NextBio-specific terminology to help you get started on using the website.
Shorthand for application. Apps allow users to ask focused questions about a query term. Each app represents a different way of categorizing and displaying correlations with your query. To learn more about a query term:
- Go to the NextBio Dashboard.
- Enter your query in the query field.
- Click an app icon at the top of the page.
When you click an app’s icon, that app is the one that processes your query. When you enter a query term and press the Enter key, your query depends on what page you were on. If you were already viewing an app’s home page or results, the query will run in that app. Otherwise, the query will run in the QuickView app by default.
A collection of genes that are associated with a specific biological function, pathway, or similar criteria. No numerical information is directly associated with a biogroup. Canonical gene lists represented as biogroups by NextBio include those from the Gene Ontology Consortium and the Broad Institute’s MSigDB.
An app that shows whether your query term is enriched for genes belonging to a particular biogroup. Use a query term that is a bioset, phenotype, tissue or compound.The Biogroups app identifies biogroups that overlap your query term, and displays a ranked list of correlated biogroups. You can use Biogroups to discover experiments that have a significant representation of genes common to a biogroup, or an experimental investigation.
A single set of genes or proteins that represent results of experimental analysis. Also: A set of genes that is of interest to a researcher. A bioset is usually derived from one experiment that identifies genes that have been found to be differentially expressed or significantly associated with a condition. Biosets have standard fields that are recognized and used for ranking (fold change, p-value, score, rank, correlation), as well as custom columns with numbers and any user-defined titles.
An app that shows the tissues, cell types, and cell lines in which a gene or bioset is significantly expressed or enriched. Body Atlas finds correlations between your query term and NextBio’s normalized, proprietary database of hundreds of tissue- and cell-specific expression and enrichment studies.
An app that matches your query with trials from ClinicalTrials.gov. Results are text-based.
A significant association with your query term. A correlation may signify statistical associations among diseases and mutations/SNPs, significantly up- or down-regulated genes, biogroups with a significant number of genes that overlap with a queried bioset, and diseases whose studies contain a large number of correlations. (There are many other possibilities.)
The process of annotating an imported bioset with semantic tags, and precalculating correlations with all of the other data available in NextBio libraries. There is a short delay between import and curation. (See import.) After curation, the imported bioset is immediately available for query.
Curated Studies is a NextBio application (“app”) that lets you browse or query all datasets that you or NextBio have imported.
An app that uses customized, proprietary algorithms created by NextBio to find and rank the diseases, traits, conditions, and surrogate endpoints most significantly correlated with a gene, sequence region, biogroup, or bioset. Disease Atlas query results are grouped according to SNOMED Clinical Terms® and appear as a ranked list of correlated phenotypes.
An option that allows you to narrow your query results or browse studies. You can filter by organism, data type, keyword, experimental design, sample source, and more.
An app that finds genes and SNPs that are significantly linked to a phenotype, tissue, or compound.
An app that lets you visualize the physical relationships between queried biosets and genomic elements. Results include genes, miRNA targets, CNVs, CpG islands, and SNPs. (This app opens in a new window.)
The process of uploading a bioset into a study created by a NextBio user. NextBio calculates correlations between the bioset and all other biosets within NextBio, resulting in a short delay between import and actual availability.
An app that shows the genes that affect a query term (gene, sequence region, biogroup, or bioset) when knocked out, overexpressed, or otherwise perturbed. You can also find gene perturbation studies with significant correlations to your query, grouped by gene perturbed.
An app that matches your query with biomedical literature and news articles. Results are text-based.
An app that lets you see which genes are significantly regulated in common, across up to 50 biosets of your choice. This app opens in a new window.
An app that shows which compounds affect a particular gene, sequence region, biogroup, or bioset. This app also finds published studies of compounds that have significant correlations to your query. Results display as a ranked list of correlated compounds.
A collection of studies that you can create. A project may contain only public or enterprise studies, or a mix of both. Projects typically focus on a single theme of interest to the user.
The method of accessing NextBio’s dynamic, regularly updated library of precomputed biological data correlations. A query has two elements: the query term and the app that you enter your query term into.
The phrase that is entered into the query field of a NextBio app. Query terms include: gene, SNP, sequence region, biogroup, bioset, phenotype, compound, tissue or keyword. Some apps (like Biogroups) do not accept certain query terms, while others (such as Literature) can accept a string of text as a query term.
An app that acts as a “home base,” or home page, for information about a queried gene, SNP, sequence region, biogroup, disease, compound, or tissue. Use this app to search a knowledge base that pulls from curated NextBio data, PubMed, and other public data sources such as ClinicalTrials.gov.
A group of biosets that correspond to a single published research paper or a single experiment.
A standard biomedical or chemistry concept; used to help identify biosets in a study. NextBio uses tags as keywords to identify and index a study’s content for database search and retrieval.
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