Coronascape Quick Guide

Table of Contents

• Introduction
• Coronascape Functions
  • User's Gene List
  • Reference Lists to Compare
  • Recommendation
  • Search
  • GO Heatmap
  • Browse All
• Coronascape Data Processing
• Coronascape Usage Examples
  • Example 1. Find similar gene lists from Coronascape by user’s gene list
  • Example 2. Compare user’s gene list to gene lists from a specific public study
  • Example 3. Compare user’s gene list to the interactome data from A549 cell line
  • Example 4. Perform Metascape re-analysis for gene lists from Coronascape

Introduction

Coronascape is a data hub depositing public available COVID-19 research related omics data sets. It includes more than 200 processed gene lists for SARS-CoV-2 from more than 20 studies. These gene lists were generated using several omics technologies, including transcriptome (RNA-Seq and scRNASeq), proteome, phosphoproteome, ubiquitome, and interactome, providing a comprehensive picture of SARS-CoV-2 infection in various host cell and tissue types. All data sets deposited in Coronascape were retrieved from published scientific articles and data sets. If publicly available, the gene lists were downloaded from supplementary tables in the publications, then processed according to the criteria suggested by the publications. Coronascape has a friendly simple user interface and convenient search function for different SARS-CoV-2 omics data sets. Users can search for similar gene lists from public data sets compared to user provided gene list, and perform system level analysis for the selected multiple gene lists using Metascape. Coupled with Metascape, Coronascape provides quick access to numerous published COVID-19 omics data sets, and a comprehensive system level data analysis toolkit for data mining.

Coronascape Functions

Coronascape Functions

Comma separated gene symbols or any other types of IDs supported by Metascape. You can click try example to test an example list of gene symbols.

Reference Lists to Compare

Use the below functions to add gene lists from public data sets for Metascape Analysis

Recommendation

Recommendation provides Similarity Search function to compare the user provided gene list to the gene lists deposited in Coronascape. After user uploads a gene list using User’s Gene List panel, click Similarity Search, then you will see the results. Click Download Similarity will download the similarity score and genes overlapping with your list to text file. By clicking Use Selected or Append Selected button, you can add the selected gene lists to the Reference Lists to Compare panel, and perform Metascape Analysis for the lists.

Search

Search function provide a convenient way to search for published gene lists using defined criteria. For example, you can search for the SARS-CoV-2 interactome data from A549 cell by choosing Interactome in Technology and A549 in Source. See example below.

GO Heatmap

GO Heatmap shows the pre-computed Gene Ontology (GO) heatmap for the top GO terms for all the gene lists.

Browse All

Browse All provides detailed information for each study and gene list, including author, title of the paper, link to the resource, technology and other useful information. You can select the gene lists, and add or append to reference lists.

Coronascape Data Processing

If publicly available, the gene lists were downloaded from supplementary tables in the publications, then processed according to the criteria suggested by the publications. The gene lists were ordered by p value, and trimmed to 300 maximum genes. If there is no clear cutoff suggested in the publication, the genes were selected based on Log2FC>1 or <-1 and BH correct P<0.01. If there were too few genes selected based on this threshold, a relaxed threshold may be used and shown in the comment column of the gene list.

Coronascape Usage Examples

Example 1. Find similar gene lists from Coronascape by user’s gene list

1. Paste your gene list to User’s Gene List.
2. In Recommendation, click Similarity Search.
3. You will be able to see the gene lists ranked by similarity comparing to user’s gene list. You can click Download Similarity to obtain the detailed gene list.
4. You can click Use Selected or Append Selected to add selected gene lists to Refence Lists to Compare.
5. After the gene lists have been added, click Metascape Analysis for system analysis of user’s gene list and selected gene lists from Coronascape.

Example 2. compare user’s gene list to gene lists from a specific public study

1. Paste your gene list to User’s Gene List.
2. In Browse All, look for the study you are interested. Click the gene list you would like to add to reference list.
3. Click Use Selected to add the gene lists to the reference lists, or Append Selected to append to existing gene lists.
4. This step can be skipped. Click Download Reference Lists if you want to save the selected gene lists for future use. This list can be directly submitted to Metascape for analysis.
5. Click Metascape Analysis to perform system analysis.

Example 3. Compare user’s gene list to the interactome data from A549 cell line

1. Paste your gene list to User’s Gene List.
2. In Search, in Technology, select Interactome, and in Source, select A549.
3. Click Search to find the matched gene lists.
4. Click Use Selected to add the gene lists to reference list, or Append Selected to append to exisiting gene lists.
5. Click Metascape Analysis to perform system analysis.

Example 4. Perform Metascape re-analysis for gene lists from Coronascape

1. Use either Recommendation, Search, GO Heatmap, or Browse All function to add selected gene lists to Reference Lists to Compare.
2. Click Metascape with or without User’s Gene List for system analysis.