ArticleCancer research2010
Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers.
Article in Cancer research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 60 citations in OpenAlex.
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- Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Strategies for Genomic and Proteomic Profiling of Cancers.Statistics in biosciences · 2016Article
- Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.Journal of proteome research · 2015Article
- Differential mRNA expression profiling of oral squamous cell carcinoma by high-throughput RNA sequencing.Journal of biomedical research · 2015Article
- Mapping Splicing Quantitative Trait Loci in RNA-Seq.Cancer informatics · 2015Article
- Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence.Proteomics · 2014Article
- Onco-proteogenomics: cancer proteomics joins forces with genomics.Nature methods · 2014Article
- A large-scale RNAi-based mouse tumorigenesis screen identifies new lung cancer tumor suppressors that repress FGFR signaling.Cancer discovery · 2014Article
- SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples.Nucleic acids research · 2014Article
- The emerging era of genomic data integration for analyzing splice isoform function.Trends in genetics : TIG · 2014Review
- A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines.Journal of proteomics · 2014Review
- Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics.Journal of proteome research · 2014Review
- SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.Molecular & cellular proteomics : MCP · 2014Article
- Application of genetic algorithms and constructive neural networks for the analysis of microarray cancer data.Theoretical biology & medical modelling · 2014Article
- Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins.Biochimica et biophysica acta · 2014Article
- Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes.Journal of proteome research · 2014Article
- Mapping Splicing Quantitative Trait Loci in RNA-Seq.Cancer informatics · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Multifaceted alternative splicing in cancer cells greatly diversifies protein structure independently of genome changes, but the characterization of cancer-associated splice variants is quite limited. In this study, we used mass spectrometric data to interrogate a custom-built database created with three-frame translations of mRNA sequences from Ensembl and ECgene to find alternative splice variant proteins. In mass spectrometric files from liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses of normal mouse mammary glands or mammary tumors derived from conditional human epidermal growth factor receptor 2 (Her2)/neu transgenic mice, we identified a total of 608 alternative splice variants, of which peptides from 216 proteins were found only in the tumor sample. Among the 608 splice variants were 68 novel proteins that were not completely matched to any known protein sequence in mice, for which we found known functional motifs. Biological process enrichment analysis of the splice variants identified suggested the involvement of these proteins especially in cell motility and translation initiation. The cancer-associated differentially expressed splice variant proteins offer novel biomarker candidates that may function in breast cancer progression or metastasis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.