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Institute of Bioinformatics
   
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Molecular Biology Lab
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TGFR Pathway
 
 

 
 
 

HUMAN PROTEINPEDIA

Human Proteinpedia is a community portal for sharing and integration of human protein data. It allows research laboratories to contribute and maintain protein annotations. Human Protein Reference Database (HPRD) integrates data, that is deposited in Human Proteinpedia along with the existing literature curated information in the context of an individual protein. All the public data contributed to Human Proteinpedia can be queried, viewed and downloaded.

  
 
 

HUMAN PROTEIN REFERENCE DATABASE (HPRD)

First of its kind, a database hosting over 25000 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 is 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 database host annotations of all the known human proteins and update them on an ongoing basis.

  
 
 

PLASMA PROTEOME DATABASE (PPD)

The Plasma Proteome Database, the first of its kind ensures a comprehensive resource for all human plasma proteins along with their isoforms. The database includes information pertaining to isoform specific expression, disease, localization, post translational modification and single nucleotide polymorphism. The information provided in this database is through manual annotation done by exhaustive literature research.

  
 
 

NETPATH

'NetPath' is a curated resource of signal transduction pathways in humans. It is a collaboration between the PandeyLab at Johns Hopkins University and the Institute of Bioinformatics. At this time, 10 cancer and 10 immune signaling pathways are available. For example Transforming growth factor-beta (TGF-beta) is a multifunctional growth factor with a wide range of biological activities such as cell differentiation, cell proliferation, apoptosis and tumor suppression. TGF-beta signalling involves a direct pathway from the cell surface receptors to the nucleus. TGF- beta, binding to its receptors initiates the degradation of several key components of its signaling pathway. The degradation of these components, including both positive and negative transducers, is mediated by the ubiquitinated proteasome system. Recent cellular, biochemical, and structural studies have shown significant insight into the mechanisms of the activation of TGF-beta receptors through ligand binding, the activation of Smad proteins through phosphorylation, the transcriptional regulation of target gene expression, and the control of Smad protein activity and degradation.

 
 
 

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.

  
 
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