**7. References**

[1] Akula, S.; Miriyala, R.; Thota, H.; Rao, A.; Gedela, S. Techniques for Integrating –omics Data, Bioinformation, Views and Challenges, 2009.

Hierarchical Biological Pathway Data Integration and Mining 29

[19] Liu, Y.; Wang, Y.; Liu, Y.;, Tan, Z. Data Integration of Bioinformatics Database Based on Web Services, International Journal of Web Applications, Volume 1, Number 3, 2009.

[21] IntAct: open source database system and analysis tools for molecular interaction

[23] Zanzoni, A. Montecchi-Palazzi, L. Quondam, M. Ausiello, G. Helmer-Citterich, M. Cesareni, G. *MINT: A Molecular INTeraction database. Elsevier FEBS Letters, 2002, Volume* 

[24] Coessens B. et.al, *INCLUSive: A Web Portal and Service Registry for Microarray and Regulatory Sequence Analysis*, *Nucleic AciDS research, 2003, vol. 31, No.13. pp. 3468-3470.*

[25] Achard, F.; Vaysseix, G.; Barillot, E. XML, Bioinformatics, and Data Integration,

[27] Hsing, M., Cherkasov, A. Integration of Biological Data with Semantic Networks,

[28] Chung, M., Lim, M., Bae, M., Park, S. Customized Biological Database Integration for cDNA Microarray, RECOMB 2005, Research in Computational and Molecular Biology,

[29] Gopalcharyulu, P. Lindfors, E. et.al. Data integration and visualization system for enabling conceptual biology, BioInformatics, Vol.21, Suppl 1 2005, pp. i177-i185. [30] Rzhetsky, A et.al, GeneWays: A System for Extracting, Analyzing, Visualizing and

[31] Zucker, J.,Luciano, J., Brandes, A. Lin, X. Semantic Aggregation Integration and

[32] Hu, Z., Mellor, J., Wu, J., Yamada, T., Holloway, D., DeLisi, C. VisANT: Data integrating visual framework for biological networks and modules, Nucleic AciDS

[33] Zhang Z.; Bajic, V.; Yu, J.; Cheung, K.; Townsend, J. Data Integration in Bioinformatics: Current Efforts and Challenges. Bioinformatics: Trends and Methodologies, Intech,

[34] Zhang, D. and Jing, L., *Context based Numerical information*, *IEEE conference on Ecommerce Technology 2005*Arredondo, T., Seeger, M., Dombrovskaia, L., Avarias, J., Calderón, F., Candel, D., Muñoz, F., Latorre, V., Agulló, L., Cordova, M., and Gómez, L.: "Bioinformatics Integration Framework for Metabolic Pathway Data-Mining". In: Ali, M., Dapoigny, R. (eds): Innovations in Applied Artificial Intelligence. Lecture Notes in

Artificial Intelligence, Vol. 4031. Springer-Verlag, Berlin (2006) pp. 917-926.

[37] TRANSPATH. http://www.ncbi.nlm.nih.gov/pubmed/12519957

http://www.iam.metu.edu.tr/research/groups/compbio/PATIKA\_METU04.pdf

Integrating Molecular Pathway Data, Journal of Bioinformatics, 2004, 43-53.

[20] UCLA-DOE Institute for Genomics and Proteomics.

[22] GRID: http://www.moldiscovery.com/soft\_grid.php/

http://tomcatbackup.esat.kuleuven.be/inclusive/

[26] Pathway Data List. http://cbio.mskcc.org/prl

Current Bioinformatics, 2006, 1 000-000.

Inference: Three case studies, ISMB 2005.

Bioinformatics Review, Evry, France, 2001, pp. 115-125.

http://dip.doe-mbi.ucla.edu/dip/Main.cgi

data.http://www.ebi.ac.uk/intact/

*513, Issue 1, Pages 135-140.*

Cambridge, 2005.

research, 2005 vol. 33.

[36] INHO: http://www.inoh.org/

[38] ReactomeSTKE. http://stke.sciencemag.org/

2011.

