STEP 18

Recovery of known STRING interactions in yeast-related published datasets

For all datasets considered for the ROC-analysis (Step 19), the distribution of Pearson correlation coefficients for protein-protein pairs with STRING interaction score > 700 (combined score), known interaction (combined score >0) and random protein-protein pairs is analyzed. The Mann-Whitney U-test was used to assess significance of the respective shifts.

Data/Code Requirements for downloading

yeast3_quant_Proteome_carbonSources_MAPPED_complexes_pathways_NORM2.tsv.gz (213KB)

Proteome data published in Martin-Perez & Judit Villén(2017), Cell Systems

yeast4_quant_Proteome_naclStress_MAPPED_complexes_pathways_NORM2.tsv.gz (179KB)

Proteome data published in Martin-Perez & Judit Villén(2017), Cell Systems

yeast5_quant_Proteome_MAPPED_complexes_pathways_NORM2_IBAQ.tsv.gz (301KB)

Proteome data published in Skelly et al.(2013), Genome Research; re-analyzed with MaxQuant

yeast10_quant_RNA_MAPPED_complexes_pathways_NORM2.tsv.gz (568KB)

RNA-seq data published in Lahtvee et al.(2017), Cell Systems

yeast11_quant_proteome_MAPPED_complexes_pathways_NORM2.tsv.gz (208KB)

Proteome data published in Lahtvee et al.(2017), Cell Systems

yeast14_quant_proteome_MAPPED_complexes_pathways_NORM2.tsv.gz (282KB)

Proteome data published in Picotti et al.(2013), Nature

yeast16_quant_proteome_MAPPED_complexes_pathways_NORM2.tsv.gz (120KB)

Proteome data published in Pavelka et al.(2010), Nature

yeast18_quant_proteome_MAPPED_complexes_pathways_NORM2.tsv.gz (140KB)

Proteome data published in Janssens et al.(2015), Elife

yeast19_quant_transcriptome_MAPPED_complexes_pathways_NORM2.tsv.gz (520KB)

RNA-seq data published in Janssens et al.(2015), Elife

yeast20_quant_proteome_MAPPED_complexes_pathways_NORM2.tsv.gz (248KB)

Proteome data published in Varland et al.(2018), Molecular & Cellular Proteomics

yeast21_quant_proteome_MAPPED_complexes_pathways_NORM2_REP.tsv.gz (258KB)

Proteome data published in Zelezniak et al.(2018), Cell Systems

4932.STRING.data.zip (37.5MB)

STRING data (v10.5) extracted for yeast

Download all input files here. (40MB)

wp_step18_code.py

Recovery of known STRING interactions in different published yeast datasets.

string_corrs.zip (1.1G)

Python object containing correlation values for all protein pairs (STRING and others) for each of the yeast datasets; unzip and unpickle to open.

suppFigure1_additional_yeast.png

Density plots displaying correlation values for STRING interactors.