Proteomics

Dataset Information

0

Identification of differentially expressed splice variants by the proteogenomic pipeline SPLICIFY


ABSTRACT: Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, SPLICIFY, which is able to detect differentially expressed protein isoforms. SPLICIFY is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions. Proof of concept was obtained by applying SPLICIFY to RNA sequencing and mass spectrometry data obtained from colorectal cancer cell line SW480, before and after siRNA-mediated down-modulation of the splicing factors SF3B1 and SRSF1. These analyses revealed 2172 and 149 differentially expressed isoforms, respectively, with peptide confirmation upon knock-down of SF3B1 and SRSF1 compared to their controls. Splice variants identified included RAC1, OSBPL3, MKI67 and SYK.

OTHER RELATED OMICS DATASETS IN: PRJNA422579

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Colon

DISEASE(S): Colon Cancer

SUBMITTER: Sander Piersma  

LAB HEAD: Connie Ramona Jimenez

PROVIDER: PXD006486 | Pride | 2017-07-28

REPOSITORIES: pride

Dataset's files

Source:
Action DRS
IsoSeq.zip Other
MaxQuant.zip Other
QE1_160915_OPL4019_GK_ALT_splice_SW480_A1.raw Raw
QE1_160915_OPL4019_GK_ALT_splice_SW480_A10.raw Raw
QE1_160915_OPL4019_GK_ALT_splice_SW480_A2.raw Raw
Items per page:
1 - 5 of 157
altmetric image

Publications


Proteogenomics, <i>i.e.</i> comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which can detect differentially expressed protein isoforms. Splic  ...[more]

Similar Datasets

2010-02-21 | E-GEOD-15548 | biostudies-arrayexpress
2013-02-23 | E-GEOD-41786 | biostudies-arrayexpress
2015-12-17 | E-GEOD-71195 | biostudies-arrayexpress
2015-09-16 | E-GEOD-62854 | biostudies-arrayexpress
2010-11-07 | E-GEOD-23694 | biostudies-arrayexpress
2012-11-28 | E-GEOD-42538 | biostudies-arrayexpress
2024-09-30 | GSE242550 | GEO
2013-03-05 | E-GEOD-42006 | biostudies-arrayexpress
2015-12-31 | E-MTAB-2515 | biostudies-arrayexpress
2011-09-08 | E-GEOD-22917 | biostudies-arrayexpress