Conclusions - HeidiOttesen/GenomeAnalysis GitHub Wiki
In this project I have learned about many different bioinformatic analysis tools used for genome assembly and differential expression, it has been a bumpy ride with a lot of troubleshooting and frustration, but also plenty of joys when things finally work.
I started off trying to follow the tools and options as used in the article but soon went in my own direction according to the student manual.
From the DeSeq2 results we found som genes that seem to be very important for survival in human serum (vs in rich medium):
| No. | Gene | Gene name | Product | log2FoldChange | pvalue |
|---|---|---|---|---|---|
| 1 | FKFLPFNF_01449 | purS | Phosphoribosylformylglycinamidine synthase subunit | 9.47689 | 0.00000e+00 |
| 2 | FKFLPFNF_01450 | purQ | Phosphoribosylformylglycinamidine synthase subunit | 9.17443 | 4.36682e-75 |
| 3 | FKFLPFNF_01448 | purC | Phosphoribosylaminoimidazole-succinocarboxamide synthase | 9.01904 | 3.63111e-119 |
| 4 | FKFLPFNF_01451 | purL | Phosphoribosylformylglycinamidine synthase subunit | 8.93882 | 2.35838e-90 |
| 5 | FKFLPFNF_01452 | purF | Amidophosphoribosyltransferase | 8.82134 | 3.03795e-141 |
| 6 | FKFLPFNF_01453 | purM | Phosphoribosylformylglycinamidine cyclo-ligase | 8.46419 | 3.17345e-241 |
| 7 | FKFLPFNF_01455 | purH | Bifunctional purine biosynthesis protein | 8.35599 | 4.26558e-175 |
| 8 | FKFLPFNF_01456 | purD | Phosphoribosylamine--glycine ligase | 8.25687 | 1.39884e-194 |
| 9 | FKFLPFNF_01454 | purN | Phosphoribosylglycinamide formyltransferase | 8.22430 | 4.60185e-158 |
| 10 | FKFLPFNF_01510 | - | Hypothetical protein | 7.75820 | 0.00000e+00 |
many of these top genes are involved in the nucleotide synthesis, and they could be potential targets for new antibiotics.