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Covid-19 Gene Expression Work Group (Private project)

Hackathon team: gene expression analysis for Covid-19 Virtual Biohackathon (vBH)

Link to vBH Github

https://github.com/virtual-biohackathons/covid-19-bh20

Official Gene Expression Work Group Page (Public page)

https://github.com/virtual-biohackathons/covid-19-bh20/wiki/GeneExpression

Main Objective

We want to perform RNAseq-based analyses on published datasets in order to better understand the interaction between human host and virus.

Fig.1 - We want to focus on already known genes (such as ACE2 and TMPRSS2) but also on new candidate ones that may play a punctual or a general role in the interaction between host and virus. To this end, we will perform extensive RNAseq analyses as described in the workflow section below

Deliverables

Biological: Perform a global RNA-Seq analysis with SARS-CoV-2 infected datasets to search for new candidate genes for testing experimentally

Methodological: Create a packaged reproducible pipeline in Docker to help scientists to easily treat their RNA-Seq data and for us if any new dataset comes out

Projects

We have four main projects going on. To summarize them :

  1. SARS-CoV-2 infection global analyses: will include global gene expression, functional and regulation of gene expression analyses.
  2. Human-virus interaction analyses : will try to search RNA-binding proteins that might be key in the interaction between human and SARS-CoV-2.
  3. Increased risk factors analyses: will look for gene expression data in other datasets to compare especially with selected genes from previous analyses.
  4. Subtyping of expression response to drugs after COVID infection: will focus on trying to search for potential drugs that could impact in important genes for the interaction of human and virus.
  5. Reporting findings to electronic medical records : will try to make these findings arrive at the hands of clinicians.

Please see the project folder for details on each individual project.

Progress tracking

We are tracking progress on project-specific boards here: https://github.com/avantikalal/covid-gene-expression/projects