Psa RNAseq
| MCP,meR,enolase... | dctT | lysR | cata/lipo |
|---|
| Tn6212 | | | | |
|---|
| Δ3 | X | X | | |
|---|
| ΔlysR | X | X | | X |
|---|
| ΔdctT | X | | X | X |
|---|
- All (4329 lines) (csv)
- All - Genome order (4329 lines) (csv)
- Only glucose (0 lines) (csv)
- Only succinate (0 lines) (csv)
- Only citrate (0 lines) (csv)
- Only ΔTn6212 (0 lines) (csv)
- Only Δ3 (0 lines) (csv)
- Only ΔLysR (0 lines) (csv)
- Only ΔdctT (0 lines) (csv)
- Identical effect for all sugars (152 lines) (csv)
- Only removed lysR i.e., ('ΔLysR', 'ΔTn6212', 'Δ3') - (0 lines) (csv)
- Only removed dctT i.e., ('ΔTn6212', 'ΔdctT') - (0 lines) (csv)
- Only removed cata or lipo i.e., ('ΔTn6212', 'Δ3') - (0 lines) (csv)
- Consistent to deletion of removed lysR i.e., ('ΔLysR', 'ΔTn6212', 'Δ3') - (4234 lines) (csv)
- Consistent to deletion of removed dctT i.e., ('ΔTn6212', 'ΔdctT') - (4292 lines) (csv)
- Consistent to deletion of removed cata or lipo i.e., ('ΔTn6212', 'Δ3') - (4300 lines) (csv)
INFO: Script run at 15:41:19 01/27/20 CET
INFO: Load RNAseq data. (Using log2FoldChange)
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13suc_vs_NZ13d3suc.txt
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13cit_vs_NZ13d3cit.txt
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13suc_vs_NZ13dTn6212suc.txt
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13glu_vs_NZ13ddctTglu.txt
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13glu_vs_NZ13dLysRglu.txt
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13glu_vs_NZ13dTn6212glu.txt
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13cit_vs_NZ13dLysRcit.txt
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13cit_vs_NZ13ddctTcit.txt
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13suc_vs_NZ13ddctTsuc.txt
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13cit_vs_NZ13dTn6212cit.txt
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13glu_vs_NZ13d3glu.txt
INFO: Load 81 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/plasmid/NZ13suc_vs_NZ13dLysRsuc.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13suc_vs_NZ13d3suc.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13cit_vs_NZ13d3cit.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13suc_vs_NZ13dTn6212suc.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13glu_vs_NZ13ddctTglu.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13glu_vs_NZ13dLysRglu.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13glu_vs_NZ13dTn6212glu.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13cit_vs_NZ13dLysRcit.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13cit_vs_NZ13ddctTcit.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13suc_vs_NZ13ddctTsuc.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13cit_vs_NZ13dTn6212cit.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13glu_vs_NZ13d3glu.txt
INFO: Load 5753 lines from data/raw/200109_raw_rnaseq_comparison/deseq2/chromosome/NZ13suc_vs_NZ13dLysRsuc.txt
INFO: 70008 entries
INFO: (5834, 12) Genes
INFO: (4329, 12) Genes after filtering (pval<0.05)
INFO: Load sequences data
INFO: Load 5883 entries from data/raw/PsaNZ13_genebank.gb
INFO: Load 84 entries from data/raw/PsaNZ13_plasmid_genebank.gb
INFO: Loaded 5974 genes description from data/raw/Pseudomonas_syringae_pv_actinidiae_ICMP_18884_7747.csv
INFO: Loaded 3455 lines from data/kofam_koala.txt, e-val in (0.0, 6e-06)
INFO: Loaded 23 lines from data/kofam_koala_plasmid.txt, e-val in (5.499999999999997e-200, 1.3000000000000002e-10)
INFO: 3478 unique mapping KO<->IYO
WARNING: Bad index K06955 - dropping.
INFO: Loaded 2337 KEGG entries from the local kegg database data/raw/kegg_annotation.pkle
INFO: 3935 BRITE entries (8 level 0, 44 level 1, 279 level 3)
INFO: There are unique 894 expression motifs
INFO: Create a file for kegg mapper and map 01100
INFO: Loaded 454 KEGG pathways from data/kegg/maps/*.xml
INFO: 248/454 Kegg pathways have differentially expressed genes