TABLE OF CONTENTS

• Introduction
• 1 Selecting the gene lolliplot alogirthm
• 2 Selecting data  
• 3 Setting parameters 
• 4 Creating the lolliplot
• 5 Lolliplot visualization

Introduction

A gene lollipop plot is a data visualization technique used in genomics and bioinformatics to represent information about a gene's structure and mutations. With the "Gene lolliplot" algorithm, you can generate a concise and informative plot that showcases the 2D structure of a gene, its protein domains, secondary structure, as well as the presence of known SNPs, including their frequency and pathogenicity, for a gene you are interested in. 

1 Selecting the gene lolliplot alogirthm

The first step of the analysis is to create a plot by clicking on the create plot icon. This will lead to a section where the algorithm of interest can be selected. Here you can select the "Gene lolliplot" algorithm. Click on the "Select algorithm" button to proceed to the next step.

2 Selecting data  

The lolliplot creation is based on information collected from three publicly available on-line repositories.

Particularly, information about SNPs is retrieved from ClinVar and the Genome Aggregation Database (gnomAD). ClinVar is a large initiative sponsored by the US National Library of Medicine, which has the objective of cataloguing and characterize all variantions in the human genome. GnomAD is a initiative that aims at harmonizing sequencing data from a variety of large scale projects. Among other information, gnomAD provides frequency estimates for SNP variants. Infromation of the known protein domains is retrieved from UniProt, a freely accessible database of protein sequences and functional information.

These three databases are already selected as input by default. Click on the "Select database" button to proceed to the next step. 

Only the most recent version of all datatabases is provided for input.

3 Setting parameters 

Once the input databases have been selected, the "Set parameters" field will be displayed. Here you can specify for which single gene you want the lolliplot to be created. 

4 Creating the lolliplot

When the parameters are all set-up, you can click on the Run button to perform the analysis. As soon as the analysis is over, a newly created plot will become interactive. You can now click its "View interactively" button to explore the lolliplot in the interactive plot page.

5 Lolliplot visualization

In the interactive plot page, you can explore your newly created lolliplot. In the panel on the left you can zoom in and navigate the lolliplot and the various points of interest. 

The gene of interest is represented as a rightmost vertical line, with exons (coding regions), UTRs (untranslated regions) and introns (non-coding regions) marked along it. Exons and UTRs are shown as rectangles, while introns are represented as lines. Mutations within the gene are indicated using horizontal lines or "lollipops" that protrude from the gene structure. The height of each lollipop corresponds to the frequency of the mutation. The pin shape indicates the pathogenicity of the mutation, which can range from benign to pathogenic, while the pin color indicates wheter the mutation is a missense or synonymous. Additional tracks on the lolliplot indicate all the known protein domains associated with the gene and are color-coded for protein domain type (e.g Leucine zipper, bHLH etc.) 

You can export your lolliplot in the "Export settings" tab.