ArticleJournal of proteome research2011
Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers.
Article in Journal of proteome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 44 citations in OpenAlex.
- Calumenin, A Calcium-Binding Modulatory Protein, Effective in Pathological Calcifications and Cancers, With Therapeutic Application Promise.FASEB bioAdvances · 2025Review
- Silencing Calumenin Expression via Artificial MicroRNA, a Potential Breakthrough for Inhibiting Proliferation, Halting Migration, and Triggering Apoptosis in Breast Cancer Cells.Advanced pharmaceutical bulletin · 2025Article
- Concordant Gene Expression and Alternative Splicing Regulation under Abiotic Stresses in Arabidopsis.Genes · 2024Article
- Advances and Utility of the Human Plasma Proteome.Journal of proteome research · 2021Review
- IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation.Bioinformatics (Oxford, England) · 2021Article
- Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years.Molecular & cellular proteomics : MCP · 2021Article
- Structural basis of the selective activation of enzyme isoforms: Allosteric response to activators of β1- and β2-containing AMPK complexes.Computational and structural biotechnology journal · 2021Article
- Computational Methods for Predicting Functions at the mRNA Isoform Level.International journal of molecular sciences · 2020Review
- Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications.Journal of proteome research · 2016Article
- A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling.Briefings in bioinformatics · 2016Article
- Comprehensive landscape of subtype-specific coding and non-coding RNA transcripts in breast cancer.Oncotarget · 2016Article
- A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.PLoS computational biology · 2016Article
- Strategies for Genomic and Proteomic Profiling of Cancers.Statistics in biosciences · 2016Article
- A Network of Splice Isoforms for the Mouse.Scientific reports · 2016Article
- Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.Journal of proteome research · 2015Article
- Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study.Journal of proteome 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
- The emerging era of genomic data integration for analyzing splice isoform function.Trends in genetics : TIG · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Alternative splicing allows a single gene to generate multiple mRNA transcripts, which can be translated into functionally diverse proteins. However, experimentally determined structures of protein splice isoforms are rare, and homology modeling methods are poor at predicting atomic-level structural differences because of high sequence identity. Here we exploit the state-of-the-art structure prediction method I-TASSER to analyze the structural and functional consequences of alternative splicing of proteins differentially expressed in a breast cancer model. We first successfully benchmarked the I-TASSER pipeline for structure modeling of all seven pairs of protein splice isoforms, which are known to have experimentally solved structures. We then modeled three cancer-related variant pairs reported to have opposite functions. In each pair, we observed structural differences in regions where the presence or absence of a motif can directly influence the distinctive functions of the variants. Finally, we applied the method to five splice variants overexpressed in mouse Her2/neu mammary tumor: anxa6, calu, cdc42, ptbp1, and tax1bp3. Despite >75% sequence identity between the variants, structural differences were observed in biologically important regions of these protein pairs. These results demonstrate the feasibility of integrating proteomic analysis with structure-based conformational predictions of differentially expressed alternative splice variants in cancers and other conditions.
Indexed as
Identifiers
What OpenQuestion holds
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.