Monthly Archives: January 2012


Query curiosity: NextBio queries using biosets

Posted on January 30, 2012 by NextBio. Filed under Tutorials

In Part III of the NextBio tutorials, we demo bioset queries with the Curated Studies, Biogroups and Genome Browser apps

Incorporating different kinds of data into a single system means that every experiment included has to be normalized and compared with other curated studies in the NextBio platform. One way we accomplish this is by standardizing different kinds of results into biosets.

A bioset usually represents the results from a single experiment. For this tutorial video, we used a bioset that compares colon cancer cells that have metastasized to the liver to normal liver tissue.  The tutorial walks you through using this bioset to query Biogroups, which shows groups of genes or pathways that are enriched in this particular comparison.   Read more…

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Epigenetic changes mark up ovarian cancer cells

Posted on January 3, 2012 by Jyoti M.. Filed under Case Studies, Paper Trail, Research

A genome wide methylation screen finds a potential new biomarker for ovarian cancer

In the forty years since the ‘War on Cancer’ was declared, ovarian cancer is the only form of the disease where mortality rates remain unchanged, in part due to a lack of early detection tests and specific treatments. In 2011, an estimated 15,000 women in the U.S will die of ovarian cancer.

A recent study in PLoS One by Campan et al. describes the identification of a new candidate biomarker, IFFO1, in a genome-wide DNA methylation screen of blood samples from ovarian cancer patients. Less invasive than tests that require tissue samples, and chemically and biologically more stable than RNA markers for gene expression, DNA methylation changes that can be tracked in blood samples are promising biomarkers for cancer detection and treatment. Read more…

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