scholarly journals Integrative Visual Analysis of the Effects of Alternative Splicing on Protein Domain Interaction Networks

2008 ◽  
Vol 5 (2) ◽  
Author(s):  
Dorothea Emig ◽  
Melissa S. Cline ◽  
Karsten Klein ◽  
Anne Kunert ◽  
Petra Mutzel ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Protein Interactions ◽  
Visual Analysis ◽  
Protein Isoforms ◽  
Interaction Networks ◽  
Protein Domain ◽  
Domain Interaction ◽  
Exon Arrays ◽  
Exon Expression ◽  
Splicing Patterns

SummaryProteins and their interactions are essential for the functioning of all organisms and for understanding biological processes. Alternative splicing is an important molecular mechanism for increasing the protein diversity in eukaryotic cells. Splicing events that alter the protein structure and the domain composition can be responsible for the regulation of protein interactions and the functional diversity of different tissues. Discovering the occurrence of splicing events and studying protein isoforms have become feasible using Affymetrix Exon Arrays. Therefore, we have developed the versatile Cytoscape plugin DomainGraph that allows for the visual analysis of protein domain interaction networks and their integration with exon expression data. Protein domains affected by alternative splicing are highlighted and splicing patterns can be compared.

scholarly journals The functional impact of alternative splicing in cancer

2016 ◽  
Author(s):  
Héctor Climente-González ◽  
Eduard Porta-Pardo ◽  
Adam Godzik ◽  
Eduardo Eyras
Keyword(s):  
Alternative Splicing ◽  
Negative Correlation ◽  
Protein Interactions ◽  
Somatic Mutations ◽  
Protein Domain ◽  
Protein Protein Interactions ◽  
Systematic Analysis ◽  
Functional Impact ◽  
Functional Consequences ◽  
Functional Transformations

SummaryAlternative splicing changes are frequently observed in cancer and are starting to be recognized as important signatures for tumor progression and therapy. However, their functional impact and relevance to tumorigenesis remains mostly unknown. We carried out a systematic analysis to characterize the potential functional consequences of alternative splicing changes in thousands of tumor samples. This analysis revealed that a subset of alternative splicing changes affect protein domain families that are frequently mutated in tumors and potentially disrupt protein protein interactions in cancer-related pathways. Moreover, there was a negative correlation between the number of these alternative splicing changes in a sample and the number of somatic mutations in drivers. We propose that a subset of the alternative splicing changes observed in tumors may represent independent oncogenic processes that could be relevant to explain the functional transformations in cancer and some of them could potentially be considered alternative splicing drivers (AS-drivers).

Protein Domain Annotation with Predicted Domain-Domain Interaction Networks

2008 ◽  
Vol 15 (5) ◽  
pp. 456-462 ◽  
Author(s):  
Xing-Ming Zhao ◽  
Yong Wang ◽  
Luonan Chen ◽  
Kazuyuki Aihara
Keyword(s):  
Interaction Networks ◽  
Protein Domain ◽  
Domain Interaction ◽  
Domain Annotation

scholarly journals Protein-Protein Interactions Inferred from Domain-Domain Interactions in Genogroup II Genotype 4 Norovirus Sequences

2013 ◽  
Vol 2013 ◽  
pp. 1-7
Author(s):  
Chuan-Ching Huang ◽  
Chuan Yi Tang
Keyword(s):  
Protein Interactions ◽  
Protein Domain ◽  
Protein Protein Interactions ◽  
Domain Interaction ◽  
Genotype 4 ◽  
Interaction Database ◽  
Domain Interactions ◽  
Severe Gastroenteritis ◽  
Worldwide Phenomenon ◽  
Infection Processes

Severe gastroenteritis and foodborne illness caused by Noroviruses (NoVs) during the winter are a worldwide phenomenon. Vulnerable populations including young children and elderly and immunocompromised people often require hospitalization and may die. However, no efficient vaccine for NoVs exists because of their variable genome sequences. This study investigates the infection processes in protein-protein interactions between hosts and NoVs. Protein-protein interactions were collected from related Pfam NoV domains. The related Pfam domains were accumulated incrementally from the protein domain interaction database. To examine the influence of domain intimacy, the 7 NoV domains were grouped by depth. The number of domain-domain interactions increased exponentially as the depth increased. Many protein-protein interactions were relevant; therefore, cloud techniques were used to analyze data because of their computational capacity. The infection relationship between hosts and NoVs should be used in clinical applications and drug design.

scholarly journals Alternative splicing of a Drosophila tropomyosin gene generates muscle tropomyosin isoforms with different carboxy-terminal ends.

