S1 - Ottawa & DiOGenes cohorts
Average anthropometric, glycemic and total lipid characteristics of the Ottawa and DiOGenes cohorts. The sample sizes correspond to subjects having genotype data in at least one of the proteomic data types (MS or SomaLogic). The p-value was obtained using a two-sided t-test for continuous variables, and using a Fisher’s exact test for gender. Standard deviations are in parentheses.
Column types:
Ottawa (n = 404)
DiOGenes (n = 572)
p-value
S2 - discovery pQTLs
pQTL associations discovered by LOCUS in the Ottawa cohort, using the mass-spectrometry and SomaLogic datasets.
Column types:
SNP
Protein
Protein name
UniProt ID
Protein SOMAID
Platform
Type
LOCUS PPI
LOCUS FDR
Validated
S3 - validation pQTLs
pQTL associations discovered by LOCUS in the Ottawa cohort and validated in the DiOGenes cohort.
Column types:
SNP
Protein
Protein name
UniProt ID
Protein SOMAID
Platform
LOCUS PPI
LOCUS FDR
Valid beta
Valid SE
Valid p-value MS
Valid adjusted p-value MS
Validated with MS
Valid p-value SomaLogic
Valid adjusted p-value SomaLogic
Validated with SomaLogic
Protein coding gene
Coding gene chr
Coding gene start
Coding gene end
Type
SNP chr
SNP position
SNP closest gene
Overlap with public pQTLs
S4 - overlap with public pQTLs
Overlap of the validated pQTL associations with public pQTL associations (PhenoScanner).
Column types:
Novelty
SNP
Protein
Protein name
UniProt ID
Protein SOMAID
Platform
Type
Gene names
Studies
Nb of studies
Proxy search r2 > 0.8
Isoform
S5 - comparison with univariate analysis, individual SNP-protein pairs
Comparison with univariate two-stage analysis using GEMMA, individual hits.
Column types:
Locus ID
LOCUS analysis: validated
GEMMA analysis: validated
SNP
SNP chr
SNP position
SNP in LOCUS panel
Protein
Protein name
UniProt ID
Protein SOMAID
Platform
Type
GEMMA disc p-value
GEMMA valid p-value
S6 - comparison with univariate analysis, sentinel SNP-protein pairs
Comparison with univariate two-stage analysis using GEMMA, hits summarized by loci. The star after `GEMMA only` refers to the fact that the locus was missed because the corresponding SNPs were not tagged and is correctly identified by LOCUS when rerunning after adding these SNPs in the panel (see `LOCUS extended panel` column which lists the SNPs identified by LOCUS after rerun for these loci).
Column types:
Locus ID
Locus identified by
Top disc SNP(s) LOCUS
Top disc SNP(s) GEMMA
SNP chr
SNP position
SNP in LOCUS panel
Protein
Protein name
UniProt ID
Protein SOMAID
Platform
Type
LOCUS PPI
GEMMA p-value
Valid p-value
LOCUS extended panel
S7 - overlap with public eQTLs
Overlap of the validated pQTL associations with public eQTL associations (GTEx Consortium).
Column types:
SNP
Protein
Protein name
Protein coding gene
Type
Platform
Controlled genes (public eQTLs)
S8 - overlap with risk loci
Overlap of the validated pQTL associations with disease risk loci (GWAS Catalog).
Column types:
SNP
Mapped gene
Trait/Disease
p-value
PubMed id
Date
First author
S9 - pQTLs vs clinical
Associations between proteins under genetic control and clinical parameters measuring dyslipidemia, insulin resistance and visceral fat, in the Ottawa and DiOGenes cohorts.
Column types:
Protein
Protein name
UniProt ID
Endpoint
Platform
Cohort name
Beta
SE
p-value
Adjusted p-value
Type
S10 - pathways covered by the SomaLogic panel
Pathways represented by the SomaLogic proteomic panel. Enrichment analysis using KEGG (2019) and Reactome (2016) and a false discovery rate threshold of 5%.
Column types:
Database
Pathway
Overlap
p-value
Adjusted p-value
S1 - Ottawa & DiOGenes cohorts
S2 - discovery pQTLs
S3 - validation pQTLs
S4 - overlap with public pQTLs
S5 - comparison with univariate analysis, individual SNP-protein pairs
S6 - comparison with univariate analysis, sentinel SNP-protein pairs
S7 - overlap with public eQTLs
S8 - overlap with risk loci
S9 - pQTLs vs clinical
S10 - pathways covered by the SomaLogic panel