Frequently Asked Questions

LENS takes lists of human genes and links them together by protein-protein interactions, and performs enrichment analyses on the resulting network.

LENS takes one or two lists of genes, separated by commas, spaces, or new lines. The genes may be HGNC-approved symbols, Entrez ids, or Uniprot ids. All elements in the list should be of the same type of ID. You can also give input genes by choosing a disease, drug, pathway, or GWAS from the text box on the right. The text box offers auto-complete options. When you select one of these options, the associated genes are automatically loaded into the box on the left.

There are two common causes of this issue:

1. If you are using gene symbols, you are not using an HGNC-approved symbol. You can try looking for your gene in the HUGO Gene Symbol Database.
2. LENS only has information on the human interactome. You may be providing non-human genes/proteins.

GWAS data comes from the NHGRI GWAS catalogue. LENS combines results from multiple GWASs so long as they are examining the same trait.

Pathways and their associated genes are collected from REACTOME.

Drugs and their target genes are collected from DrugBank.

Diseases and their associated genes are collected from the KEGG DISEASE Database.

Protein-protein interactions are collected from biophysical interactions found in HPRD and BioGRID.

We do not manually evaluate any of the data we acquire from other databases, and we rely on their methods for data curation.

We update our local copies of these databases once a month.

If you click on any circle representing a gene, or any line between genes, you will be linked to Wiki-Pi for more information on the gene or interaction.

We use a force layout provided by Data Driven Documents (d3).

The number of nodes can be reduced by clicking the "Hide Non-connecting Nodes" button. This will remove all gray circles that are not part of a shortest path. You may also consider reducing the number of genes you give as input, or move genes from the candidate gene list to the target gene list.

LENS uses a semantic zoom method. If you scroll within the network view, the distance between connected genes can be increased or decreased.

Clicking and dragging in the white-space of the interactome will allow you to select multiple genes, which will be outlined in green. You can then move, scale, or reapply the layout to just those selected genes. You can make multiple selections by holding the shift key while clicking and dragging. Clicking anywhere within the whitespace without dragging will clear the selection.

Several files are available for download:

• The structure of the interactome can be downloaded as a SIF file, compatible with Cytoscape.
• Just the shortest paths between genes can also be downloaded as a SIF file. This is the network as it would appear after pressing the "Hide Non-connecting Nodes" button.
• The list of all genes in the interactome is also downloadable as a plain text file.
• The raw XML code for the network can be downloaded as an SVG, clear of coloring and formatting.
• The network, as it appears, can be downloaded as a high-resolution PNG image as well.

LENS saves your results indefinitely, and they can be shared with a static URL. While your results are being computed, you can see two URLs: one for viewing and sharing your results, and another for viewing and editing your results. You can send the "view and share" link to collaborators to show them the results, or send the "view and edit" link to allow collaborators to add their own notes.

The average shortest path length is the average shortest path distance from each candidate gene to its nearest candidate neighbor, or target neighbor if target genes were given. Multiple paths between nodes of equal length are not double counted. If a node is entirely disconnected, the distance between it and its nearest neighbor is 17. Shortest path lengths taken into account are only from candidate genes to their neighbors; disconnected target genes do not affect the average. This also applies to the number of disconnected nodes reported. That is, only the number of disconnected candidate genes is given.

These numbers, alone, may not be very informative. To put them in perspective, the same numbers are reported for randomly generated networks. If only candidate genes were provided, five networks are generated using randomly selected genes in equal number to the original input size. The minimum shortest path length, average shortest path length, and number of disconnected nodes are averaged from the five networks and reported. If target genes were given, three sets of random networks are generated for more comparisons. The first selects random candidate genes as before, but retains the list of target genes. The second keeps the candidate genes from the input and randomizes the target genes. The last randomizes both gene sets.

Because we store gene associations as true/false values, the procedure for testing for significance is the same for each dataset.

By default, when you view the overlaps you will see only the enrichment for candidate genes. To see the overlap with the entire network, click the "Entire Network" button in the overlap view.

The p-value for statistical significance for LENS is computed using a hypergeometric distribution.

Any disease, drug, pathway or GWAS with at least one associated gene in the candidate genes given by the user, or in the interactome generated by LENS, will be displayed and have a p-value computed.

The Links tab contains two links to your results. One allows people to view your results and make changes to the notes and title, and the other will let users view the results but not make changes. You can bookmark these links for your own use, or send them to others to let them see your findings.

If you have the link to edit the results, at the top of the page you should see text that says, "Click here to change the title." Clicking the title will turn it into a text box for you to edit. When you're done, you can click anywhere outside of the text box to apply the change. Don't forget to save the changes if you want it to be persistent though.

If you are using the link to edit your results, you should see a button beside the Download link that says, "Save View." If you click this button, any changes to the title and notes will be viewable to anyone with a link to your results.

If you can't edit the notes page, you are not using the link that allows you to edit the results. Double check the link you used to get to the page.

If you can't change the title, you are not using the link that allows you to edit the results. Double check the link you used to get to the page.