1984 ◽  
Vol 4 (12) ◽  
pp. 2828-2836 ◽  
Author(s):  
G S Basi ◽  
M Boardman ◽  
R V Storti
Keyword(s):  
Alternative Splicing ◽  
Transcription Unit ◽  
Protein Isoforms ◽  
Tropomyosin Isoforms ◽  
Exon Splicing ◽  
Muscle Tropomyosin ◽  
Specific Mrnas ◽  
Carboxy Terminal ◽  
Splicing Patterns ◽  
I Gene

The muscle tropomyosin I (mTm I) gene from Drosophila melanogaster has been analyzed and shown to express a complex transcription unit consisting of two sets of tissue-specific mRNAs. A 1.3- and 1.6-kilobase set of mRNAs is expressed during myogenesis in embryos, and in myogenic cell cultures. The mRNAs encode a 34,000-dalton muscle tropomyosin isoform. The same mTm I gene expresses a different set of 1.7- and 1.9-kilobase mRNAs in thoracic flight muscle tissue of the adult. The thorax RNAs encode a new tropomyosin isoform resolved on two-dimensional gels. The structure of the gene has been determined, and we show that the embryonic and thoracic mRNAs are generated by alternative splicing. The alternate exon splicing patterns determine a different 27 amino acids at the carboxy-terminal end of the two tropomyosin isoforms. These results show that the carboxy-terminal domain of tropomyosin is highly regulated in determining tropomyosin function. The results also show that contractile protein isoforms can be generated by single as well as multiple genes.

Alternative splicing of a Drosophila tropomyosin gene generates muscle tropomyosin isoforms with different carboxy-terminal ends

1984 ◽  
Vol 4 (12) ◽  
pp. 2828-2836
Author(s):  
G S Basi ◽  
M Boardman ◽  
R V Storti
Keyword(s):  
Alternative Splicing ◽  
Transcription Unit ◽  
Protein Isoforms ◽  
Tropomyosin Isoforms ◽  
Exon Splicing ◽  
Muscle Tropomyosin ◽  
Specific Mrnas ◽  
Carboxy Terminal ◽  
Splicing Patterns ◽  
I Gene

The muscle tropomyosin I (mTm I) gene from Drosophila melanogaster has been analyzed and shown to express a complex transcription unit consisting of two sets of tissue-specific mRNAs. A 1.3- and 1.6-kilobase set of mRNAs is expressed during myogenesis in embryos, and in myogenic cell cultures. The mRNAs encode a 34,000-dalton muscle tropomyosin isoform. The same mTm I gene expresses a different set of 1.7- and 1.9-kilobase mRNAs in thoracic flight muscle tissue of the adult. The thorax RNAs encode a new tropomyosin isoform resolved on two-dimensional gels. The structure of the gene has been determined, and we show that the embryonic and thoracic mRNAs are generated by alternative splicing. The alternate exon splicing patterns determine a different 27 amino acids at the carboxy-terminal end of the two tropomyosin isoforms. These results show that the carboxy-terminal domain of tropomyosin is highly regulated in determining tropomyosin function. The results also show that contractile protein isoforms can be generated by single as well as multiple genes.

scholarly journals DISPOT: a simple knowledge-based protein domain interaction statistical potential

2019 ◽  
Vol 35 (24) ◽  
pp. 5374-5378 ◽  
Author(s):  
Oleksandr Narykov ◽  
Dmytro Bogatov ◽  
Dmitry Korkin
Keyword(s):  
Protein Interactions ◽  
Experimental Studies ◽  
Protein Domain ◽  
Supplementary Information ◽  
Protein Protein Interactions ◽  
Domain Interaction ◽  
Statistical Potential ◽  
Knowledge Based ◽  
Scop Family

