Bio Saga Blog - A Chronicle of Life Sciences & Informatics

This something really interesting to PPI, Systems biology  and molecular networks people, I just recently came across, Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. However, recent functional genomic experiments have identified thousands of interactions for the signalling canonical proteins, challenging the traditional view of pathways as independent functional entities. Combining information from pathway databases and interaction networks obtained from functional genomic experiments is therefore a promising strategy to obtain more robust pathway and process representations, facilitating the study of cancer-related pathways.  Results: We present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them t...

Entrez gene is the most widely used data resource for Gene based information worldwide. To enable researchers to obtain high quality manually annotated information from XTractor when they search for a Gene on Entrez Gene, we are now providing direct links from Entrez Gene records to corresponding Gene Reports in XTractor. To use this outlinked option- when in Entrez Gene, for any human gene select the “Link Out” option from the Display menu in Entrez Gene and click on the XTractor link. You will be taken directly to the XTractor graphical report for the Gene of interest and also manually annotated facts on the associated Diseases, Drugs and the Biological Processes for the Gene. http://www.xtractor.in/ncbiSearch.do?xid=XT_15377&symbol=BRCA1 XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis Innovati...

BANGALORE, Indian Researchers have achieved a breakthrough, identifying a protein pathway that triggers cancer in the human body owing to its erratic behaviour. Researchers at Bangalore’s National Centre for Biological Sciences (NCBS) led by Satyajit Mayor and Neha Vyas have identified what is known as the Hedgehog pathway and the ways in which it forms and leads to cancer. The researchers, who have published their work in the journal, Cell, say this pathway is formed when the proteins (called hedgehog), which are separate, get drawn to each other by electrostatic interactions between amino acids present around the proteins. A small cluster of proteins then gets formed and goes on to form a mega-cluster. This travels to other cells and creates effects that are good or bad — the cluster could be normal and help organ regeneration or tissue repair, or the cluster could get hyperactive and affect other cells, which is the sign that cancer is coming. Simply put, the NCBS research indicates...

XTractor Knowledgebase XTractor is the first of its kind web 2.0 application which enables researchers to analyze the most current complex biological and chemical relationships published in PUBMED everyday. XTractor Knowledgebase now contains more than 100000 relationships on interactions, regulations and modulations between proteins, drugs, processes and disease. It is the only knowledgebase that updates its data content on a daily basis. The Approach: The Data behind XTractor comes from manual annotation, which is carried out by qualified scientists at Molecular Connections, INDIA ( www.molecularconnections.com ). Our scientists regularly handpick and annotate the most relevant sentences to public ontologies. Each of the data points is quality checked to ensure the highest levels of data accuracy. The extracted facts are also referenced back to the PubMed abstract(s).The sentences in XTractor are also manually c...