Human response to viruses

SARS-CoV-2 is a highly infectious coronovirus that enables to infect human beings and causes the global pandemic COVID-19. It not only threatens public health but also leads to economic downturn worldwide. The virus has caused > 50 millions confirmed cases and killed > 1 million people as of 2020-11-11, reported by WHO.

During the outbreak of SARS (caused by SARS-CoV) in 2002-2003, approximately 8000 individuals were infected and 800 died. MERS-CoV has a case fatality rate of ~34% and has caused ~2500 confirmed cases and ~900 deaths since 2012.

There are neither approved drugs nor vaccines for the three highly pathogenic coronaviruses. The viruses depend on the human cell to complete their life cycle which includes genomic RNA replication, mRNA translation, virion assembly and release. This suggests that the human body has to react to viral activities. The response of human to virus at the molecular level can be manifested by the analysis of DEGs, PPIs, DEPs, DPPs, DTPs, DUPs, and SAPs.

Browse datasets

DEGs

DEGs are listed in table on the page using the DataTables library. In the table, official symbol, HGNC ID, UniProt identifiers of the encoded protein, and confidence score are shown. On the right top of the table, a search box is provided to search content in the table.

Clicking on the gene will direct to a page showing details of the gene. On that page, the temporal profile of how the gene changes over time post infection is shown.

Also, that page shows a list of drugs which are known to target this gene or the gene product.

PPIs

The first way is to browse PPIs in table, where interacting pairs and corresponding information are shown.

Another way to browse PPIs is using Network view, which will visualize PPIs in a network on the page. In the network, virus proteins are shown as red nodes, human protein are shown as blue nodes.

The NCBI's sequence viewer has been embedded on the page to easily browse virus genome. Clicking on a virus gene in the table or network will show its annotation in the sequence viewer.

DEPs

Please refer to the guide for DEGs.

DPPs

The list page of DPPs is similar to that of DEPs but comes with an additional column that shows which site has been modified.

DTPs

Please refer to the guide for DEGs.

DUPs

Please refer to the guide for DPPs.

SAPs

The list page of SAPs is similar to that of DEPs but comes with an additional column that shows the comparison groups.

Use utilities

Enrichment analysis

In panel 1, set dataset and score. The score denotes the number of studies where the genes or proteins are identified from. Setting the score limits the analysis to a specific subset of genes/proteins. When the setting is done, click the button on the bottom left to start analyzing enriched PANTHER Pathways.

When the analysis finishes, panel 2 lists the input genes/proteins that have been analyzed, and panel 3 shows the enrichment results.

Drug finder

Drug finder searches targeting drugs of a given protein. Please only use the UniProt accession as protein identifier at this moment. Drugs are retrieved from the DrugBank database via the UniProt's API.

For example, enter Q9BYF1 and then click the Find button, found drugs appear below the search box.

Data animation

Want to make data alive? Here you go!

Please set the setting panel and then click Show to initiate the animation. Click the play button on the bottom right of the plot to inspect the dynamics of all genes or proteins in the animation.

Download data

Please go to the Download data page for downloading.

Submit data

We appreciate your contribution. Please go to the Submit data page and follow the rules on that page to submit data to H2V.

Feedback

We value your voice. Please send an email to the webmaster, admin@zhounan.org, if you have any suggestions.

Human response to coronaviruses