Gene Information eXtension (GIX)

Settings

Activation method

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 enable the "CTRL/⌘ required" option then double-clicking (or dragging) on its own will not initiate a query. On Linux and Windows systems you will have to hold the CTRL key while clicking to perform a query, or on Mac it is the Command/⌘ key. This restriction can ensure that the extension only activates when you want, rather than whenever you double-click.

If you wish to completely disable the extension, simply click the disable button.

Display options

The extension can display information in two ways:

1. Detailed report: a panel spanning the full height of the browser window displaying links to external resources and the information from those resources.
2. Tooltip report: a small box that opens at the point of the mouse click with only links to external resources.

Species

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
• Escherichia coli (strain K12)
• Gallus gallus
• Mus musculus
• Saccharomyces cerevisiae
• Salmonella Typhimurium (strain LT2)
• Schizosaccharomyces pombe
• 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 organisms we support: Arabidopsis, C. elegans, Drosophila, human, mouse and yeast.

Query type

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)
• 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. Loci were specifically included for yeast and ORFs for flies and worms to enable querying by commonly used nomenclature of the following formats:

• YGL190C (yeast locus for gene CDC55)
• CG12217 (fly ORF for gene PpV)
• C14A4.11 (worm ORF for gene ccm-3)

You can query by locus or ORF for other species by selecting the appropriate option from the settings dropdown, however it will only autodetect these query types in yeast, flies and worms as these species adhere to specific naming formats that do not necessarily hold in other species.

Some organism-specific selectors can also be automatically detected:

• neXtProt, H. sapiens (e.g. NX_Q9BUL8)
• Wormbase, C. elegans (e.g. WBGene00007561)

Search

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.

Information options

Each pierce of information provided by GIX can be toggled off in the extension popup and will be hidden on subsequent queries.

The GO term, Localization, Protein expression 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 Protein and RNA expression you can choose which cell lines and tissues to display by default in the information panel. There are 135 cell lines and 58 tissues for protein expression, and 64 cell lines and 37 tissues for RNA.

You can control the order in which information appears on the results panel by dragging and dropping the settings in the extension popup.

Certain data is only available for specific species as outlined above in the Species section.

Information panel

Multiple results

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 as the initial result to display in the case of multiple matches.

Buttons

• close the extension
• reposition the extension horizontally
• go back to the previous result
• resize the extension (bottom left corner)

Database

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.

Integrated resources

We integrate several databases to generate the database used for GIX. The resources, urls and citations are listed below in alphabetical order:

• BioGRID, thebiogrid.org (PMID:16381927)
• Compartments, compartments.jensenlab.org (PMID:24573882)
• DepMap, depmap.org (PMID:29083409)
• Gene Ontology, www.geneontology.org (PMID:10802651, PMID:27899567)
• HGNC, www.genenames.org (PMID:27799471)
• Human Protein Atlas, www.proteinatlas.org (PMID:25613900, PMID:28495876)
• IntAct, www.ebi.ac.uk/intact (PMID:24234451)
• OMIM, www.omim.org (PMID:30445645)
• Pfam, pfam.xfam.org (PMID:30357350)
• ProteomicsDB, proteomicsdb.org (PMID:31665479)
• Reactome, reactome.org (PMID:29145629)
• UniProt, www.uniprot.org (PMID:29425356)

Feature requests

If you would like to request a new feature or the addition of a species, please use our issue tracker. You can make requests via the Chrome Web Store's support page but unfortunately developers do not receive e-mail notifications when that happens and users do not receive notifications when we reply, so GitHub is the preferred place to make requests.

Alternatively if you would like to add a feature yourself, please fork the code on GitHub and submit a pull request with your changes.

Unsupported websites

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.

Browsers block extensions from running on the tab homepage - the page you see when opening a new tab - as well as a few other privileged pages, and so neither double clicking nor the search bar will work in these contexts. The extension will alert you to this with a warning at the bottom of the popup.

Permissions

When you install the extension it will alert you that it can "Read and change all your data on the websites you visit" on Chrome or "Access your data for all websites" in Firefox.

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 the page. 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 in Chrome, 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.

Logging & privacy policy

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 collect, store or share any personal information or IP addresses and the extension does not use analytics.

Source code

Source code is available at GitHub.

Issues

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 GIX, please use our issue tracker.

Browser support

Firefox

GIX should work in Firefox as of version 57.0 (2017-11-14) but please update to the latest version to ensure full compatibility.

Microsoft Edge

To add the extension to Edge, first ensure you have their latest Chromium-based version installed. Information about it can be found here: Edge.

Safari

The extension works in Safari 14, which is available on macOS 10.14 and above (Mojave, Catalina, Big Sur). To install, follow the App Store link and allow your browser to open the link at the App Store, then Install the extension. When you open Safari it will display a notification with instructions on how to activate the extension. Once activated, you'll then need to click on the extension's icon from the toolbar and grant it access to read the web sites you visit (ideally "Always allow on every website"). Finally, you'll need to refresh the page you are on or navigate to a new page.

Chromium browsers

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. Other browsers in this category the extension is known to work in are Brave and Opera.

To add the extension to Brave, simply go to the Chrome Web Store and click the "Add to Brave" button.

To add the extension to Opera, first go to the Chrome Web Store. Click the "Add to Opera" button. A notification will appear at the top of the page asking if you want to install extensions from the Chrome Web Store. Confirm that you do.

Manuscript & citation

If you find the extension helpful and would like to cite us, please reference our manuscript published in Nature Methods.

• PubMed
• bioRχiv

Funding

This project was supported by funding from CIHR, Compute Canada, Genome Canada, National Institutes of Health, Ontario Genomics and the Ontario Research Fund.