The app I produced is tool that should help domain scientists explore and generate hypotheses based on RNA expression data from lung cells infected with SARS-CoV.
In 2007, Sims et al. published a time series dataset where they inoculated cultured human lung cells with a virus designated SARS-CoV and measured RNA expression for 72 hours. This dataset is available online under reference GSE33267.
First, I had to transform data from wide to long format. This is the result:
| probe | sample_name | time_point | replicate | value |
|---|---|---|---|---|
| A_23_P100001 | DORF6 | 0H | 1 | 10.14091 |
| A_23_P100001 | DORF6 | 0H | 2 | 10.21428 |
| A_23_P100001 | DORF6 | 0H | 3 | 10.21319 |
| A_23_P100001 | DORF6 | 3H | 1 | 10.28294 |
| A_23_P100001 | DORF6 | 3H | 2 | 9.97440 |
| A_23_P100001 | DORF6 | 3H | 3 | 10.12804 |
Expressions are reported for regions that do not have pretty gene symbol names, so I translated that into something human readable. Dataset with nice gene symbols can be found here.
In the end, completely transformed dataset looks like this:
| probe | sample_name | time_point | replicate | value | GENE_SYMBOL |
|---|---|---|---|---|---|
| A_23_P100001 | DORF6 | 0H | 1 | 10.14091 | FAM174B |
| A_23_P100001 | DORF6 | 0H | 2 | 10.21428 | FAM174B |
| A_23_P100001 | DORF6 | 0H | 3 | 10.21319 | FAM174B |
| A_23_P100001 | DORF6 | 3H | 1 | 10.28294 | FAM174B |
| A_23_P100001 | DORF6 | 3H | 2 | 9.97440 | FAM174B |
| A_23_P100001 | DORF6 | 3H | 3 | 10.12804 | FAM174B |