Molecular Biology Lab
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EGFR1 Signaling Pathway


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.



'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.



PathBuilder is an open source software to annotate biological information pertaining to signaling pathways and, with minimal additional effort, to create web-based pathway resources. PathBuilder enables annotation of molecular events including protein-protein interactions, enzyme-substrate relationships and protein translocation events via manual or automatic methods. The features of PathBuilder include automatic validation of data formats, built-in modules for visualizing pathways, automated import of data from other pathway resources, export of data in several standard data exchange formats and an application programming interface for retrieving pathway datasets.


Resource of Asian Primary Immunodeficiency Diseases

To build a PID informational platform and also as a part of action to initiate a network of PID research in Asia, we have constructed a web-based compendium of molecular alterations in PID, named Resource of Asian Primary Immunodeficiency Diseases (RAPID) in collaboration with RIKEN, Japan. It hosts information on sequence variations and expression at the mRNA and protein levels of all genes reported to be involved in PID patients. The main objective of this database is to provide detailed information pertaining to genes and proteins involved in primary immunodeficiency diseases along with other relevant information about protein-protein interactions, mouse studies and microarray gene-expression profiles in various organs and cells of the immune system. RAPID also contains list of candidate PID genes predicted using support vector machine learning approach.Thus, information contained in this database should help physicians and other biomedical investigators to further investigate the role of these molecules in PID.



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.



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.



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.



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.



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.



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.



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'.



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.



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.