | biostudies-arrayexpress

Gene expression profile of human colorectal carcinoma

Project description:Despite steady progress in the diagnosis and treatment of colorectal cancer (CRC), overall therapeutic outcomes remain unsatisfactory. Therefore, a better understanding of the molecular mechanisms of CRC is urgently needed. Fourteen pairs of cancerous and matched non-cancerous tissues (at least 5 cm away) were obtained from CRC patients undergoing surgical resection. Affymetrix human GeneChip primeview array was conducted to identify differentially expressed genes (DEGs) between CRC tissues and matched adjacent normal tissues. cDNA microarray analysis of cancerous and paired noncancerous tissues from CRC patients revealed 1,868 DEGs, of which 778 in primary lesions were up-regulated and 1,090 were down-regulated.

2018-04-24 | GSE113513 | GEO

Post-transcriptional mechanisms modulate the consequences of adaptive copy number variation

Project description:Copy-number variants (CNVs) are large-scale amplifications or deletions of DNA that can drive rapid adaptive evolution and result in large-scale changes in gene expression. Whereas alterations in the copy number of one or more genes within a CNV can confer a selective advantage, other genes within a CNV can decrease fitness when their dosage is changed. Dosage compensation - in which the gene expression output from multiple gene copies is less than expected - is one means by which an organism can mitigate the fitness costs of deleterious gene amplification. Previous research has shown evidence for dosage compensation at both the transcriptional level and at the level of protein expression; however, the extent of compensation differs substantially between genes, strains, and studies. Here, we investigated sources of dosage compensation at multiple levels of gene expression regulation by defining the transcriptome, translatome and proteome of experimentally evolved yeast (Saccharomyces cerevisiae) strains containing adaptive CNVs.

2023-11-01 | PXD046587 | Pride

Integrated analysis of copy number variation-associated lncRNAs identifies candidates contributing to the etiologies of congenital kidney anomalies.

Project description:We analyzed lncRNAs located in CNV loci associated with congenital anomalies of the kidney and urinary tract (CAKUT). HSALNG0134318 at CNV 22q11 was identified as CAKUT related lncRNA, which was coexpressed with multiple known CAKUT associated genes. To validate our findings, we performed knockdown experiments in HEK293 cell line to characterize the trascriptomic profiles regulated by HSALNG0134318 in human embryonic kidney cells.

2023-05-01 | GSE223312 | GEO

Selective Akt inhibition by MK-2206 eleminates colorectal cancer-initiating stem cells

Project description:To identify the regulatory mechanisms and signalling pathways involved in colorectal cancer (CRC) development, we compared the transcriptome of patient-derived tumor-initiating cells (TICs) with their normal stem cell counterparts of the same patient. This study demonstrates the relevance of AKT-signalling in colonic TIC proliferation and survival. Functional testing uncovered the selective AKT-inhibitor MK-2206 as a potential therapeutic for TIC-directed therapy in CRC. Gene expression profiling of tumor and normal tissues from 5 patients.

2016-07-06 | E-GEOD-70018 | biostudies-arrayexpress

Adaptive evolution by copy number variation in fall armyworms

Project description:CNV in fall armyworms

| PRJEB34915 | ENA

Great Ape Copy Number Variation

Project description:Intra-specific polymorphism in copy number is documented in many organisms, including human and chimpanzee, but very little is known for other great apes. This study aims to provide CNVs data for orangutan, gorilla, bonobo and chimpanzee, and compare the CNV patterns among these species, as well as with human CNVs and segmental duplications from public databases.

2011-08-03 | GSE30559 | GEO

Evaluation of somatic copy number variation detection by NGS techonologies and bioinformatics tools

Project description:We have benchmarked the performance of cancer CNV calling by six most recent software tools on their detection accuracy, sensitivity, and reproducibility. We also explored the consistency of CNV calling across different orthogonal technologies, including optical mapping and microarrays. Using consensus results from six CNV callers and confirmation from three orthogonal methods, we established a high-confidence CNV call set for the reference sample.

2023-08-25 | GSE212051 | GEO

Copy number variation in the porcine genome

Project description:Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, are currently being associated with phenotypes of clinical relevance, mostly in humans and mice. Notwithstanding, little is known about the extent of CNV that contributes to genetic variation in farm animals, including pig. This Nimblegen experiment reports a genome-wide high resolution map of copy number variation in the porcine genome. After remapping the initial CNV sequences to the latest genome assembly (Sus scrofa v.9), 84 CNV regions (CNVRs) were identified among the genomes of 21 related porcine samples from Duroc breed. We used a set of NimbleGen CGH arrays that tile across the assayable portion of the pig genome with approximately 2.1 million probes, at a 502 bp average probe spacing (Sus scrofa pre assembly version 6). These CNVRs covered 2 Mb of the genome, and ranged in size from 4 to 352 kb (median size of 12 kb). Together, this analysis provides a useful resource to assist with the assessment of CNVs in the contexts of porcine variation, health and productive efficiency.

2010-05-01 | GSE19047 | GEO

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