Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteogenomic Landscape of Squamous Cell Lung Cancer

ABSTRACT: Proteogenomic Landscape of Squamous Cell Lung Cancer

PROVIDER: PRJNA520937 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Proteogenomic Landscape of Squamous Cell Lung Cancer

Project description:Proteogenomic Landscape of Squamous Cell Lung Cancer

| PRJNA520938 | ENA

Proteogenomic Landscape of Squamous Cell Lung Cancer 2: Tandem Mass Tag Datasets

Project description:We report an integrated analysis incorporating DNA copy number analyses, somatic exon mutations, mRNA expression via RNA-sequencing, and shotgun mass spectrometry analysis of protein abundance in 108 surgically resected squamous cell lung cancers (SCC) with accompanying clinical outcome, evaluation of tumor pathology, and other clinically relevant data. We identified three major subtypes of SCC at the proteomic level, with two groups associated with inflammation/immune response or oxidation-reduction biology. Inflamed tumors could be further sub-classified based on neutrophil infiltration or antigen presentation proteomes and reflected patterns of infiltrating immune cells. No gene mutations, mRNA signatures, or proteomic subclasses were associated with outcomes; however, the presence of B-cell rich tertiary lymph node structures could be associated with better patient outcomes. By integrating our proteogenomic data with publicly available RNA interference screen data, we identified TP63, PSAT1, and AKR1C3 as vulnerabilities in SCC, particularly in the redox proteomic group. This cohort and its deep molecular data serves as an important resource to better understand biology and targets associated with SCC.

2019-05-24 | PXD010429 | Pride

The Proteogenomic Landscape of Curable Prostate Cancer [microarray]

Project description:The Proteogenomic Landscape of Curable Prostate Cancer [microarray]

| PRJNA419650 | ENA

Proteogenomic landscape of squamous cell lung cancer.

Project description:How genomic and transcriptomic alterations affect the functional proteome in lung cancer is not fully understood. Here, we integrate DNA copy number, somatic mutations, RNA-sequencing, and expression proteomics in a cohort of 108 squamous cell lung cancer (SCC) patients. We identify three proteomic subtypes, two of which (Inflamed, Redox) comprise 87% of tumors. The Inflamed subtype is enriched with neutrophils, B-cells, and monocytes and expresses more PD-1. Redox tumours are enriched for oxidation-reduction and glutathione pathways and harbor more NFE2L2/KEAP1 alterations and copy gain in the 3q2 locus. Proteomic subtypes are not associated with patient survival. However, B-cell-rich tertiary lymph node structures, more common in Inflamed, are associated with better survival. We identify metabolic vulnerabilities (TP63, PSAT1, and TFRC) in Redox. Our work provides a powerful resource for lung SCC biology and suggests therapeutic opportunities based on redox metabolism and immune cell infiltrates.

| S-EPMC6687710 | biostudies-literature

Proteogenomic Landscape of Squamous Cell Lung Cancer 1: Digestion QC with DIA LC-MS/MS

2019-05-24 | PXD010357 | Pride

Proteogenomic landscape of medulloblastoma subgroups

Project description:Proteogenomic landscape of medulloblastoma subgroups

| PRJNA420382 | ENA

Proteogenomic Landscape of Squamous Cell Lung Cancer

Project description:<p>To provide a detailed analysis on how genomic and transcriptomic alterations related to proteome level changes in squamous cell lung cancer (SCC), we performed an integrated analysis incorporating DNA copy number, somatic mutations, expression RNA-sequencing, and expression proteomics in 108 SCC nested within clinical outcome, tumor pathology, and other clinically relevant data.</p>

| phs001781 | dbGaP

Proteogenomic landscape of medulloblastoma subgroups [methylation]

Project description:Proteogenomic landscape of medulloblastoma subgroups [methylation]

| PRJNA413673 | ENA

Proteogenomic landscape of medulloblastoma subgroups [SNP]

Project description:Proteogenomic landscape of medulloblastoma subgroups [SNP]

| PRJNA420381 | ENA

Proteogenomic characterization analysis of human large cell lung cancer

Project description:Current clinical therapy of non-small cell lung cancer depends on histo-pathological classification. This approach poorly predicts clinical outcome for individual patients. Proteogenomic characterization analysis holds promise to improve clinical stratification, thus paving the way for individualized therapy. We investigated proteogenomic characterization and performed comprehensive integrative genomic analysis of human large cell lung cancer. Here we analyzed proteomes of 29 paired normal lung tissues and large cell lung cancer, identified significantly deregulated proteins associated with large cell lung cancer.

2019-01-16 | PXD012393 |

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