Abstract
Recent advances have provided a working interactome map for the human malaria parasite Plasmodium falciparum. The aforementioned map, generated from genome-scale analyses, has provided a basis for proteomic studies of the parasite; however, such large-scale approaches commonly suffer from undersampling and lack of coverage. The current map bears no exception, containing only one-quarter of the organism's proteins. Inspired by the needs of the current map and the wealth of bioinformatics data, we assembled a map of 19 979 interactions among 2321 proteins in P. falciparum. The resultant map was generated by computationally inferring protein-protein interactions from evolutionarily conserved protein interactions, underlying domain interactions, and experimental observations. To compile this information into a repository of meaningful data, we assessed interaction quality by applying a logistic regression method, which correlated the presence of an interaction with relevant cellular parameters. Interestingly, it was found that sub-networks from different sources are quite dissimilar in their topologies and overlap to a very small extent. Applying Markov clustering, we observe a typical cluster composition, featuring common cellular functions that were previously reported absent, making this map a valuable resource for understanding the biology of this organism.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1461-1470 |
| Number of pages | 10 |
| Journal | Journal of Proteome Research |
| Volume | 6 |
| Issue number | 4 |
| DOIs | |
| State | Published - Apr 2007 |
| Externally published | Yes |
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Keywords
- Human malaria parasite
- Interactome
- P. falciparum
ASJC Scopus subject areas
- Biochemistry
- Biotechnology
- Genetics
Cite this
A draft of protein interactions in the malaria parasite P. falciparum. / Wuchty, Stefan; Ipsaro, Jonathan J.
In: Journal of Proteome Research, Vol. 6, No. 4, 04.2007, p. 1461-1470.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - A draft of protein interactions in the malaria parasite P. falciparum
AU - Wuchty, Stefan
AU - Ipsaro, Jonathan J.
PY - 2007/4
Y1 - 2007/4
N2 - Recent advances have provided a working interactome map for the human malaria parasite Plasmodium falciparum. The aforementioned map, generated from genome-scale analyses, has provided a basis for proteomic studies of the parasite; however, such large-scale approaches commonly suffer from undersampling and lack of coverage. The current map bears no exception, containing only one-quarter of the organism's proteins. Inspired by the needs of the current map and the wealth of bioinformatics data, we assembled a map of 19 979 interactions among 2321 proteins in P. falciparum. The resultant map was generated by computationally inferring protein-protein interactions from evolutionarily conserved protein interactions, underlying domain interactions, and experimental observations. To compile this information into a repository of meaningful data, we assessed interaction quality by applying a logistic regression method, which correlated the presence of an interaction with relevant cellular parameters. Interestingly, it was found that sub-networks from different sources are quite dissimilar in their topologies and overlap to a very small extent. Applying Markov clustering, we observe a typical cluster composition, featuring common cellular functions that were previously reported absent, making this map a valuable resource for understanding the biology of this organism.
AB - Recent advances have provided a working interactome map for the human malaria parasite Plasmodium falciparum. The aforementioned map, generated from genome-scale analyses, has provided a basis for proteomic studies of the parasite; however, such large-scale approaches commonly suffer from undersampling and lack of coverage. The current map bears no exception, containing only one-quarter of the organism's proteins. Inspired by the needs of the current map and the wealth of bioinformatics data, we assembled a map of 19 979 interactions among 2321 proteins in P. falciparum. The resultant map was generated by computationally inferring protein-protein interactions from evolutionarily conserved protein interactions, underlying domain interactions, and experimental observations. To compile this information into a repository of meaningful data, we assessed interaction quality by applying a logistic regression method, which correlated the presence of an interaction with relevant cellular parameters. Interestingly, it was found that sub-networks from different sources are quite dissimilar in their topologies and overlap to a very small extent. Applying Markov clustering, we observe a typical cluster composition, featuring common cellular functions that were previously reported absent, making this map a valuable resource for understanding the biology of this organism.
KW - Human malaria parasite
KW - Interactome
KW - P. falciparum
UR - http://www.scopus.com/inward/record.url?scp=34248164526&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=34248164526&partnerID=8YFLogxK
U2 - 10.1021/pr0605769
DO - 10.1021/pr0605769
M3 - Article
C2 - 17300188
AN - SCOPUS:34248164526
VL - 6
SP - 1461
EP - 1470
JO - Journal of Proteome Research
JF - Journal of Proteome Research
SN - 1535-3893
IS - 4
ER -