Table 2 Normalised enrichment scores and numbers of core genes for the Gene Set Enrichment Analysis (GSEA) of SWATH-MS proteomics data and mRNA expression data.

From: Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells

FC

Protein gene set

Enrichment score

Number of core genes

↑ UM-CLL

Combat S (n = 238)

1.85

80

Combat U (n = 234)

1.87

78

limma S (n = 216)

1.88

74

linear M (216)

2.07

81

↓ UM-CLL

Combat S (n = 157)

− 1.71

36

Combat U (n = 149)

− 1.65

33

limma S (n = 141)

− 1.65

40

linear M (n = 139)

− 1.80

37

Negative P.Corr IGHV

Combat S (n = 174)

2.03

84

Positive P.Corr IGHV

Combat S (n = 254)

− 2.15

55

  1. GSEA was used to compare an mRNA ranked t-statistic gene expression signature (GEO database, accession number GSE28654)21, representing genes found to be differentially expressed between UM-CLL and M-CLL samples (≤ 10% FDR, n = 3008), to proteins found to be differentially expressed (≤ 10% FDR) in batch corrected (by Combat supervised (Combat S), Combat unsupervised (Combat U), limma supervised (limma S) or limma with batch information incorporated into the linear model design (linear M)) SWATH-MS data. In addition, the mRNA signature was compared to proteins found to be significantly positively or negatively correlated to the percentage of IGHV mutation by partial correlation analysis (P. Corr) after Combat S batch correction (FDR < 10%). All GSEA results were significant (0% FDR).
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