What is it about?
It is a web application that may be used freely (without fees) and without having to register to use, where users may upload a set of human genes, and find out what pathways, diseases (including GWAS) and drugs are associated with their protein products. It gives these annotations not only for the input gene set but for their protein interactome which includes the protein-protein interactions of the input genes and also the shortest paths that connect them to each other. Also, the tool gives not only the associations but their statistical significance of association. It presents a visualization of the interactome, and also makes the network available for download (in plain text format as as well .SIF format that would be compatible with applications like Cytoscape).
Featured Image
Why is it important?
Often biologists find specific genes of their interest - often, these genes could be what are differential expressed in disease cases, or those whose mutations are significantly associated to diseases. The next step in understand what the role of these genes is to that disease is to understand what these genes play a role in. There are commercially available tools for comprehensive analysis of gene sets, but they are very expensive. So, a majority of scientists may not own a license to use them. Here, we make a freely accessible website where biologists (or others) can upload a set of genes and get a picture of what they are involved in, at the click of a button. Of course, those can have a license to commercial applications may get more details than what are presented here, but for others, this website presents a pretty detailed set of annotations. Also we integrated interactome network into the analysis - thus, the users see not only annotations of the proteins that they have input but also association and statistical enrichment when the set is expanded to include their protein-protein interactions.
Perspectives
We designed this website so that it can reduce the burden of biologists in manually using different tools.. we reduced the number of clicks/steps to get to the results. My co-author, who was a graduate student at that time, made a Video demo and web-based interactive demo, wrote Help pages and answered FAQs to make it easy to understand the application. I really like how he made information available that caters to different preferences of people (watch video, versus go step-by-step versus peruse everything in a single page). Watching this material after a few years of publication motivated me to share this publication here on Kudos.
Madhavi K Ganapathiraju
University of Pittsburgh
Read the Original
This page is a summary of: LENS: web-based lens for enrichment and network studies of human proteins, BMC Medical Genomics, December 2015, Springer Science + Business Media,
DOI: 10.1186/1755-8794-8-s4-s2.
You can read the full text:
Resources
LENS Demo
LENS is a web-based analysis tool for analyzing sets of human proteins or genes using protein-protein interaction networks. It finds out what the interactome is of the input genes, and then finds out which of the functional, pathway, disease, GWAS and other such annotations are over represented in the original gene set or in its interactome. It computes all these with the click of a button and presents a comprehensive set of results. It also allows presents a network visualization of the interactome and allows this to be downloaded.
Interactive Demo
To get familiar with what LENS is and how it may be used, you could either watch the demo, or follow this interactive tutorial.
FAQ (Frequently Asked Questions)
Answers to Frequently Asked Questions (FAQ)
LENS - Web-Application
It is the link to the web-application
LENS - Publication
Link to Open Access Publication
Contributors
The following have contributed to this page