Abstract Motivation The complexity of protein–protein interactions (PPIs) is further compounded by the fact that an average protein consists of two or more domains, structurally and evolutionary independent subunits. Experimental studies have demonstrated that an interaction between a pair of proteins is not carried out by all domains constituting each protein, but rather by a select subset. However, determining which domains from each protein mediate the corresponding PPI is a challenging task. Results Here, we present domain interaction statistical potential (DISPOT), a simple knowledge-based statistical potential that estimates the propensity of an interaction between a pair of protein domains, given their structural classification of protein (SCOP) family annotations. The statistical potential is derived based on the analysis of >352 000 structurally resolved PPIs obtained from DOMMINO, a comprehensive database of structurally resolved macromolecular interactions. Availability and implementation DISPOT is implemented in Python 2.7 and packaged as an open-source tool. DISPOT is implemented in two modes, basic and auto-extraction. The source code for both modes is available on GitHub: https://github.com/korkinlab/dispot and standalone docker images on DockerHub: https://hub.docker.com/r/korkinlab/dispot. The web server is freely available at http://dispot.korkinlab.org/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals DIGGER: exploring the functional role of alternative splicing in protein interactions

2020 ◽  
Vol 49 (D1) ◽  
pp. D309-D318 ◽  
Author(s):  
Zakaria Louadi ◽  
Kevin Yuan ◽  
Alexander Gress ◽  
Olga Tsoy ◽  
Olga V Kalinina ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Protein Interactions ◽  
Functional Role ◽  
Protein Protein Interactions ◽  
Exon Expression ◽  
Specific Effects ◽  
Domain Interactions ◽  
Essential Resource ◽  
User Friendly

Abstract Alternative splicing plays a major role in regulating the functional repertoire of the proteome. However, isoform-specific effects to protein-protein interactions (PPIs) are usually overlooked, making it impossible to judge the functional role of individual exons on a systems biology level. We overcome this barrier by integrating protein-protein interactions, domain-domain interactions and residue-level interactions information to lift exon expression analysis to a network level. Our user-friendly database DIGGER is available at https://exbio.wzw.tum.de/digger and allows users to seamlessly switch between isoform and exon-centric views of the interactome and to extract sub-networks of relevant isoforms, making it an essential resource for studying mechanistic consequences of alternative splicing.

scholarly journals DISPOT: A simple knowledge-based protein domain interaction statistical potential

2019 ◽  
Author(s):  
Oleksandr Narykov ◽  
Dmitry Korkin
Keyword(s):  
Protein Interactions ◽  
Source Code ◽  
Experimental Studies ◽  
Protein Domain ◽  
Protein Protein Interactions ◽  
Domain Interaction ◽  
Statistical Potential ◽  
Link Type ◽  
Knowledge Based ◽  
Scop Family

AbstractMotivationThe complexity of protein-protein interactions (PPIs) is further compounded by the fact that an average protein consists of two or more domains, structurally and evolutionary independent subunits. Experimental studies have demonstrated that an interaction between a pair of proteins is not carried out by all domains constituting each protein, but rather by a select subset. However, finding which domains from each protein mediate the corresponding PPI is a challenging task.ResultsHere, we present Domain Interaction Statistical POTential (DISPOT), a simple knowledge-based statistical potential that estimates the propensity of an interaction between a pair of protein domains, given their SCOP family annotations. The statistical potential is derived based on the analysis of more than 352,000 structurally resolved protein-protein interactions obtained from DOMMINO, a comprehensive database on structurally resolved macromolecular interactionsAvailability and implementationDISPOT is implemented in Python 2.7 and packaged as an open-source tool. DISPOT is implemented in two modes, basic and auto-extraction. The source code for both modes is available on Github: (https://github.com/KorkinLab/DISPOT) and standalone docker images on DockerHub: (https://cloud.docker.com/u/korkinlab/repository/docker/korkinlab/dispot).

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