HUMAN PROTEIN REFERENCE DATABASE (HPRD)

First of its kind, a database hosting over 6000 human proteins and disease genes. The main objective of this database is to make available all related fields of a protein including Interactions, Post Translational Modifications, Substrates and other information so as to help the scientists working in the areas of Proteomics. This makes HPRD a reliable source for protein data. HPRD will be the first ever database to implement the standardization protocol put forward by the Proteomics Standards Initiative for molecular interactions (PSI MI). The annotations are manually done by scientists working at IOB and each annotation undergoes multiple levels of reviews before being made publicly available, to ensure the quality. The plans are to complete 10000 proteins by the end of April 2004.

ANALYSIS OF HUMAN 'X' CHROMOSOME

Involves a careful and comprehensive analysis of Human 'X' chromosome. Using comparative genomic approach, we have identified novel protein coding regions; we have performed an extensive pseudogene analysis of the 'X' chromosome and have documented alternative splicing events. In order to help the scientific community working on X-Linked Mental Retardation, the domain is linked to HPRD where the user can view the annotations of all the genes on 'X'.

BREAST CANCER DATABASE

A database which contains all the “Known molecular alterations related to Breast Cancer”. This database comprises of information related to known molecular alterations at the chromosome, mRNA and protein levels. The database will also comprise all the SAGE analysis and Microarray data relevant to breast cancer. The data includes information on regulation (up/down) of all the reported genes and its proteins related to breast cancer. This database is linked to the HPRD for manually curated protein annotations, ONCOMINE, Geneontology, Unigene, and Genecard, where the user can have a comparative account of cancerous and normal state for a particular gene of their interest.

ANALYSIS OF HUMAN PROTEIN TYROSINE PHOSPHATASES FOR ALTERNATIVE SPLICING

A thorough analysis of the protein tyrosine phosphatases encoded by the human genome using computational biology methods. Primary aim of the study is to identify novel tyrosine phosphatases and novel transcript variants for all the known protein tyrosine phosphatases. The findings are then experimentally validated by experts using techniques such as RT-PCRs and Northern blots.

ONCOMINE

IOB in collaboration with Chinnaiyan Lab has created a microarray database whose goal is to curate publicly available cancer microarray studies and provide data mining tools to generate biologically relevant information in a user friendly manner. Links to various bioinformatics resources have been implemented including Unigene, Swissprot, Biocarta, HPRD, and KEGG, among others. IOB was involved in implementing the technical aspect for the database and Chinnaiyan Lab provided the normalized expression data. This database has been published in January/February issue of Neoplasia.

BIO-BUILDER

A content management system, designed for easy modifications and management of HPRD using web interface. The administration of annotation process and the multi-level review carried out round the globe is made easy by the implementation of this tool. This user friendly tool is created using Python and Zope.

GENOME BROWSER

An application which would comprise the basic sequence data along with the higher-level, location-based annotations on the sequence: These annotations would relate the sequence data to various genomic aspects like SNPs and expression profiling data such as that derived from DNA microarray and SAGE studies and also mass spectrometry derived data in order to understand various post translational modifications. This would add value to the analysis of the genomic sequence, as it would provide several different contexts in which to interpret the genomic/transcriptomic/proteomic data. With this application, when exploring a genomic region, biologists would be able to interact with the interface in a richer fashion than is currently possible using simple, hyperlinked images.

TAGmapper

Is a comprehensive tool used to perform tag-to-gene mapping. The 10 base pair sequences of each of the SAGE tags, which are generated experimentally in the lab, are submitted to the tool as input. The output results in mapping the SAGE tags to their respective genes by performing an extensive search across the ‘dbEST’ and ‘non redundant’ database.

NOVEL GENES

Through comparative genomics approach we have predicted several novel genes, which we are experimentally verifying in our laboratory. Identification, isolation and characterization of the predicted novel genes are the ultimate goals are being accomplish by a variety of molecular biological techniques. RT-PCR and Northern blot experiments are being performed to validate the predicted genes and RNAi experiments are being planned to check their function.

PROTEOMICS

IOB has kept in pace with tremendous advances in proteomics, a powerful tool to unravel the protein machinery of the cell. Understanding the complexities of proteomics such as protein structure, function, protein-protein interaction, sub cellular localization and post-translational modifications is facilitated because of the availability of completely sequenced human genome and the use of high through-put mass spectrometry technology. We are employing the recent strategies of quantitative protein profiling in different biological systems delivering more insights into the human health and diseases. Our proteomics experiments are also intended to complement the findings of microarray analysis and comparative genomics, which are underway at IOB.