Systems biology via redescription and ontologies (III): Protein classification using malaria parasite's temporal transcriptomic profiles

Antonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, Bud Mishra

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

This paper addresses the protein classification problem, and explores how its accuracy can be improved by using information from time-course gene expression data. The methods are tested on data from the most deadly species of the parasite responsible for malaria infections, Plasmodium falciparum. Even though a vaccination for Malaria infections has been under intense study for many years, more than half of Plasmodium proteins still remain uncharacterized and therefore are exempted from clinical trials. The task is further complicated by a rapid life cycle of the parasite, thus making precise targeting of the appropriate proteins for vaccination a technical challenge. We propose to integrate protein-protein interactions (PPIs), sequence similarity, metabolic pathway, and gene expression, to produce a suitable set of predicted protein functions for P. falciparum. Further, we treat gene expression data with respect to various changes that occur during the five phases of the intraerythrocytic developmental cycle (IDC) (as determined by our segmentation algorithm) of P. falciparum and show that this analysis yields a significantly improved protein function prediction, e.g., when compared to analysis based on Pearson correlation coefficients seen in the data. The algorithm is able to assign "meaningful" functions to 628 out of 1439 previously unannotated proteins, which are first-choice candidates for experimental vaccine research.

Original languageEnglish (US)
Title of host publicationProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
Pages278-283
Number of pages6
DOIs
StatePublished - 2008
Event2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 - Philadelphia, PA, United States
Duration: Nov 3 2008Nov 5 2008

Other

Other2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
CountryUnited States
CityPhiladelphia, PA
Period11/3/0811/5/08

Fingerprint

Systems Biology
Malaria
Ontology
Parasites
Proteins
Gene expression
Plasmodium falciparum
Gene Expression
Vaccination
Plasmodium
Falciparum Malaria
Protein Transport
Vaccines
Metabolic Networks and Pathways
Infection
Life Cycle Stages
Life cycle
Clinical Trials
Research

ASJC Scopus subject areas

  • Molecular Biology
  • Information Systems
  • Biomedical Engineering

Cite this

Mitrofanova, A., Kleinberg, S., Carlton, J., Kasif, S., & Mishra, B. (2008). Systems biology via redescription and ontologies (III): Protein classification using malaria parasite's temporal transcriptomic profiles. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 (pp. 278-283). [4684903] https://doi.org/10.1109/BIBM.2008.82

Systems biology via redescription and ontologies (III) : Protein classification using malaria parasite's temporal transcriptomic profiles. / Mitrofanova, Antonina; Kleinberg, Samantha; Carlton, Jane; Kasif, Simon; Mishra, Bud.

Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. p. 278-283 4684903.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Mitrofanova, A, Kleinberg, S, Carlton, J, Kasif, S & Mishra, B 2008, Systems biology via redescription and ontologies (III): Protein classification using malaria parasite's temporal transcriptomic profiles. in Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008., 4684903, pp. 278-283, 2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, Philadelphia, PA, United States, 11/3/08. https://doi.org/10.1109/BIBM.2008.82
Mitrofanova A, Kleinberg S, Carlton J, Kasif S, Mishra B. Systems biology via redescription and ontologies (III): Protein classification using malaria parasite's temporal transcriptomic profiles. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. p. 278-283. 4684903 https://doi.org/10.1109/BIBM.2008.82
Mitrofanova, Antonina ; Kleinberg, Samantha ; Carlton, Jane ; Kasif, Simon ; Mishra, Bud. / Systems biology via redescription and ontologies (III) : Protein classification using malaria parasite's temporal transcriptomic profiles. Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. pp. 278-283
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