Table 3. Bipartite graphs.

Data types 1 and 2 (nodes in Neo4j) are defined in Supplementary Table S5, and indices refer to numbered bipartite graphs in Supplemental Figure S7 as well as their narrative description in Supplementary Data p.11–14. Data type names are given as implemented in the Neo4j database.

Index	Data type 1	Data type 2	Statistical method/ association type	Multiple testing correction	Cutoff (corrected P-value)	Implementation	Description and Biological implication	Reference(s)
1	PROBETYPE	SYMBOL	mapping	N/A	N/A	getSYMBOL function in lumi package	Reference mapping of all probes on the chip to genes (platform-specific)	14
2	PROBE	SYMBOL	mapping	N/A	N/A	topTable function in limma	Mapping of experiment-specific probes to genes	18
3	PROBE	wgcna	mapping	N/A	N/A	WGCNA	Indicates membership of specific probes in enumerated WGCNA modules	14
4 X	PROBE	PROBE	Connectivity (weight in topological overlap matrix)	N/A	Maximum of 2000 per module	Custom function: at least the top 10 % of edges in the module network, capped at 2000	Subset of probes in WGCNA modules with high connectivity	14
5	SYMBOL	reactomePW	mapping	N/A	N/A	lumi, ReactomePA (uses reactome. db)	Mapping of gene symbols to reactome pathways in the current dataset	14, 22
6	SYMBOL	PalWangPW	mapping	N/A	N/A	WGCNA (uses PWLists included with WGCNA)	Mapping of gene symbols to a manually curated list of pathways in the current dataset	14
7	SYMBOL	ImmunePW	mapping	N/A	N/A	WGCNA (uses ImmunePathwayLists included with WGCNA)	Mapping of gene symbols to a manually curated list of immune pathways in the current dataset	14
8	SYMBOL	cellEx	mapping	N/A	N/A	WGCNA (uses BloodLists included with WGCNA)	Mapping of gene symbols to a manually curated list of cell-type specific genes in the current dataset	14
9	SYMBOL	cellEx	mapping	N/A	N/A	CellMix (HaemAtlas dataset)	Mapping of gene symbols to the Watkins, et al. list of cell-type specific genes in the current dataset	19, Supp. Ref 30
10	SYMBOL	cellEx	mapping	N/A	N/A	CellMix (Abbas dataset)	Mapping of gene symbols to the Abbas, et al. list of cell-type specific genes in the current dataset	19, Supp. Ref 11
11	wgcna	baylor (Chaussabel modules)	Hypergeometric test	BH	<0.05	WGCNA (UserListEnrichment function with Chaussabel module genes as input)	Enrichment of WGCNA modules for Chaussabel modules, allowing functional comparison of the two approaches	14
12	baylor (Chaussabel modules)	reactomePW	Hypergeometric test	BH	<0.05 *	WGCNA (UserListEnrichment function with Reactome genes as input)	Enrichment of Chaussabel modules for Reactome pathways, allowing functional annotation of the module	14, 22
13	baylor (Chaussabel modules)	PalWangPW	Hypergeometric test	BH	<0.05 **	WGCNA (UserListEnrichment function with a custom list of pathway genes as input)	Enrichment of Chaussabel modules for a manually curated list of pathways, allowing functional annotation of the module	14
14	baylor (Chaussabel modules)	ImmunePW	Hypergeometric test	BH	<0.05 ***	WGCNA (UserListEnrichment function with a custom list of immune pathway genes as input)	Enrichment of Chaussabel modules for a manually curated list of immune pathways, allowing functional annotation of the module	14
15	wgcna	reactomePW	Hypergeometric test	BH	<0.05 *	WGCNA (UserListEnrichment function with Reactome genes as input)	Enrichment of WGCNA modules for Reactome pathways, allowing functional annotation of the module	14, 22
16	wgcna	PalWangPW	Hypergeometric test	BH	<0.05 **	WGCNA (UserListEnrichment function with a custom list of pathway genes as input)	Enrichment of WGCNA modules for a manually curated list of pathways, allowing functional annotation of the module	14
17	wgcna	ImmunePW	Hypergeometric test	BH	<0.05 ***	WGCNA (UserListEnrichment function with a custom list of immune pathway genes as input)	Enrichment of WGCNA modules for a manually curated list of immune pathways, allowing functional annotation of the module	14