[35] PATIKA:


Eve Syrkin Wurtele

Julie Dickerson

**7. References** 

*Department of Genetics, Development and Cell Biology, Iowa State University, USA* 

[1] Akula, S.; Miriyala, R.; Thota, H.; Rao, A.; Gedela, S. Techniques for Integrating –omics

[5] Thimm, O; Blasing, O; Gibon, Y; Nagel, A; Meyer, S; Kruger, P; Selbig, J; Muller, L; Rhee, S; and Stitt, M. MAPMAN: a user driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes, The Plant journal (2004) 37, pp 914-939. http://www.uky.edu/~aghunt00/PLS620/papers.htm/

http://metadatabase.org/wiki/BIND\_-\_Biomolecular\_Interaction\_Network\_Database [7] Bajic VB, Veronika M, Veladandi PS, Meka A, Heng MW, Rajaraman K, Pan H, Swarup S. Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical

[8] Pandey R, Guru R K, Mount D W. Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression

microarray data, Bioinformatics. 2004 Sep 1;20(13):2156-8. Epub 2004 May 14.

[10] PlantCare a database. http://bioinformatics.psb.ugent.be/webtools/plantcare/html/

[16] Friedman N, Linial, M; Nachman,I; and Pe'er, D. Using Bayesian Networks to Analyze Expression Data, Journal of computational biology, Volume 7, Numbers 3/4, 2000, pp.

[17] Schadt, et.al, *An Integrative Genomics Approach to Infer Causal Associations Between Gene Expression and Disease*, *Nature Genetics, vol.37, number 7, July 2005, pp, 710-717*.

[9] RegulonDB database: Escheichia Coli k-12 transcriptional network.

[15] TRANSFAC: http://www.gene-regulation.com/pub/databases.html/

[18] The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/).

[11] PLACE: a database of Plant Cis-acting regulatory netowrk.

[12] EPD: Eukaryotic promoter database. http://epd.vital-it.ch/

[13] TRRD: transcription regulatory regions database http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/

[3] KEGG: Kyoto Encyclopedia of Genes and Genomes. http://www.genome.jp/kegg/

*Electrical and Computer Engineering, Iowa State University, USA* 

Data, Bioinformation, Views and Challenges, 2009.

[4] TAIR- AraCyc: http://www.arabidopsis.org/biocyc/

Systems%20approaches%20copy/MAPMAN.pdf [6] BIND: Biomolecular Interaction Network Database

terms list, Plant Physiol. 2005 Aug; 138(4):1914-25.

http://regulondb.ccg.unam.mx/

[14] Athamap: http://www.athamap.de/

601-620.

http://www.dna.affrc.go.jp/PLACE/

[2] Saccharomyces genome database. http://www.yeastgenome.org/


**Chapter 2** 

© 2012 Yahya et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

© 2012 Yahya et al., licensee InTech. This is a paper distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

**Investigation on Nuclear Transport of** 

Umi Marshida Abdul Hamid and Farida Zuraina Mohd Yusof

Mohd Fakharul Zaman Raja Yahya,

http://dx.doi.org/10.5772/47448

**1. Introduction** 

**1.1. Trypanosomiasis** 

Additional information is available at the end of the chapter

*Trypanosoma brucei***: An** *in silico* **Approach** 

A group of animal and human diseases caused by parasitic protozoan trypanosomes is called trypanosomiases. The final decade of the 20th century witnessed a frightening revival in sleeping sickness (human African trypanosomiasis) in sub-Saharan Africa. Meanwhile, Chagas' disease (American trypanosomiasis) remains one of the most widespread infectious diseases in South and Central America. Arthropod vectors are responsible for the spread of African and American trypanosomiases, and disease restraint through insect control programs is an attainable target. However, the existing drugs for both illnesses are far from ideal. The trypanosomes are some of the earliest diverging members of the Eukaryotae and share several biochemical oddities that have inspired research into discovery of new drug targets. Nevertheless, discrepancies in mode of interactions between trypanosome species and their hosts have spoiled efforts to design drugs effective against both species. Heightened awareness of these neglected diseases might result in progress towards control

through increased financial support for drug development and vector eradication [1].

Trypanosome is a group of unicellular parasitic flagellate protozoa which mostly infects the vertebrate genera. A number of trypanosome species cause important veterinary diseases, but only two cause significant human diseases. In sub-Saharan Africa, *Trypanosoma brucei* causes sleeping sickness or human African trypanosomiasis whilst in America, *Trypanosoma cruzi* causes Chagas' disease (Figure 1) [2]. Meanwhile, the life cycle of these parasitic protozoa engage insect vectors and mammalian hosts (Figure 2) [1]. All trypanosomes require more than one obligatory host to complete their life cycle and are transmitted via vectors. Most of the species are transmitted by blood-feeding invertebrates, however there


**Chapter 2** 
