Dataset Information

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

ACCESS DATA

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

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Publications

Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify.

Komor Malgorzata A MA Pham Thang V TV Hiemstra Annemieke C AC Piersma Sander R SR Bolijn Anne S AS Schelfhorst Tim T Delis-van Diemen Pien M PM Tijssen Marianne M Sebra Robert P RP Ashby Meredith M Meijer Gerrit A GA Jimenez Connie R CR Fijneman Remond J A RJA

Molecular & cellular proteomics : MCP 20170726 10

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]

PMID: 28747380

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