Table 2.

Clusters of genes differentially expressed between TB patients with good or poor TB treatment outcomes to TB treatment in MaSigPro analysis of combined RNA-Seq data from South Africa and Indonesia.

Cluster number	Overall pattern	Number of gene transcripts	Gene function				Top Functions from g:Profilerbwith adjusted P < 0·05
			Protein coding	Processed transcript	Pseudo-gene	Regulatory RNAsa
1	↓ through treatment; Higher in Good at M0.5	26	20	1	0	5	GO:MF – Opsonin Binding; GO:CC – Intracellular Vesicles; Endomembrane System
2	↑ through treatment; Higher in Poor throughout	14	13	0	0	1	GO:BP – B cell receptor (BCR) signaling; GO:CC – BCR complex KEGG – BCR signaling; primary immunodeficiency; REAC – BCR signaling WP – BCR signaling CORUM – CIN85-BLNK complex
3	↑ through treatment; Higher in Good at M6	25	17	2	0	6	No significant results
4	↓ through treatment; Higher in Poor throughout	47	37	2	2	6	GO:CC – Arp2/3 complex; KEGG – Shigellosis; E.coli, Yersinia, Salmonella infection; Endocytosis; REAC – Ephrin signaling; Rho GTPAses activate WASPs and WAVEs; TF – ZNF544 CORUM – Arp2/3 complex
5	Small ↓ through treatment; Higher in Poor throughout	11	6	1	1	3	GO:MF – L-tyrosine transmembrane transporter activity; GO:BP – positive regulation of fatty acid transport.
6	No change; Higher in Poor throughout	4	0	0	3	1	No significant results
7	↑ to M0.5, then ↓; Higher in Poor at M0.5	4	4	0	0	0	GO:BP – mitotic cell cycle process WP – Retinoblastoma Gene in Cancer
8	↑ in Good through treatment; No change in Poor	7	3	0	2	2	GO:MF - RNA polymerase III activity
9	↓ through treatment; Much greater change Good	10	10	0	0	0	GO:MF – immunoglobulin receptor binding GO:BP – phagocytosis, recognition; complement activation, classical pathway; immunoglobulin mediated immune response; B cell activation GO:CC – immunoglobulin complex; E/C space; plasma membrane REAC – Classical antibody-mediated complement activation; FCGR activation; phagocytosis.

^aRetained introns, Antisense, LncRNA, miRNA, nonsense-mediated decay, sense overlapping, sense intronic, snoRNA,

^bRedundant G:Profiler results are not shown.