Backpain exercise therapy remodels human epigenetic profiles in buccal and human peripheral blood mononuclear cells: An exploratory study in young male participants

###### Files description #####
Notes. 1) "BT" refers to before therapy and "AT" to after therapy.
2) 0 refers to FALSE and 1 to TRUE for binary variables.
The provided files have tab-separated columns except the .RDS which is and R output of the mixOmics DIABLO integration analysis.

# Questionnaire
> participants_categories.tsv: per participant (rows), output of the clustering with the participant ("ID") category ("category") per class ("class")
> questionnaire_agility_metrics.tsv: questionnaire and agility metrics per participant (rows) for the participants ("ID") with at least one
paired AT+BT data in one type of biological sample (indicated in the columns "swab", "PBMC", and "plasma")

# PTMs
Samples´ names are encoded as PBMC_AT_8_batch1, i.e. cells origin_time upon therapy_ID_batch (we removed _batch column suffix for the processed files).
NA indicates an undetected intensity.
> raw_PBMC_light_labelled_intensities.tsv: raw intensity of light/endogenous peptides (row) by precursor per sample (column) from PBMC
> raw_swab_light_labelled_intensities.tsv: idem from buccal cells
> raw_PBMC_heavy_labelled_intensities.tsv: raw intensity of light/endogenous peptides (row) by precursor per sample (column) from PBMC
> raw_swab_heavy_labelled_intensities.tsv: idem from buccal cells
> raw_PBMC_heavynormalized_intensities.tsv: raw intensity of light peptides normalized by heavy peptides intensity (row) by precursor per sample (column)
> raw_swab_heavynormalized_labelled_intensities.tsv: idem from buccal cells
> processed_cleaned_PBMC_log2intensities.tsv: processed (heavy normalized, imputed, batch-corrected) intensity of peptides
aggregated by modification (PTM, row) by precursor per sample (column) after log2-transformation.
The relative abundances are computed from this file.
Rows without me/ac suffix represents the amount of unmodified peptide for the considered site.
> processed_cleaned_swab_log2intensities.tsv: idem from buccal cells
> rel_abundance_PTM_PBMC.tsv: relative abundance computed per precursor, e.g. for a given sample, the H3_K4+H3_K4me1+H3_K4me2+H3_K4me3 relative abundance values must sum to 100, with the relative abundance of H3_K4 representing the absence of modified K4.
> rel_abundance_PTM_swab.tsv: idem from buccal cells
> tests_from_rel_abundance_PTM_swab_PBMC.tsv: per type of samples ("Sample.origin", i.e.swab of PBMC) and per PTM (rows, "PTM"), report the output of classic (p-values, adjusted with Benjamini-Hochberg (BH), or Benjamini-Yekutieli procedure (BY), from raw and arcsin square root transformed percentage) and PLS-DA tests (VIP - Variable Importance score - and its 95% confidence interval). The percentage of changeof each PTM after therapy relative tobefore therapy is reported in "perc_change.AT.over.BT" column.
The "is_candidate" indicates if the PTM has been considered as a hit in the swab or PBMC.

# Plasma
Samples´ names are encoded as PLASMA_AT_8_batch1, i.e. cells origin_time upon therapy_ID_batch.
NA indicates an undetected intensity.
> raw_plasma_maxquant_log2ibaq_intensities.tsv: raw data from protein group MaxQuant file. The iBAQ columns are used in later steps.
> processed_cleaned_plasma_log2intensities.tsv: processed (imputed, batch-corrected) intensity of protein groups after log2-transformation.
> tests_from_intens_plasma.tsv: per protein group ("Proteins.ID"), report the output of classic (p-values, adjusted Benjamini-Hochberg (BH),or Benjamini-Yekutieli procedure (BY), from log2-transformed intensities) and PLS-DA tests (VIP and its 95% confidence interval). The log2 fold change after therapy relative to before therapy is reported in "log2FC.AT.over.BT" column.
The "is_candidate" indicates if the protein group has been considered as a hit.

# Integration
> circos_input: output of DIABLO analysis with correlation threshold set to 0.7. Use the readRDS R function to open.