Table 1 Datasets used for module construction.

Dataset	Category	Population	# Samples (Cases)	# Samples (Control)	# Samples (Total)
1 Staphylococcus aureus infection	Bacterial Infection	Pediatric	99	44	143
2 Sepsis	Bacterial Infection	Adult	35	12	47
3 Tuberculosis	Bacterial Infection	Adult	23	11	34
4 Influenza	Viral Infection	Pediatric	25	14	39
5 RSV	Viral Infection	Pediatric	70	14	84
6 HIV	Viral Infection	Adult	28	35	63
7 Systemic lupus erythematosus	Autoimmune	Pediatric	55	14	69
8 Multiple sclerosis	Autoimmune	Adult	34	22	56
9 Juvenile dermatomyositis	Autoimmune	Pediatric	40	9	49
10 Kawasaki disease	Autoinflammatory	Pediatric	21	23	44
11 Systemic onset juvenile idiopathic arthritis	Autoinflammatory	Pediatric	62	23	85
12 COPD	Inflammatory	Adult	19	24	43
13 Melanoma	Malignancy	Adult	22	5	27
14 Pregnancy	Physiologic variant	Adult	25	20	45
15 Liver transplant recipients	Immunosuppressed	Adult	94	30	124
16 B-cell deficiency	Immunodeficiency	Adult	20	13	33

Sixteen distinct datasets were used as the input for module repertoire construction. Each dataset corresponds to a different condition or physiological state and comprises both cases and matched controls. Each dataset was processed as a single batch at the same facility with the data generated using Illumina HumanHT-12 v3.0 Gene Expression BeadChips. The collection comprises a total of 985 individual transcriptome profiles.

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