ViRAL

querying a gene of interest across respiratory virus infections


Gene Expression in Symptomatic cases v.s. Control samples
(Wilcoxon rank-sum test, ***: P < 0.001; **: P < 0.01; *: P < 0.05; ns: P > 0.05)

CSV PDF
Gene Expression in Asymptomatic cases v.s. Control samples
(Wilcoxon rank-sum test, ***: P < 0.001; **: P < 0.01; *: P < 0.05; ns: P > 0.05)

CSV PDF
ROC Analysis Between Symptomatic cases v.s. Control samples

CSV PDF
ROC Analysis Between Asymptomatic cases v.s. Control samples

CSV PDF

IFV: Influenza Virus
RSV: Respiratory Syncytial Virus
HRV: Human Rhinovirus
SARS-CoV-2: Severe Acute Respiratory Syndrome Coronavirus 2
Seasnal CoVs: Seasonal Coronavirus including HKU-1, OC43, etc.
Re-standardized severity:
Symptomatic: symptomatic individuals with the viral infection.
Asymptomatic: individuals who tested positive for a virus but presented no symptoms
Controls: uninfected healthy individuals

Step3: Select a Dataset


ROC Analysis


Select a Multiple Infection Dataset



ROC Analysis


Select the single cell RNA dataset










Tutorial for respiratory Virus Response AnaLysis & Visualization

Introduction


rViRAL is a database for facilitating the use of publicly available transcriptomics in the field of host responses to virus infections. It has integrated 1,489 blood samples from both asymptomatic and symptomatic individuals infected with one of the following viruses: SARS-CoV-2, seasonal coronavirus (Seasonal CoVs), influenza virus (IFV), respiratory syncytial virus (RSV), or human rhinovirus (HRV) from 10 independent cohorts across continents of Asia, Europe, and North America. A suite of advanced functions is provided to understand a gene of interest across multiple viral infections.


When querying a gene of interest, by default, the results will be automatically generated for : (i) pan-respiratory-virus differential expression (DE) analysis to determine if the gene of interest is differentially expressed between infected and un-infected samples presenting symptoms or not, and ROC analysis is performed to measure the performance of the gene biomarker in distinguishing infected samples from control samples with a forest plot, (ii) The DE and ROC analyses can also be implemented for a selected single or multiple viral infection project to show more detailed information about the dynamics of the gene and its associated diagnostic power for a viral infection type of interest.


By using rViRAL, experimental biologists can easily ask specific questions and test their hypotheses. For example, one can easily find the gene RBBP6 specifically expressed in SARS-CoV-2 infection regardless of symptom (Figure 1).

Figure 1. Overview of the ViRAL.

Query a Gene of Interest


Users can query a gene of interest by typing the gene symbol in the 'Search a Gene' field and selecting the gene from the dropdown list. In addition to the general information including Ensembl ID, Alias, and Description of the queried gene, links to several public databases including ENSEMBL, NCBI, GeneCards, DrugBank, and EBI are also provided.

Figure 1. Overview of UI for Querying a Gene of Interest

Pan-Viral Infection


Pan-respiratory-virus differential expression (DE) analysis to determine if the gene of interest is differentially expressed between infected and un-infected samples presenting symptoms or not. Wilcoxon rank sum test is used for DE analysis. The expression levels and statistical significances of the gene of interest can be visualized in a box plot.


Receiver operating characteristic (ROC) analysis is performed to measure the performance of the gene biomarker in distinguishing infected samples from control samples with a forest plot. A forest plot with the number of Infected and uninfected samples, area under the curve (AUC), and 95% confidence interval (CI) of the AUC for each project is used to visualize the result.

Figure 1. Pan-respiratory-virus Infection Analysis

Single-Viral Infection


rViRAL provides functions to focus the DE analysis and ROC analysis for the gene of interest in a selected project.


To explore the gene of interest in a selected project, the steps were:

(1) Select the virus, including one of the followings:

IFV: Influenza Virus

RSV: Respiratory Syncytial Virus

HRV: Human Rhinovirus

SARS-CoV-2: Severe Acute Respiratory Syndrome Coronavirus 2

Seasnal CoVs: Seasonal Coronavirus including HKU-1, OC43, etc.

(2) Select the infected cases presenting symptoms or not:

Symptomatic: symptomatic individuals with the viral infection.

Asymptomatic: individuals who tested positive for a virus but presented no symptoms.

(3) Select the dataset of interest from the data table.

Figure 1. Single-Viral Infection Analysis

Multiple-Viral Infection


Multiple-Viral infection, also known as viral co-infection, is associated with increased rates of hospitalization.
ViRAL provides functions to focus the DE analysis and ROC analysis for the gene of interest in such a dataset with multiple-viral infection.


Figure 1. Multiple-Viral Infection Analysis

Contacts


The rViRAL would not be possible without the contributions of the community. Any comments or suggestions from you will highly appreciated:


1. An interesting dataset;


2. A new feature requested;


3. Anything else.


Please feel free to contact us: yeli7068 AT outlook.com