Skip to main content
  • Poster presentation
  • Open access
  • Published:

Functional variation of alternative splice forms in their protein interaction networks: a literature mining approach

Analyzing protein interactions and protein functions is crucial for the analysis of complex biological processes as well as the consequences from aberrant gene products [1]. Protein-Protein Interaction Networks (PPIN) are invaluable means enabling scientists to get a global understanding of interactomes, while analyzing individual protein functions [2]. High-throughput experiments and complete literature mining analyses have been used to deliver well-structured data into scientific databases reporting on proteins, their interactions and functions. These repositories form a precious resource to scientists, but only cover a portion of the proteome and often underrepresented alternative splice forms [3].

Alternative splicing (AS) is a cellular process that produces from a single gene different physical variants of a given protein which may differ in its structure or its function. This process produces molecular variability and contributes to the complexity of the proteomes and their interactomes. The analysis of AS shows that this process is most relevant to molecular regulation processes. In this research, we attempt to identify functional variability linked to alternative splice forms within their PPINs from the scientific literature. For this purpose, we gather AS events and analyze the transcript data for 16,826 different genes from the HumanSDB3 database [4, 5]. We have collected around 4 million abstracts from NCBI’s PubMed by utilizing a rich search term set for each individual isoform by using Gene DB, Swissprot DB and synonym generation. We then utilize an SVM classifier which uses in-domain features together with standard term weights and have trained it on the BioCreative-II IAS corpus (81.31% F1-measure on test set) for selecting those abstracts which are likely to contain interaction data. Finally, we employ another SVM classifier based on syntactic features and have trained it on the AIMed corpus (F1-measure of 54.20% cross validation performance) for extracting PPI information from the selected abstracts. The obtained PPIN comprises a total of 31,819 distinct interactions between 7,161 distinct proteins out of which 5,615 are considered to represent an isoform from HumanSDB3.

To the best of our knowledge, neither a genome-wide PPIN for the human protein isoforms has been built nor has their variability concerning interactions and functions been analyzed. Currently, we analyze the distribution of functional annotations based on the GO terms from the literature for all the isoforms. Both PPIN and functional annotations of the isoforms will be suitable for identifying potential interactions or functional variations of AS. Our findings are linked to the HumanSDB3 database and will be available through a publicly accessible web interface for further use.


  1. Jaeger S, Gaudan S, Leser U, Rebholz-Schuhmann D: Integrating Protein-Protein Interactions and Text Mining for Protein Function Prediction. BMC Bioinformatics 2008, 9(Suppl.8):S2. 10.1186/1471-2105-9-S8-S2

    Article  PubMed Central  PubMed  Google Scholar 

  2. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, Mering C: STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2008, 37(Database Issue):D412-D416.

    PubMed Central  PubMed  Google Scholar 

  3. Mathivanan S, Periaswamy B, Gandhi TKB, Kandasamy K, Suresh S, Mohmood R, Ramachandra YL, Pandey A: An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics 2006, 7(Suppl. 5):S19. 10.1186/1471-2105-7-S5-S19

    Article  PubMed Central  PubMed  Google Scholar 

  4. Taneri B, Novoradovsky A, Snyder B, Gaasterland T: Databases for comparative analysis of human-mouse orthologous alternative splicing. Lecture Notes in Bioinformatics 2005, 3388: 123–131.

    Google Scholar 

  5. Taneri B, Snyder B, Novoradovsky A, Gaasterland T: Alternative splicing of mouse transcription factors affect their DNA-binding domain architecture and is tissue specific. Genome Biol 2004, 5: R75. 10.1186/gb-2004-5-10-r75

    Article  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations


Corresponding author

Correspondence to Şenay Kafkas.

Rights and permissions

Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution 2.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Reprints and permissions

About this article

Cite this article

Kafkas, Ş., Varoğlu, E., Rebholz-Schuhmann, D. et al. Functional variation of alternative splice forms in their protein interaction networks: a literature mining approach. BMC Bioinformatics 11 (Suppl 5), P1 (2010).

Download citation

  • Published:

  • DOI: