Tag Archives: NextBio Public

Predicting drug responses: Clinical Trials and Meta-analysis in NextBio

Posted on February 8, 2012 by Samara M.. Filed under Tutorials

In part IV of the NextBio tutorials, we use the Clinical Trials and Meta-analysis apps to explore the effects of the drug tibolone

High through-put technology is churning out data faster than human beings can process and sift through this abundance of information. However, not all of the results obtained are included in the finished product of a study. A recent paper by Lisa Bero and her colleagues investigates the effect of omitted trial outcome data from the Food and Drug Administration. By examining studies included in the Cochrane reviews, the researchers found that approximately half of these clinical trials exclude data. Meta-analyses and systemic reviews based on partial data may overestimate the efficacy of the drug, a practice that can be harmful to patients. Bero and her colleagues found that 19 out of 41 trials included in their reanalysis showed decreased efficacy with the addition of unpublished data. Read more…

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…

NextBio Public Tutorials: Exploring the experimental details behind NextBio results

Posted on November 30, 2011 by NextBio. Filed under Tutorials

In part II of the NextBio Public tutorials, we show you how to find the experimental details underlying your NextBio query results.

Critics of GWAS are quick to point out that the genetic associations identified in such studies rarely reach clinical significance. However, integrating associations identified in genome-wide studies with evidence from more directed experiments can speed up the process of taking genomic variants from the bench to the clinic. Watch our tutorial to find out how to dig down into the experimental results associated with a gene query in NextBio, or read on to learn more about our study* on one particular gene, POU5F1B. Read more…

NextBio Public Video Tutorials: Using NextBio to explore a gene

Posted on October 31, 2011 by NextBio. Filed under Tutorials

In part I of the NextBio tutorials, we explain how and why NextBio helps explore data relevant to a gene query

A single gene can be studied in many ways- genome-wide analysis for associations with diseases, experimental studies of function in cell lines or animal models, or pharmaceutical research as a potential drug target. At NextBio, we aggregate these diverse kinds of data, normalize and integrate them on a common platform, coalescing diffuse “data clouds” to address focused research questions.

In the first of our NextBio Public tutorials, we explain how to use simple NextBio functions to find this aggregated data relevant to a gene, beginning with GWAS associations, to descriptions of tissues and cell lines and results from pharmacological experiments, all in a matter of minutes.

Announcing: NextBio Public

Posted on August 30, 2011 by Jyoti M.. Filed under News

If you’re a user of NextBio Basic, you’re probably aware that NextBio lets you access thousands of gene expression studies from sources such as GEO. NextBio has done the heavy lifting of importing, normalizing, and curating publicly available genomic data so that biologists can ask and answer biological questions completely in silico—even with little computational expertise.

Which makes our recent updates very exciting: We’ve made data from GWAS, CNV studies, and more freely available* through the NextBio Public site. These numbers update on a near-daily basis. Because our curators tag each imported study using a controlled vocabulary and custom disease ontology, you’ll easily be able to perform meta-analyses of multiple studies across different diseases through a simple, web-based interface.

Correlating genomic data from thousands of studies linked to different diseases, compounds, tissues, cells and more is complicated. We’re constantly trying to make the job a little easier, which is why we’ve also given the NextBio Public user interface a major overhaul.
Read more…