Differential analysis of proteomics datasets — PROTEOME

Timewise summary statistics and training FDR from differential analysis (DA) that tests the effect of training on each proteomics feature (protein, phosphosite, acetylsite, ubiquitlsite) within each sex. One data frame per data type per tissue.

Usage

PROT_CORTEX_DA

PROT_SKMGN_DA

PROT_HEART_DA

PROT_KIDNEY_DA

PROT_LUNG_DA

PROT_LIVER_DA

PROT_WATSC_DA

PHOSPHO_CORTEX_DA

PHOSPHO_SKMGN_DA

PHOSPHO_HEART_DA

PHOSPHO_KIDNEY_DA

PHOSPHO_LUNG_DA

PHOSPHO_LIVER_DA

PHOSPHO_WATSC_DA

ACETYL_HEART_DA

ACETYL_LIVER_DA

UBIQ_HEART_DA

UBIQ_LIVER_DA

Format

A data frame 18 variables:

feature: character, unique feature identifier in the format 'ASSAY_ABBREV;TISSUE_ABBREV;feature_ID' only for training-regulated features at 5% IHW FDR. For redundant differential features, 'feature_ID' is prepended with the specific platform to make unique identifiers. See REPEATED_FEATURES for details.
assay: character, assay abbreviation, one of ASSAY_ABBREV
assay_code: character, assay code used in data release. See MotrpacBicQC::assay_codes.
tissue: character, tissue abbreviation, one of TISSUE_ABBREV
tissue_code: character, tissue code used in data release. See MotrpacBicQC::bic_animal_tissue_code.
feature_ID: character, MoTrPAC feature identifier
sex: character, one of 'male' or 'female'
comparison_group: character, time point of trained animals compared to the sex-matched sedentary control animals, one of '1w', '2w', '4w', '8w'
p_value: double, unadjusted p-value for the difference between 'comparison_group' and the group of sex-matched sedentary control animals
adj_p_value: double, adjusted p-value from 'p_value' column. P-values are BY-adjusted across all datasets within a given assay/ome.
logFC: double, log fold-change where the numerator is 'comparison_group', e.g., '1w', and the denominator is the group of sex-matched sedentary control animals
logFC_se: double, standard error of the log fold-change
tscore: double, t statistic
covariates: character, comma-separated list of adjustment variables or NA
numNAs: integer, number of missing values in the current 'comparison_group' and sex-matched sedentary control animals
comparison_average_intensity: double, average intensity among the replicates in 'comparison_group'
reference_average_intensity: double, average intensity among the replicates in the group of sex-matched sedentary control animals
selection_fdr: double, adjusted training p-value used to select training-regulated analytes. P-values are IHW-adjusted across all datasets within a given assay with tissue as a covariate.

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Details

Reproduce our analysis with MotrpacRatTraining6mo::proteomics_timewise_da() and MotrpacRatTraining6mo::proteomics_training_da().