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DATABASES
 
Proteomic Databases developed at IOB:
 
Defining the 'Proteome'
The term "Proteome" defines the complete protein complement of a genome, has become the key research frontier in the post-genomic era. Recent advances in proteomic technologies, apart from the basic applications of gel-electrophoresis and mass spectrometric procedures, have helped in deciphering the primary protein sequence/structure as well as in knowing certain post-translational modifications or subtle protein-protein interactions. Even a decade after the human genome has been decoded; we are no where close to answering many of the biological questions. As genomic sequence information becomes available in unprecedented amounts, the lack of corresponding functional correlation with their gene transcripts and proteins, however, represent a significant roadblock. To bridge this gap and improve the efficiency of biological discoveries, Institute of Bioinformatics has developed various databases to identify and analyze protein products in a cell or tissue. These resources are freely available over the World Wide Web and can be easily accessed by the scientific community.
 
Proteomic Resources
   
The Human Proteome Map (HPM) (http://humanproteomemap.org/) portal is an interactive resource to the scientific community by integrating the massive peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. All mass spectrometry data including precursors and HCD-derived fragments were acquired on the Orbitrap mass analyzers in the high-high mode. Currently, the HPM contains direct evidence of translation of a number of protein products derived from over 17,000 human genes covering >84% of the annotated protein-coding genes in humans based on >290,000 non-redundant peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. This includes 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues. The HPM portal provides an interactive web resource by reorganizing the label-free quantitative proteomic data set in a simple graphical view. In addition, the portal provides selected reaction monitoring (SRM) information for all peptides identified.
   
NetPath (http://www.netpath.org) and NetSlim (http://www.netpath.org/netslim/) NetPath constitutes an extensive database of signal transduction pathways in humans, that at present contains all information pertaining to 10 cancer and 10 immune signaling pathways. NetSlim represents a subset of reactions depicted in NetPath and was developed by applying a set of stringent criteria to generate high-confidence signaling maps and also to enable easy visualization and interpretation of the pathways.
 
Human Protein Reference Database (http://www.hprd.org/) This database represents a centralized platform to visually depict and integrate the information related to protein-protein interactions, post-translational modifications, tissue expression, expression in cell lines, sub-cellular localizations and enzyme-substrate relationships and disease associations for each protein in the human proteome. All information in this resource has been manually extracted from literature by expert biologists and researchers.
 
Human Proteinpedia (http://www.humanproteinpedia.org/) Developed as a community portal for sharing and integrating human protein data, this resource allows research labs around the world to contribute and maintain protein annotations derived from various platforms like mass spectrometry, immunochemistry and fluorescence based experiments.
 
Plasma Proteome Database (http://www.plasmaproteomedatabase.org/) This is a manually curated exhaustive collection of all human plasma proteins along with their isoform information, particularly expression, disease localization, post-translational modifications and Single Nucleotide Polymorphisms.
 
More Data Resources:
   
The Pancreatic Cancer Database (http://pancreaticcancerdatabase.org/) is a resource of experimentally demonstrated molecular alterations associated with pancreatic cancer in cancer tissues or cancer cell lines. It currently contains information pertaining to changes at the mRNA, protein and miRNA levels. The data can be queried or browsed at mRNA, protein or miRNA levels or based on specific cancer subtypes. Individual entries are also linked to Entrez Gene, OMIM, Human Protein Reference Database (HPRD), HGNC and miRBase.
   
Resource of Asian Primary Immunodeficiency Diseases (http://rapid.rcai.riken.jp/RAPID) RAPID is a web-based compendium of molecular alterations in primary immunodeficiency diseases that contain detailed information about genes and proteins that are affected along with information about protein-protein interactions, microarray gene expression profiles and deleterious and novel mutations associated with them.
 
TBnet (http://tbnetindia.ibioinformatics.org/) As part of an initiative by Department of Biotechnology, Government of India, this portal was developed with special focus on contributions by Indian researchers on various issues related to tuberculosis. The clinical, epidemiological and molecular manifestation of this disease and the development of multiple drug resistance in recent times pose a major health concern in third world countries like India
   
India Cancer Research Database (http://www.incredb.org/) This database provides details of scientists and physicians involved in cancer research in India along with the information about their areas of expertise, research publications and funded grants. The main goal of the database was to foster collaborations among researchers and to provide a snapshot of ongoing research initiatives and activities in India.