1 Compare DEs in DrugA and DrugB show 3 clusters

Venn diagram showing little overlapping between DEs in DrugA condition and Drug B condition. DrugB only have 13 DE genes (AbsLog2FC>1 and Padj <0.05), while Drug B have 223 DE genes.

The interactive heatmap for log2 fold changes (cutted into 3 clusters) for all the DEs in both Drug A and Drug B.

The final heatmap

2 Gene enrichment analysis (use KEGG pathway database)

Initial analysis shown:

2.1 Drug A have significant enrichment

2.1.1 KEGG:msm02010 - ABC Transporters

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Table 1: msm02010 in Drug A
kegg.node log2FC mapped_gene
MSMEG_0134 -12.245461 MSMEG_0134,MSMEG_0135,MSMEG_0136,MSMEG_0137,MSMEG_0138,MSMEG_0139,MSMEG_0346,MSMEG_0347,MSMEG_0348,MSMEG_0349,MSMEG_0350,MSMEG_0351,MSMEG_1144,MSMEG_2856,MSMEG_2857,MSMEG_4792,MSMEG_4793,MSMEG_5818,MSMEG_5895,MSMEG_5896,MSMEG_5897,MSMEG_5898,MSMEG_5899,MSMEG_5900,MSMEG_6540
MSMEG_0132 -6.082959 MSMEG_0132,MSMEG_0133,MSMEG_0344,MSMEG_0345,MSMEG_1141,MSMEG_1142,MSMEG_2853,MSMEG_2854,MSMEG_4795,MSMEG_4796,MSMEG_5901,MSMEG_5902
MSMEG_2925 3.113872 MSMEG_2925,MSMEG_2927,MSMEG_6331,MSMEG_6332
MSMEG_0549 -2.379863 MSMEG_0549,MSMEG_3854,MSMEG_4588,MSMEG_5530
MSMEG_0508 -2.249968 MSMEG_0508,MSMEG_0556,MSMEG_3108,MSMEG_5058,MSMEG_5571
MSMEG_6553 1.888710 MSMEG_6553,MSMEG_6554
MSMEG_1373 -1.797986 MSMEG_1373,MSMEG_3090,MSMEG_3601,MSMEG_4171
MSMEG_2926 1.717902 MSMEG_2926,MSMEG_6333
MSMEG_1374 -1.458813 MSMEG_1374,MSMEG_3095,MSMEG_3598,MSMEG_3599,MSMEG_4172
MSMEG_0550 -1.419377 MSMEG_0550,MSMEG_3852,MSMEG_4586,MSMEG_5529
MSMEG_1706 -1.206374 MSMEG_1706
MSMEG_1217 -1.083213 MSMEG_1217,MSMEG_3251
MSMEG_4470 1.073128 MSMEG_4470,MSMEG_6725
MSMEG_2924 1.054581 MSMEG_2924,MSMEG_6334

2.1.2 KEGG:msm00920 - Sulfur Metabolism

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Table 2: msm00920 in Drug A
kegg.node log2FC mapped_gene
MSMEG_0549 -4.690427 MSMEG_0549,MSMEG_0550,MSMEG_0551,MSMEG_3852,MSMEG_3853,MSMEG_3854,MSMEG_4586,MSMEG_4587,MSMEG_4588,MSMEG_5529,MSMEG_5530,MSMEG_5531
MSMEG_0113 -1.635513 MSMEG_0113,MSMEG_0114,MSMEG_0116
MSMEG_4530 -1.452507 MSMEG_4530,MSMEG_4531,MSMEG_4532,MSMEG_4533
MSMEG_2651 -1.298951 MSMEG_2651,MSMEG_2800,MSMEG_3850,MSMEG_4103,MSMEG_4539

2.1.3 KEGG:msm03010 - Ribosome

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Table 3: msm03010 in Drug A
kegg.node log2FC mapped_gene
MSMEG_3757 -1.470656 MSMEG_3757,MSMEG_4931

2.2 Drug B have significant enrichment

2.2.1 KEGG:msm02010 - ABC Transporters

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Table 4: msm02010 in Drug B
kegg.node log2FC mapped_gene
MSMEG_0134 -8.998712 MSMEG_0134,MSMEG_0135,MSMEG_0136,MSMEG_0137,MSMEG_0138,MSMEG_0139,MSMEG_0346,MSMEG_0347,MSMEG_0348,MSMEG_0349,MSMEG_0350,MSMEG_0351,MSMEG_1144,MSMEG_2856,MSMEG_2857,MSMEG_4792,MSMEG_4793,MSMEG_5818,MSMEG_5895,MSMEG_5896,MSMEG_5897,MSMEG_5898,MSMEG_5899,MSMEG_5900,MSMEG_6540
MSMEG_0132 -5.833747 MSMEG_0132,MSMEG_0133,MSMEG_0344,MSMEG_0345,MSMEG_1141,MSMEG_1142,MSMEG_2853,MSMEG_2854,MSMEG_4795,MSMEG_4796,MSMEG_5901,MSMEG_5902
MSMEG_1374 -2.059356 MSMEG_1374,MSMEG_3095,MSMEG_3598,MSMEG_3599,MSMEG_4172
MSMEG_1373 -1.992708 MSMEG_1373,MSMEG_3090,MSMEG_3601,MSMEG_4171
MSMEG_0508 -1.508841 MSMEG_0508,MSMEG_0556,MSMEG_3108,MSMEG_5058,MSMEG_5571
MSMEG_3091 -1.304093 MSMEG_3091,MSMEG_3602,MSMEG_4170
MSMEG_0639 -1.141402 MSMEG_0639,MSMEG_6120