18	baylor (Chaussabel modules)	cellEx	Hypergeometric test	BH	<0.05	WGCNA (UserListEnrichment function, uses BloodLists included with WGCNA)	Enrichment of Chaussabel modules for a manually curated list of cell-type specific genes, allowing interpretation of cellular context of the module	14
19	baylor (Chaussabel modules)	cellEx	Hypergeometric test	BH	<0.05	WGCNA (UserListEnrichment function, uses HaemAtlas list included with Cellmix)	Enrichment of Chaussabel modules for a manually curated list of cell-type specific genes, allowing interpretation of cellular context of the module	14, 19, Supp. Ref 30
20	baylor (Chaussabel modules)	cellEx	Hypergeometric test	BH	<0.05	WGCNA (UserListEnrichment function, uses Abbas list included with Cellmix)	Enrichment of Chaussabel modules for a manually curated list of cell-type specific genes, allowing interpretation of cellular context of the module	14, 19, Supp. Ref 11
21	wgcna	cellEx	Hypergeometric test	BH	<0.05	WGCNA (UserListEnrichment function, uses BloodLists included with WGCNA)	Enrichment of WGCNA modules for a manually curated list of cell-type specific genes, allowing interpretation of cellular context of the module	14
22	wgcna	cellEx	Hypergeometric test	BH	<0.05	WGCNA (UserListEnrichment function, uses HaemAtlas list included with Cellmix)	Enrichment of WGCNA modules for a manually curated list of cell-type specific genes, allowing interpretation of cellular context of the module	14, 19, Supp. Ref 30
23	wgcna	cellEx	Hypergeometric test	BH	<0.05	WGCNA (UserListEnrichment function, uses Abbas list included with Cellmix	Enrichment of WGCNA modules for a manually curated list of cell-type specific genes, allowing interpretation of cellular context of the module	14, 19, Supp. Ref 11
24	wgcna	cellprop	Pearson correlation	BH	<0.05 ***	WGCNA (WGCNA::cor function)	Correlation of WGCNA module eigengenes with estimated cell-type proportions (as output using functions in the CellMix package)	14
25	CELL	cellEx	mapping	N/A	N/A	Mapping of consensus cell type names to cell type names used in the BloodLists dataset included with WGCNA)	Convenience mapping that facilitates searching for cell types in the ANIMA database regardless of the name of the cell type in the original gene marker list	14
26	CELL	cellEx	mapping	N/A	N/A	Mapping of consensus cell type names to cell type names used in the HaemAtlas dataset included with CellMix)	Convenience mapping that facilitates searching for cell types in the ANIMA database regardless of the name of the cell type in the original gene marker list	19, Supp. Ref 30
27	CELL	cellEx	mapping	N/A	N/A	Mapping of consensus cell type names to cell type names used in the Abbas dataset included with CellMix)	Convenience mapping that facilitates searching for cell types in the ANIMA database regardless of the name of the cell type in the original gene marker list	19, Supp. Ref 11
28	CELL	cellprop	mapping	N/A	N/A	Mapping of consensus cell type names to cell type names used in the Abbas dataset included with CellMix)	Convenience mapping that facilitates searching for cell types in the ANIMA database regardless of the name of the cell type in the original gene marker list	19, Supp. Ref 11
29	wgcna	pheno	Pearson correlation	BH	<0.05 ***	WGCNA (WGCNA::cor function)	Correlation of WGCNA module eigengenes with a numeric matrix of clinical and other phenotype data	14

*a minimum of three and a maximum of ten results were included in the ANIMA database

** a minimum of four and a maximum of ten results were included in the ANIMA database

*** results were reviewed algorithmically; in the case of no hits for enrichment at the specified cutoff, less stringent criteria were applied (See Supplementary information). In all cases, the corrected P-value was included as a property of the relationship, allowing filtering of the database entries.

^X the PROBE-PROBE network is a monopartite correlation network and not a bipartite graph

Abbreviations: BH, Benjamini-Hochberg multiple testing correction