Frequently Asked Questions (FAQs)

Q1. What is vhfRNAi

A. It is an online resource for analysis of host factors involved in viral infection identified by genome wide RNAi screen.

Q2. What is the use of such a resource?

A. vhfRNAi will be useful in understanding host-virus biology, host regulatory networks as well as identification of targets for the development of antiviral therapeutics.

Q3. What information does this resource provide?

A. vhfRNAi furnishes in depth information about the target gene, virus, phenotype, assay, screen description etc. vhfRNAi has about 12000 host factors of 18 viruses along with tools of overlap, network, enrichment and interaction analysis.

Q4. How can this resource be used?

A. The resource is freely accessible at http://bioinfo.imtech.res.in/manojk/vhfrnai

Q5. How to retrieve data from vhfRNAi?

A. Desired information on viral RNAi screens can be obtained using browse and search options provided in the online resource. The results obtained from can be sorted by clicking on the column header and filtering can be done by typing in the boxes given under the headers.

Q6. How was the data curated?

A. To fetch relevant articles from the scientific literature, we used advanced search option in PubMed. We searched the database with the following text mining script having abbreviations and synonyms to retrieve maximum number of papers:

 (((((genomewide) OR genome-wide) OR *genome*wide*)) AND ((((RNA interference) OR RNAi) OR RNA*interference*) OR RNAi*)) AND ((virus) OR viral)

 

Q7. How was vhfRNAi developed?

A. vhfRNAi is developed using the open source LAMP solution stack with MySQL and Apache in back-end and front-end of web interface is programmed using PHP, HTML and JavaScript.

Q8. What are the different types analysis provided in vhfRNAi?

A. vhfRNAi provides seven types of analysis. They are: vhfRNAi overlap analysis, network analysis, gene ontology (GO) analysis, vhfRNAi involved in disease (GWAS), vhfRNAi interaction with virus, virus interacting proteins and pathway enrichment analysis.

Q9. What is overlap analysis?

A. The overlap analysis provides the list of common host factors from different viruses/families/groups and are displayed in the form of clickable heat maps as well as chord diagrams using Circos.

Q10. What is network analysis?

A. The network analysis displays the interaction between the host and the virus. All the host factors for the user selected virus are shown in graphical view. The host factors are colored "blue" with virus ("green color") at the center and cellular proteins on the periphery for distinction. While the viruses sharing host factors of other viruses are given "yellow color". This analysis was performed using cytoscape.

Q11. What is gene ontology (GO) analysis?

A. Gene Ontology (GO) analysis is used to determine GO categories that are significantly overrepresented and map the predominant functional themes by using using host factors of different viruses.It is performed using BiNGO tool in cytoscape.

Q12. What is genome wide association studies (GWAS) analysis?

A. In the genome wide association studies analysis users can analyze candidate disease host genes of which the common genetic variants, e.g., single-nucleotide polymorphisms (SNPs), in different individuals are associated with a trait/disease. These were identified from genome wide association studies (GWAS) (The NHGRI GWAS Catalog).

Q13. What is "vhfRNAi interaction with virus" analysis?

A. "vhfRNAi interaction with virus" analysis displays the interaction of host factors with virus. It was displayed using D3 (Data-Driven Documents) which is a JavaScript library for visualizing data with HTML, SVG, and CSS.

Q14. What is "virus interacting proteins" analysis?

A. "virus interacting proteins" contains list of genes whose protein products are experimentally validated. These pathogen interacting proteins (PIP) data are from VirHostNet and VirusMINT.

Q15. What is pathway enrichment analysis?

A. Pathway enrichment analysis is performed using KEGG Mapper. This analysis provides functional annotation of the host factors involved in cellular pathways.