NDLI: Systems Biology via Redescription and Ontologies (III): Protein Classification Using Malaria Parasite's Temporal Transcriptomic Profiles

Content Provider	IEEE Xplore Digital Library
Author	Mitrofanova, A. Kleinberg, S. Carlton, J. Kasif, S. Mishra, B.
Copyright Year	2008
Description	Author affiliation: Dept. of Med. Parasitology, New York Univ., New York, NY (Carlton, J.) \|\| Biomed. Eng., Boston Univ., Boston, MA (Kasif, S.) \|\| Comput. Sci. Dept., New York Univ., New York, NY (Mitrofanova, A.; Kleinberg, S.; Mishra, B.)
Abstract	This paper addresses the protein classification problem, andexplores how its accuracy can be improved by using information fromtime-course gene expression data. The methods are tested on datafrom the most deadly species of the parasite responsible for malariainfections, Plasmodium falciparum. Even though avaccination for Malaria infections has been under intense study formany years, more than half of Plasmodiumproteins still remain uncharacterized and therefore are exemptedfrom clinical trials. The task is further complicated by arapid life cycle of the parasite, thus making precisetargeting of the appropriate proteins for vaccination a technicalchallenge. We propose to integrate protein-protein interactions (PPIs),sequence similarity, metabolic pathway, andgene expression, to produce a suitable set of predicted proteinfunctions for P.falciparum. Further,we treat gene expression data withrespect to various changes that occur during the five phases of theintraerythrocytic developmental cycle (IDC) (as determinedby our segmentation algorithm) ofP.falciparum and show that this analysis yields asignificantly improved protein function prediction, e.g., whencompared to analysis based on Pearson correlation coefficients seenin the data. The algorithm is able to assign ``meaningful''functions to 628 out of 1439 previously unannotated proteins, whichare first-choice candidates for experimental vaccine research.
Starting Page	278
Ending Page	283
File Size	523145
Page Count	6
File Format	PDF
ISBN	9780769534527
DOI	10.1109/BIBM.2008.82
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2008-11-03
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Protein engineering Sequences Information resources temporal transcriptomic profiles Ontologies protein function Gene expression malaria Diseases Computer science Plasmodium falciparum temporal gene expression Systems biology Bioinformatics data integration protein classification Testing
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Systems biology via redescription and ontologies (iii): protein classification using malaria parasite’s temporal transcriptomic profiles.

Heavy path mining reveals novel protein-protein associations in the malaria parasite plasmodium falciparum

Systems biology via redescription and ontologies (i): finding phase changes with applications to malaria temporal data (2008).

Systems biology via redescription and ontologies (I): finding phase changes with applications to malaria temporal data

Stage-Specific Expression of the Calmodulin Gene in Plasmodium falciparum

Deconvolution of Microarray Data Predicts Transcriptionally Regulated Protein Kinases of Plasmodium falciparum

Systems Biology via Redescription and Ontologies : Untangling the Malaria Parasite Life Cycle

Polyamine uptake in the malaria parasite, Plasmodium falciparum, is dependent on the parasite's membrane potential

Polyamine uptake in the malaria parasite, Plasmodium falciparum, is dependent on the parasite's membrane potential

Systems Biology via Redescription and Ontologies (III): Protein Classification Using Malaria Parasite's Temporal Transcriptomic Profiles

Similar Documents

Systems biology via redescription and ontologies (iii): protein classification using malaria parasite’s temporal transcriptomic profiles.

Heavy path mining reveals novel protein-protein associations in the malaria parasite plasmodium falciparum

Systems biology via redescription and ontologies (i): finding phase changes with applications to malaria temporal data (2008).

Systems biology via redescription and ontologies (I): finding phase changes with applications to malaria temporal data

Stage-Specific Expression of the Calmodulin Gene in Plasmodium falciparum

Deconvolution of Microarray Data Predicts Transcriptionally Regulated Protein Kinases of Plasmodium falciparum

Systems Biology via Redescription and Ontologies : Untangling the Malaria Parasite Life Cycle

Polyamine uptake in the malaria parasite, Plasmodium falciparum, is dependent on the parasite's membrane potential

Polyamine uptake in the malaria parasite, Plasmodium falciparum, is dependent on the parasite's membrane potential

Systems Biology via Redescription and Ontologies (III): Protein Classification Using Malaria Parasite's Temporal Transcriptomic Profiles