STEP 17
In this step the abundances of complex-associated subunits are normalized to the trimmed mean of the complexes (as previosuly described in Ori et al., 2013; Ori et al., 2016). Briefly, proteins belonging to the same complex were normalized by the respective trimmed mean (or interquartile mean) of the complex subunits across all individuals/samples. In case of proteins involved in multiple complexes, the average value from all the corresponding complexes was taken into account. Given the complex-normalized abundances, the variance of each subunit in a given complex was calculated. The output-directory of this step summarizes these results.
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
Download all input files here (3MB)Python code required for normalization within complexes & pathways.
Python object containing complex-normalized values for each input dataset unzip and unpickle to open.
modulewise_norm_pathway_stoichiometry.zip (665KB)Python object containing pathway-normalized values for each input dataset unzip and unpickle to open.