The default method for querying a gene is to double click on it. You can instead choose the drag method that requires you to mouse down on one side of the gene name, drag the selection box to the other side and release the mouse button. This can be useful on websites where double clicking selects more that one word (this is a rare occurrence and depends on the markup used by the website). The drag method is also necessary for gene names that have certain special characters in them. For example, double clicking a gene name with a dash '-' will only capture text before or after the dash but not including it.
If you wish to disable the extension, simply click the disable button.
The extension can display information in two ways:
- Detailed report: a panel spanning the full height of the browser window displaying links to external resources and the information from those resources.
- Tooltip report: a small box that opens at the point of the mouse click with only links to external resources.
In addition to human gene information our database contains information for the following model organisms:
- Arabidopsis thaliana
- Caenorhabditis elegans
- Danio rerio
- Dictyostelium discoideum
- Drosophila melanogaster
- Gallus gallus
- Mus musculus
- Saccharomyces cerevisiae
- Xenopus laevis
Some information will only be available for certain species. For instance, Human Protein Atlas localization and expression information is only available for human gene entries. The Compartments subcellular localization database has information on six of the ten organisms we support: Arabidopsis, C. elegans, Drosophila, human, mouse and yeast.
The extension can retrieve information for any of the following query types:
- Ensembl gene (e.g. ENSG00000114209)
- Ensembl protein (e.g. ENSP00000376506)
- Gene name (e.g. PDCD10)
- NCBI Entrez gene ID (e.g. 11235)
- neXtProt (e.g. NX_Q9BUL8)
- RefSeq (either nucleotide or protein e.g. NM_007217.3, NP_009148.2)
- UniProt (e.g. Q9BUL8)
By default it will autodetect the query type but you can disable this option and force it to treat all queries as a specific type.
Genes may also have a locus and ORF associated with them that can be used for querying. These were specifically included for yeast and flies respectively to enable querying by commonly used nomenclature of the following formats:
- YGL190C (yeast locus for gene CDC55)
- CG12217 (fly ORF for gene PpV)
You can query by locus and ORF for other species, however it will only autodetect these query types in yeast and flies respectively as these species adhere to specific naming formats that do not hold in other species.
The search box can be used for making queries in addition to using the mouse. Simply type in a query, hit enter and the information panel will appear on the current web page. Unlike mouse events, the search box will work on websites with embedded content like Google Docs and PDF viewers.
Each pierce of information provided by Gene Info can be toggled off in the extension popup and will be hidden on subsequent queries.
The GO term, Localization and RNA expression sections have advanced display options that can be viewed by clicking the settings/ellipsis button () next to the relevant field in the extension popup. For GO terms, you can set the default namespace to display on the information panel: BP (biological process), CC (cellular compartment) or MF (molecular function). You can choose which resources to display for localization, including the Compartments subcellular localization database, the Human Protein Atlas and/or UniProt. Under RNA expression you can choose which cell lines and tissues to display by default in the information panel. There are 64 cell lines and 37 tissue types to choose from that we have incorporated from the Human Protein Atlas.
Certain data is only available for specific species as outlined above in the Species section.
If a query matches to multiple genes, as can happen since gene names are not always unique, the information panel will display one result and the others will be available from the dropdown menu that appears next to the Gene heading. A match to an official gene name will always be selected at the initial result to display in the case of multiple matches.
The database will be updated on the 15th of each month or the next business day if the 15th falls on a weekend or holiday.
We integrate several databases to generate the database used for Gene Info. The resources, urls and citations are listed below in alphabetical order:
- BioGRID, https://thebiogrid.org (PMID:16381927)
- Compartments, https://compartments.jensenlab.org (PMID:24573882)
- Gene Ontology, http://www.geneontology.org (PMID:10802651, PMID:27899567)
- Human Protein Atlas, https://www.proteinatlas.org (PMID:25613900, PMID:28495876)
- IntAct, https://www.ebi.ac.uk/intact (PMID:24234451)
- Pfam, https://pfam.xfam.org (PMID:30357350)
- UniProt, https://www.uniprot.org (PMID:29425356)
The extension is not able to capture mouse events (double clicks, etc.) on websites with embedded elements like Google Docs and PDF viewers and you can not therefore perform queries in the default way. The search box in the extension popup can however still be used for performing queries on these sites.
Chrome blocks extensions from running on the tab homepage - the page you see when opening a new tab - and so neither double clicking nor the search bar will work in this context.
When you install the extension it will alert you that it can "Read and change all your data on the websites you visit".
To capture text from websites you visit this extension needs to be granted permission to read the sites. The only thing this extension reads is the text selected via double clicking or mouse dragging (if you enable that option).
Adding an information panel or tooltip to a webpage with information about the gene you have selected requires permission to modify or "change all your data on the websites you visit". The only thing we modify about the websites you visit is the addition of the panel or tooltip.
If you would like to further restrict the access given to this extension you can right click on the icon in your browser toolbar and scroll to "This Can Read and Change Site Data" to view the options. Detailed instructions can be found at the Web Store's Help Page.
We log three pieces of information with each query: 1) whether it matched to something in our database; 2) the species; and 3) the type of query, i.e. was it a gene name, UniProt ID, etc. We do not log the actual query term itself. Recording the total number of queries allows us to ensure the server has enough hardware resources to meet the demands of the user base. Recording the species allows us to prioritize development time and add resources for the most used species. For example, if a model organism is only searched by 0.01% of the user base, it will get less priority than one used by 95% of users. Finally, recording the type of query allows us to determine whether it is worth continuing to support a particular type of accession.
We do not record an personal information or IP addresses and the extension does not use analytics.
Source code is available at GitHub.
If you find the extension does not work for you it may be that you are located behind a very strict firewall that blocks the method we are using to fetch data from our server (XMLHttpRequest) or that blocks the requests but not the method specifically. If this is the case, you'll have to discuss the matter with your IT department. If we can help to resolve the issue, please contact us.
If you would like to report a bug, request a feature or have your resource added to Gene Info, please use our issue tracker.
In addition to working with Chrome the extension can work in any browser built on top of Chromium if the developers of that browser provide support for extensions. For a complete list of Chromium browsers, see Chromium browsers. Currently the extension is known to work in the Brave browser.
To add an extension to Brave simply go to the Chrome Web Store, find the extension and click the "Add to Chrome" button.