Proteomic signatures of human visceral and subcutaneous adipocytes - Supplementary files

Supplemental Information
S File 1 – Dataset with normalized and imputed intensity values
MaxQuant search proteinGroups.txt dataset with the following modifications: a) removal of decoy hits and contaminant protein groups; b) exclusion of 4 male sample pairs and an outlying sample pair; b) protein group intensities log2 transformation, c) LoessF normalization, and d) missing values imputation using the imp4p package; e) filtration of protein groups with less than 8 measured intensity values for VA or SA, and protein groups identified to less than 2 peptides within the SA or VA group of samples. The filtered dataset with normalized and imputed intensities was used for the comparative analysis using the Limma R package.

S File 2 – Limma differential expression analysis results
Differential expression analysis using the LIMMA R package 28. The linear model used to compare paired differences between SA and VA samples was adjusted for batch effect by adding batch number as a variable in the model. The correlation between sample pairs was included in the linear model using appropriate functions from the LIMMA package 29. Subsequently, the results were adjusted for multiple hypothesis testing using the Benjamini and Hochberg procedure 30 implemented in the LIMMA package.

S File 3a – SA Reactome over-representation pathway analysis
The file was retrieved submitting the list of UniProt accessions of all significantly upregulated SA proteins into the Reactome data analysis tool.

S File 3b – VA Reactome over-representation pathway analysis
The file was retrieved submitting the list of UniProt accessions of all significantly upregulated VA proteins into the Reactome data analysis tool.

S File 4a – Pathway enrichment analysis of all differentially expressed proteins
Cytoscape ClueGO plugin Reactome pathways and reactions enrichment analysis results using all upregulated SA and VA proteins submitted as separate groups. The analysis was performed using default settings but showing only results with a p-value < 0.05.

S File 4b – Pathway enrichment analysis of SA upregulated proteins
Cytoscape ClueGO plugin Reactome pathways and reactions enrichment analysis results for SA upregulated proteins. The analysis was performed using default settings but showing only results with a p-value < 0.05.

S File 4c – Pathway enrichment analysis of VA upregulated proteins
Cytoscape ClueGO plugin Reactome pathways and reactions enrichment analysis results for VA upregulated proteins. The analysis was performed using default settings but showing only results with a p-value < 0.05.

S File 5 – SignalP prediction of putative secreted proteins
The output of putative secreted proteins analysis using SignalP-5.0 Server. This analysis was performed using the FASTA sequence of the most differentially expressed proteins with log2FC > 1 separately for SA and VA proteins.
S File 6 – Dendrogram with modules
Clustering dendrograms of the SA and VA proteins, respectively, with dissimilarity based on topological overlap, together with assigned module colours after the Dynamic tree cut and subsequent merging of highly similar modules (module eigengene correlation > 0.8). The colours were assigned independently for SA and VA dendrogram.
S File 7 – SA WGCNA and module-trait relationships results
The table contains the module membership and gene significance with the respective p-values of the WGCNA and module-trait relationship analysis for the SA protein expression. S File 8 – VA WGCNA and module-trait relationships results
The table contains the module membership and gene significance with the respective p-values of the WGCNA and module-trait relationship analysis for the VA protein expression.