Early innate immunity determines outcome of Mycobacterium tuberculosis pulmonary infection in rabbits

Table 1 List of top canonical pathways affected by SDEG

No.	Pathway														HN878	CDC1551
		1	2	3	4	5	6	7	8	9	10	11	12	13	Up / Down	Up / Down
1	REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES (41)	23	22	0	0	6	0	0	1	22	0	23	0	0	17 / 6	11/12
2	KEGG_CHEMOKINE_SIGNALING_PATHWAY (144)	1	54	3	0	10	6	0	5	26	0	22	0	0	37 / 17	34 / 20
3	REACTOME_INTERFERON_GAMMA_SIGNALING (40)	0	0.1	26	5	3	5	4	0	0	0	0	5	1	21 / 5	15 / 11
4	KEGG_GRAFT_VERSUS_HOST_DISEASE (21)	0	0	0.3	15	2	8	3	0	3	0	0	14	3	15 / 0	7/8
5	KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY (80)	0.3	0.3	0.1	0.1	29	7	0	0	8	2	6	2	2	27 / 2	17 / 12
6	KEGG_LEISHMANIA_INFECTION (55)	0	0.2	0.2	0.5	0.2	29	4	2	3	1	1	7	4	25 / 4	13 / 16
7	REACTOME_IMMUNOREGULATORY_INTERACTIONS_	0	0	0.2	0.2	0	0.2	23	6	0	2	1	3	3	21 / 2	17 / 6
	BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL (36)
8	REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_	0	0.1	0	0	0	0.1	0.3	37	2	6	2	0	3	23 / 14	27 / 10
	VASCULAR_WALL (65)
9	KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION (202)	1	0.5	0	0.2	0.3	0.1	0	0.1	66	0	22	3	13	48 / 18	43 / 23
10	PID_INTEGRIN1_PATHWAY (60)	0	0	0	0	0.1	0	0.1	0.2	0	36	0	0	3	22 / 14	28 / 8
11	REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS (121)	1	0.5	0	0	0.2	0	0	0.1	0.5	0	44	0	0	28 / 16	22 / 22
12	KEGG_ALLOGRAFT_REJECTION (25)	0	0	0.3	0.9	0.1	0.5	0.2	0	0.2	0	0	15	3	14 / 1	8/7
13	KEGG_HEMATOPOIETIC_CELL_LINEAGE (68)	0	0	0	0.2	0.1	0.1	0.1	0.1	0.4	0.1	0	0.2	34	24 / 10	25 / 9

The pathways are ranked 1 to 13 according to their p value and shown in column 1 and row 1. The numbers in parenthesis after the pathway (column 2) refers to the total number of SDEG involved. This includes unique genes and those that are shared among different pathways. The numbers along the diagonal axis (underlined) are the number of SDEG involved in a specific pathway. Numbers shown above the diagonal axis are the number of SDEG shared between the pathways. The fractional numbers shown below the diagonal axis are the portion of SDEG shared by other pathways with reference to the numbers in the diagonal axis. The last two columns at the right show the number of up and down regulated genes in each pathway.

ISSN: 1478-811X