TABLE OF CONTENTS

• Introduction
• 1 Create plot page
  • 1.1 Select algorithm
  • 1.2 Select data
  • 1.3 Set parameters
• 2 Running the gene lolliplot table
• 3 Interactive plot page
  • 3.1 Gene lolliplot table visualization
    • 3.1.1 Exporting the gene lolliplot
  • 3.2 Gene enhancer lolliplot table visualization
    • 3.2.1 Exporting the enhancer gene lolliplot

Introduction

The gene lolliplot metadata table allows you to obtain and explore all the data necessary to create a gene and gene enhancer lolliplot.

1 Create plot page

The first step of the analysis is to create a plot by clicking on the create plot icon. 

This will lead to you to the create plot page. Here you can start by filling in the plot name and plot template.

1.1 Select algorithm

Next, you can select the "Gene lolliplot metadata table" algorithm. Click on the "Select algorithm" button to proceed to the next step.

1.2 Select 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. Infromation of the known enhancers is retrieved from GeneCards.

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.

1.3 Set parameters

Once the input databases have been selected, the "Set parameters" field will be displayed. In the "Gene of interest" menu you can specify for which single gene you want the gene lolliplot metadata table to be created. 

In the "Lolliplot type" you can specify what kind of lolliplot you want to create, a "Gene lolliplot" or a "Gene enhancer lolliplot".

2 Running the gene lolliplot table

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 gene lolliplot or gene enhancer lolliplot table in the interactive plot page.

3 Interactive plot page

The "Gene lolliplot" and "Gene enhancer lolliplot" both have an unique interactive plot pages.

3.1 Gene lolliplot table visualization

In the interactive plot page, you can explore the gene lolliplot meadata via a pivot table.

Ultimately, you can create a gene lolliplot by selecting the "Gene lolliplot" visualization type in the "Display options" menu. 

On the gene lolliplot, the gene of interest is represented as a topmost horizontal 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 vertical 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 control which data is displayed on the lolliplot by subsetting the values in the individual gene metadata variables. Doing so will re-render the lolliplot and display only the selected data.

3.1.1 Exporting the gene lolliplot

Once you have finalized your gene lolliplot you can export it as a separate plot via the "Save output" menu. This will preserve any customization of the lolliplot you have made. 

The exported lolliplot can then be viewed in the interactive plot page.

3.2 Gene enhancer lolliplot table visualization

In the interactive plot page, you can explore your newly created gene enhancer lolliplot metadata table via a pivot table.

Ultimately, you can create a gene enahncer lolliplot by selecting the "Gene enhancer lolliplot" visualization type in the "Display options" menu.

The genomic region around the gene of interest is represented as a central horizontal line. The enhancers, promoters and and the gene of interest itself are represented as rectangles.

Mutations within the gene are indicated using vertical lines or "lollipops" that protrude upwards 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. The lollipops that protrude downwards indicate the transcription factors that bind to the displayed promoters and enhancers.

You can control which data is displayed on the lolliplot by subsetting the values in the individual gene metadata variables. Doing so will re-render the lolliplot and display only the selected data.

3.2.1 Exporting the enhancer gene lolliplot

Once you have finalized your gene lolliplot you can export it as a separate plot via the "Save output" menu. This will preserve any customization of the lolliplot you have made.

The exported lolliplot can then be viewed in the interactive plot page.