NextBio

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Introduction

NextBio Public is an online library of genomic data curated from sources such as GEO and dbGaP which allows users to mine billions of precomputed data correlations and thousands of public genomic studies.[1] Users can register for a free account with NextBio (with the use of an email address from a valid government, academic, or non-profit institution) in order to access the following features:[2]

  • Access to full view of search results and all search sections ("Apps").
  • Import data into NextBio and correlate it with public data.
  • Save and share search results (through My Studies, My Projects, Bookmarks, and Collaborations).

After registering, users have full access to the following search Apps:[3]

  • QuickView - Under "NextBio Summary," lists of top 5 relevant results from different search Apps (Disease Atlas, Curated Studies, Literature, Clinical Trials, etc). Under "General Info," a brief definition of the term.
  • Genomic Applications - Search and rank public genomic data through these applications.
    • Curated Studies - Query or browse all studies curated by NextBio. You can query by gene, SNP, sequence region, biogroup, bioset, phenotype, compound, tissue, or keyword. Or browse using filters and text-based search.[4]
    • Body Atlas - View the tissues, cell types, and cell lines in which a queried gene, biogroup, or bioset is significantly expressed or enriched.[5]
    • Disease Atlas - Find diseases, traits, conditions, and surrogate endpoints associated with a queried gene, sequence region, SNP, biogroup, or bioset.[6]
    • Pharmaco Atlas - Discover which compounds and treatments affect a queried gene, sequence region, biogroup, or bioset.[7]
    • Knockdown Atlas - Perform a knockdown, knockout, or overexpression experiment in reverse: See which genetic perturbations affect a queried gene, sequence region, biogroup, or bioset.[8]
    • Genetic Markers - Locate genes and SNPs that are significantly linked to a queried phenotype, tissue, or compound.[9]
    • Biogroups - Find biogroups for which your queried bioset, phenotype, tissue, or compound is highly enriched.[10]
  • Genome Browser - View experimental datasets on genomes through an interactive display.
  • Literature - Do a classic PubMed literature search, or search hundreds of biology- and health-related news sources with any query term or keyword.[11]
  • Clinical Trials - Find clinical trials with any query term or keyword.[12]
  • Meta-Analysis - Discover which genes are significantly regulated in common, across up to 50 biosets.[13]

All apps (except the interactive Genome Browser display) have two search forms: the keyword search form and the "search sequence regions" form. The "search sequence region" form allows user to select the organism type and chromosome via drop-down menus and define the start and stop points on the sequence.


Sources

  1. "Products NextBio Public." NextBio website, http://www.nextbio.com/b/corp/products_basic.nb. Accessed September 5, 2011.
  2. "Registration." NextBio website, https://www.nextbio.com/b/register/register.nb. Accessed September 5, 2011.
  3. "NextBio Public - Home." NextBio website, http://www.nextbio.com/b/nextbio.nb. Accessed September 5, 2011.
  4. "Curated Studies." NextBio website, https://www.nextbio.com/b/search/as.nb. Accessed September 5, 2011.
  5. "Body Atlas." NextBio website, https://www.nextbio.com/b/search/ba.nb. Accessed September 5, 2011.
  6. "Disease Atlas." NextBio website, https://www.nextbio.com/b/search/da.nb. Accessed September 5, 2011.
  7. "Pharmaco Atlas." NextBio website, https://www.nextbio.com/b/search/pa.nb. Accessed September 5, 2011.
  8. "Knockdown Atlas." NextBio website, https://www.nextbio.com/b/search/ka.nb. Accessed September 5, 2011.
  9. "Genetic Markers." NextBio website, https://www.nextbio.com/b/search/gm.nb. Accessed September 5, 2011.
  10. "Biogroups." NextBio website, https://www.nextbio.com/b/search/bg.nb. Accessed September 5, 2011.
  11. "Literature." NextBio website, https://www.nextbio.com/b/search/lit.nb. Accessed September 5, 2011.
  12. "Clinical Trials." NextBio website, https://www.nextbio.com/b/search/trials.nb. Accessed September 5, 2011.
  13. "Meta-Analysis." NextBio website, https://www.nextbio.com/b/search/adv.nb. Accessed September 5, 2011.

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