Prediction of novel systems components in cell cycle regulation in malaria parasite by subnetwork alignments

With 300-500 clinical cases and 1-2 million deaths yearly, malaria contributes to enormous health care and economic burden worldwide. The advent of high throughput -omics technologies is driving new approaches to the identification of potential antimalarial targets. In this paper, we propose a neighborhood subnetwork alignment approach to uncover the network components involved in cell cycle regulation of the malaria parasite Plasmodium falciparum and to assign function to previously unannotated proteins.

[1]  Damian Szklarczyk,et al.  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored , 2010, Nucleic Acids Res..

[2]  Leann Tilley,et al.  Plasmodium falciparum metabolic pathways (MPMP) project upgraded with a database of subcellular locations of gene products. , 2011, Trends in parasitology.

[3]  G. Fall,et al.  The RhopH complex is transferred to the host cell cytoplasm following red blood cell invasion by Plasmodium falciparum. , 2008, Molecular and biochemical parasitology.

[4]  Hisashi Kashima,et al.  Kernels for graph classification , 2002 .

[5]  Bonnie Berger,et al.  Global Alignment of Multiple Protein Interaction Networks , 2008, Pacific Symposium on Biocomputing.

[6]  Serafim Batzoglou,et al.  Automatic Parameter Learning for Multiple Local Network Alignment , 2009, J. Comput. Biol..

[7]  Martin Kuiper,et al.  BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks , 2005, Bioinform..

[8]  M. Vignali,et al.  A protein interaction network of the malaria parasite Plasmodium falciparum , 2005, Nature.

[9]  Wojciech Szpankowski,et al.  Pairwise Alignment of Protein Interaction Networks , 2006, J. Comput. Biol..

[10]  Roded Sharan,et al.  Torque: topology-free querying of protein interaction networks , 2009, Nucleic Acids Res..

[11]  Jonathan E. Allen,et al.  Genome sequence of the human malaria parasite Plasmodium falciparum , 2002, Nature.

[12]  Wojciech Szpankowski,et al.  Detecting Conserved Interaction Patterns in Biological Networks , 2006, J. Comput. Biol..

[13]  Y. Freund,et al.  Profile-based string kernels for remote homology detection and motif extraction. , 2005, Journal of bioinformatics and computational biology.

[14]  Neil Hall,et al.  Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry , 2002, Nature.

[15]  Hans-Peter Kriegel,et al.  Graph Kernels For Disease Outcome Prediction From Protein-Protein Interaction Networks , 2006, Pacific Symposium on Biocomputing.

[16]  Yufeng Wang,et al.  Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum , 2012, BMC Systems Biology.

[17]  Rafael C. Jimenez,et al.  The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..

[18]  B. Cairns,et al.  The biology of chromatin remodeling complexes. , 2009, Annual review of biochemistry.

[19]  Manuel Llinás,et al.  The Apicomplexan AP2 family: integral factors regulating Plasmodium development. , 2011, Molecular and biochemical parasitology.

[20]  David L. Tabb,et al.  A proteomic view of the Plasmodium falciparum life cycle , 2002, Nature.

[21]  Trey Ideker,et al.  Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..

[22]  Hisashi Kashima,et al.  Marginalized Kernels Between Labeled Graphs , 2003, ICML.

[23]  J. Derisi,et al.  The Transcriptome of the Intraerythrocytic Developmental Cycle of Plasmodium falciparum , 2003, PLoS biology.

[24]  Patricia De la Vega,et al.  Discovery of Gene Function by Expression Profiling of the Malaria Parasite Life Cycle , 2003, Science.

[25]  Isabel M. Tienda-Luna,et al.  Inferring the skeleton cell cycle regulatory network of malaria parasite using comparative genomic and variational Bayesian approaches , 2007, Genetica.

[26]  Hagai Ginsburg,et al.  The transcriptome of Plasmodium vivax reveals divergence and diversity of transcriptional regulation in malaria parasites , 2008, Proceedings of the National Academy of Sciences.

[27]  Sourav Bandyopadhyay,et al.  Systematic identification of functional orthologs based on protein network comparison. , 2006, Genome research.

[28]  Thomas Gärtner,et al.  On Graph Kernels: Hardness Results and Efficient Alternatives , 2003, COLT.

[29]  H. Kashima,et al.  Kernels for graphs , 2004 .

[30]  S. V. N. Vishwanathan,et al.  Graph kernels , 2007 .

[31]  Francis Bach,et al.  Global alignment of protein–protein interaction networks by graph matching methods , 2009, Bioinform..