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Research Unit for Immunoinformatics
S. Sujatha MOHAN
Unit Leader
S. Sujatha MOHAN (Ph.D.)
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Research Areas

Primary Immunodeficiency diseases (PID) are a class of disorders resulting from intrinsic defects in genes involved in the development and maintenance of the immune system. Despite rapid developments in the science of PID, early diagnosis and effective treatment of PID are posed with new challenges to physicians all over the world. Our main aim is to maintain informational platform that bring PID clinicians and researchers in Asia together and also to establish active Asian network among interested groups who are involved in PID that will further link to other established PID groups from other parts of the world. No such community involvement has so far been initiated for PID in Asia. Towards this, we have constructed a web-based compendium of molecular alterations in PID, named Resource of Asian Primary Immunodeficiency Diseases (RAPID), which is available as a worldwide web resource at http://rapid.rcai.riken.jp/. RAPID is an object-oriented database. We used Zope (http://www.zope.org) for the development of RAPID. Zope is a leading open source web application server and is built using the programming language Python (http://www.python.org). MySQL is used as a backend data storage system.There are 167 PID gene pages in RAPID, out of which, 145 genes are reported with pathological mutations. Sequence-variations in PID genes identified in patients are manually curated from published literature and mapped to NCBI RefSeq genomic, cDNA and protein sequences as per the recommendations of Human Genome Variations Society. Each mutation on the database is also linked to "Mutation@A glance" a web-based graphical user interface (GUI) enabled tool which can be accessed at http://rapid.rcai.riken.jp/mutBrowse.cgi. It facilitates user to visualize the mutation position both at the level of DNA and protein sequences as well as homology based three-dimensional structures with various types of information such as SNP, protein domains and functional sites. RAPID also contains protein-protein interaction from Human Protein Reference Database, expression profiles from Gene Expression Omnibus and RefDIC, mouse phenotypes from Mouse genome database (MGI).RAPID also contains mouse phenotypes from Mouse genome database (MGI). With community participation of interested groups, we anticipate that RAPID will become a primary resource of PIDs in Asia.

Research Subject

  1. Construction of web-based, integrated open access database for primary immunodeficiency diseases
  2. Annotation of reported sequence variations in PID genes from published literature
  3. Generation of PID gene-specific signaling pathway using e-Path visualization tool
  4. Prediction of novel candidate PID genes using Support Vector Machine (SVM) learning approach

Related links

  1. RIKEN Research Center for Allergy and Immunology Website_Laboratories PageNew Window

List of Selected Publications

  1. Keerthikumar, S., Raju, R., et al.:
    "RAPID: Resource of Asian Primary Immunodeficiency diseases."
    Nucleic Acids Research, 37 (Database issue): D863-7 (2009).
  2. Prasad, T. S. K., Goel, R., et al.:
    "Human Protein Reference Database - 2009 update."
    Nucleic Acids Research, 37 (Database issue): D767-72 (2009).
  3. Mathivanan S, Ahmed M. et al.:
    "Human Proteinpedia enables sharing of human protein data."
    Nature Biotechnology, 26(2): 164-7 (2008).
  4. Gandhi, T K B, Zhong, J., et al.:
    "Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets."
    Nature Genetics. 38: 285-293 (2006).
  5. Suresh, S., S. Sujatha Mohan., et al.:
    "Proteomic resources: Integrating biomedical information in humans."
    Gene. 2005; 364: 13-18.
  6. Kandasamy, K.*, Mohan, S.S*, Raju, R., Keerthikumar, S., et al.:
    "A Public Resource of Curated Signal Transduction Pathways. Genome Biology"
    Genome Biology.
  7. Kandasamy, K., Keerthikumar, S., Rajesh.:
    "PathBuilder - Open Source Software for Annotating and Developing Pathway Resources."
    Bioinformatics, 25(21):2860-2.
  8. Keerthikumar, S., Bhadra, S., Kandasamy, K., Raju, R., Ramachandra, Y.L., Bhattacharyya, C., Ohara, O., Mohan, S., and Pandey, A.:
    "Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach."
    DNA Research, 16(6):345-51.
  9. Keerthikumar, S., Raju, R., Kandaswamy, K., Hijikata, A., Ramabadran, S., Balakrishnan, L., Ahmed, M., Rani, S., Dhevi, L., Selvan, N., Somanathan, D. S., Ray, S., Bhattacharjee, M., Gollapudi, S., Ramachandra, Y.L., Bhadra, S., Bhattacharyya, C., Imai, K., Nonoyama, S., Kanegane, H., Miyawaki, T., Pandey, A., Ohara, O., and Mohan. S. S.:
    "RAPID: Primary Immunodeficiency disease database."
    Nucleic Acids Research, 37 (Database issue):D863-7. (2009)
  10. Prasad, T. S. K., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A., Balakrishnan, L., Marimuthu, A., Banerjee, S., Somanathan, D. S., Sebastian, A., Rani, S., Ray, S., Kishore, C. J. H., Kanth, S., Ahmed, M., Kashyap, M., Mohmood, R., Ramachandra, Y. L., Krishna, V., Rahiman, A. B., Mohan, S., Ranganathan, P., Ramabadran, S., Chaerkady, R. and Pandey, A.:
    "Human Protein Reference Database - 2009 update."
    Nucleic Acids Research, 37 (Database issue):D767-72.

Members

Principal Investigator

Mohan S SUJATHA
Unit Leader

Members

Suresh Kumar RAMADOSS
 
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