Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequencing of Coding and Non-coding Regions in Primary Breast Cancers and Patient-Matched Controls

ABSTRACT: Sequencing of Coding and Non-coding Regions in Primary Breast Cancers and Patient-Matched Controls

PROVIDER: PRJNA353973 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Sequencing of Coding and Non-coding Regions in Primary Breast Cancers and Patient-matched Controls

Project description:<p>Genomic analysis of tumor samples has led to the identification of hundreds of cancer genes based on the presence of mutations in protein-coding regions. By contrast, much less is known about cancer-causing mutations in non-coding regions. Here, we performed deep sequencing in 360 primary breast cancers and developed computational methods to identify significantly mutated promoters. Clear signals were found in the promoters of four genes. FOXA1, a known driver of hormone-receptor positive breast cancer, harbors a mutational hotspot in its promoter that leads to overexpression through increased E2F binding. RMRP and NEAT1, two non-coding RNA genes, carry mutations that alter protein binding to the promoter and impact expression levels. Overall, our study shows that recurrent mutations in or near gene promoters in cancers have functional consequences. Power analyses indicate that more such genes remain to be discovered through deep sequencing of adequately sized patient cohorts. </p>

| phs001250 | dbGaP

Homo sapiens

Project description:Sequencing of Coding and Non-coding Regions in Primary Breast Cancers and Patient-Matched Controls

| PRJNA353974 | ENA

Integrative identification of non-coding regulatory regions driving metastatic prostate cancer [MPRA]

Project description:Large-scale sequencing efforts have been undertaken to understand the mutational landscape of the coding genome. However, the vast majority of variants occur within non-coding genomic regions. We designed an integrative computational and experimental framework to identify recurrently mutated non-coding regulatory regions that drive tumor progression. Applying this framework to sequencing data from a large prostate cancer patient cohort revealed a large set of candidate drivers. We used (i) in silico analyses, (ii) massively parallel reporter assays, and (iii) in vivo CRISPR interference screens to systematically validate mCRPC drivers. One found enhancer region, GH22I030351, acts on a bidirectional promoter to simultaneously modulate expression of U2-associated splicing factor SF3A1 and chromosomal protein CCDC157. SF3A1 and CCDC157 promote tumor growth in vivo. We nominated a number of transcription factors, notably SOX6, to regulate expression of SF3A1 and CCDC157. Our integrative approach enables the systematic detection of non-coding regulatory regions that drive human cancers.

2025-10-01 | GSE274698 | GEO

Integrative identification of non-coding regulatory regions driving metastatic prostate cancer [CRISPR]

2025-10-01 | GSE274679 | GEO

Differential Mutations In Matched Primary and Metastatic Colorectal Cancers

Project description:Differential Mutations In Matched Primary and Metastatic Colorectal Cancers

| PRJNA314364 | ENA

Integrative identification of non-coding regulatory regions driving metastatic prostate cancer [CLIP-seq]

2025-10-01 | GSE274696 | GEO

Genomic Profile of Primary Colorectal Cancers and associated Liver Metastases

Project description:Comparison of genomic alterations of primary colorectal cancers with liver metastases of the same patient Keywords: array CGH, colorectal cancer, colon cancer, liver metastasis 21 primary colorectal cancers and 21 matched liver metastases hybridized against sex-matched control pools

2010-07-07 | E-GEOD-10179 | biostudies-arrayexpress

Gene expression in human oral mucosal fibroblasts and patient-matched skin fibroblasts

Project description:Wound healing within the oral mucosa results in minimal scar formation compared to wounds within the skin. We have recently demonstrated distinct differences in the ageing profiles of cells (oral mucosal and patient-matched skin fibroblasts) isolated from these tissues. We hypothesize that the increased replicative potential of oral mucosal fibroblasts may confer upon them preferential wound healing capacities. Passage-matched early cultures of oral mucosal fibroblasts and skin fibroblasts demonstrated distinct gene expression profiles with a number of genes linked to wound healing/tissue repair. We analyzed the gene expression profiles of oral mucosal and patient-matched skin fibroblasts for multiple patients both prior to (0h) and (6h) following a wounding stimulus.

2011-01-01 | GSE21648 | GEO

Gene expression changes in patient-matched gastric normal mucosa, adenomas, and carcinomas

Project description:sequential changes in gene expression profiles in the gastric adenoma-carcinoma sequence by analyzing eight patient-matched gastric normal mucosa, adenomas and carcinomas.

2010-09-28 | GSE24375 | GEO

Transcriptomic profiling of a glioblastoma multiforme patient with matched control brain tissue

Project description:To investigate differential gene expression, we analyzed the entire transcriptomes of tumor and matched normal brain tissues obtained from a patient who had glioblastoma multiforme. We extracted and sequenced the mRNA using Illumina GA2 platform. The raw data was analyzed using our recently developed program called RNASEQR, as well as ERANGE, MapSplice, SpliceMap, and TopHat. Tumor and matched control brain tissues were obtained from a Han-Chinese patient.

2011-10-30 | E-GEOD-33328 | 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