Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human colorectal cancer CPTAC dataset

ABSTRACT: This is a same data set generated by Vanderbilt University. 6M spectra was generated from 95 colorectal cancer samples. We used SpliceDB tool to generate a customized database which includes novel / alternative splice junction and small SNV information.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Vineet Bafna

PROVIDER: MSV000079166 | MassIVE | Thu Jun 18 13:32:00 BST 2015

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Publications

Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer.

Woo Sunghee S Cha Seong Won SW Bonissone Stefano S Na Seungjin S Tabb David L DL Pevzner Pavel A PA Bafna Vineet V

Journal of proteome research 20150721 9

Aiming toward an improved understanding of the regulation of proteins in cancer, recent studies from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) have focused on analyzing cancer tissue using proteomic technologies and workflows. Although many proteogenomics approaches for the study of cancer samples have been proposed, serious methodological challenges remain, especially in the identification of multiple mutational variants or structural variations such as fusion gene events. In add ...[more]

PMID: 26139413

Similar Datasets

Using RNA-Seq to create sample-specific proteomic databases that enable mass spectrometric discovery of splice junction peptides

Project description:Many new alternative splice forms have been detected at the transcript level using next generation sequencing (NGS) methods, especially RNA-Seq, but it is not known how many of these transcripts are being translated. Leveraging the unprecedented capabilities of NGS, we collected RNA-Seq and proteomics data from the same cell population (Jurkat cells) and created a bioinformatics pipeline that builds customized databases for the discovery of novel splice-junction peptides. Results: Eighty million paired-end Illumina reads and ~500,000 tandem mass spectra were used to identify 12,873 transcripts (19,320 including isoforms) and 6,810 proteins. We developed a bioinformatics workflow to retrieve high-confidence, novel splice junction sequences from the RNA data, translate these sequences into the analogous polypeptide sequence, and create a customized splice junction database for MS searching. Jurkat T-cell mRNA was analyzed on an Illumina HiSeq2000. ~80 million paired end reads (2x200bp, ~350bp lengths) were collected.

2013-05-17 | E-GEOD-45428 | biostudies-arrayexpress

Using RNA-Seq to create sample-specific proteomic databases that enable mass spectrometric discovery of splice junction peptides

2013-05-17 | GSE45428 | GEO

Colorectal adenocaricinomas and matched normal colonic tissues

Project description:Five colorectal adenocarcinomas and matched normal colonic tissuesÂ were analyzed with Affymetrix HG-U133-Plus-2.0 microarrays. Two labs independently generated microarray data with the same array platform on the same biological samples. Colorectal adenocarcinomas and matched normal colonic RNA sample were purchased from Oncomatrix, Inc., San Diego, CA. The RNA from each biological sample was distributed to and processed in two laboratories at Stanford University.

2012-10-03 | E-GEOD-41328 | biostudies-arrayexpress

Consensus molecular subtypes as biomarkers of FU/FA maintenance therapy with or without panitumumab in RAS wild-type metastatic colorectal cancer (PanaMa, AIO KRK 0212).

Project description:Customized Nanostring PanCancer Progression Panel performed on FFPE tumor tissue derived from treatment naive metastatic colorectal cancer patients included into the randomized phase 2 PanaMa trial.

2023-02-15 | GSE221953 | GEO

Colorectal liver metastasis profiles

Project description:Expression profiles of colorectal liver metastasis samples collected from Paul Brousse Hospital (France) and University Hospital Utrecht (The Netherlands). Patients are divided into a high-risk (DFS < 1 year) and a low-risk group (DFS < 1 year).

2012-11-29 | E-TABM-1112 | biostudies-arrayexpress

Next Generation Sequencing (NGS) for quantitative transcriptomic analysis of colorectal tumor cell lines and their ENU mutants

Project description:Purpose: To understand differences of gene expression profiles between colorectal cell lines and their ENU mutants. Methods: RNA profiles were generated by deep sequencing using Illumina Next-seq. Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (GRCm38 release-95). Conclusions: Our study represents the detailed differential transcriptomic analysis using ENU mutants of colorectal tumors, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2024-06-07 | GSE176264 | GEO

Identification of a gene expression signature in colorectal adenocarcinoma in comparison with colorectal adenoma

Project description:We showed that a lot of genes were deregulated in colorectal adenocarcinomas in comparison with colorectal adenomas. 37 colorectal adenoma and 9 colorectal adenocarcinoma samples were analyzed. We generated a comparison between adenocarcinomas and adenomas.

2013-08-27 | E-GEOD-50115 | biostudies-arrayexpress

CPTAC Colorectal Dataset - Patient 3518

Project description:CPTAC Colorectal Dataset - tumor proteomics data from patient TCGA-AA-3518-01A-11, extracted from the full dataset MSV000079852. Data was originally imported from: https://cptac-data-portal.georgetown.edu/cptac/s/S016 and https://cptac-data-portal.georgetown.edu/cptac/s/S019

2017-04-13 | MSV000080921 | MassIVE

Transcriptomic profiles of advanced colorectal adenomas from 40 Korean patients

Project description:We report the RNA-seq data of 40 advanced colorectal adenoma patients form Dongguk University Ilsan International Hospital. The polyps with a diameter of 1cm or greater were regarded as advenced colorectal adenoma and obtained through colonoscopy. The data consist of 22 tublar adenoma, 6 tublovillous adenoma, 5 sessile serrated adenoma/polyp, 1 traditional serrated adenoma, intramucosal adenocarcinoma, neuroendocrine tumor, hyperplastic polyp, inflammatory polyp, high grade dysplasia, and atypical glands with adjacent hyperplastic mucosa.

2023-08-07 | GSE154548 | GEO

Nano-HPLC-MS/MS analysis for proteins encoded by circRNA in myoblasts and myotubes

Project description:The MS/MS spectra were searched against a custom protein database from span back-splice junction circRNA open reading frame prediction.

2020-08-21 | PXD021030 |

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