PTM-SEA Results

PTM-SEA enrichment of PTMsigDB signatures in the prot-ph differential-analysis z-statistics (see PTMSEA_INPUT), run with the Broad Institute PTM-SEA / ssGSEA2.0 container, for the acute-exercise EE-CON and RE-CON contrasts. Muscle carries three post-exercise timepoints crossed with the two exercise modalities; adipose was sampled at post_3.5_4_hr only. Same layout as CAMERA_RESULTS, with NES in place of t, df and z.std, so it can be passed to plot_enrich_heatmap.

Usage

PTMSEA_RESULTS

Format

A data.frame with 3,910 rows (muscle: 506 signatures x 6 contrasts; adipose: 437 signatures x 2 contrasts) and 17 columns:

tissue

factor; "muscle" or "adipose".

assay

factor; "prot-ph".

contrast_type

factor; "exercise_with_controls".

contrast

factor; the contrast, as in CONTRAST_CONVERTER$contrast.

contrast_short

factor; abbreviated contrast label.

collection

factor; "PTMSIGDB".

database

factor; the PTMsigDB signature category, the prefix of set (e.g. "KINASE-PSP", "PERT-P100-DIA2").

set_id

factor; the PTMsigDB signature ID. Not an ID from SET_TO_ID.

set

factor; the PTMsigDB signature ID.

set_short

factor; signature name followed by database in parentheses.

set_size

integer; number of signature sites measured.

set_size_DB

integer; number of sites in the signature, as reported by PTM-SEA.

size_ratio

numeric; set_size / set_size_DB.

direction

factor; "Up" if NES > 0, else "Down".

NES

numeric; normalized enrichment score.

p_value

numeric; nominal p-value.

adj_p_value

numeric; PTM-SEA FDR, adjusted within tissue and contrast.

Source

Muscle: precovid-analyses figures/muscle/Figure5/ (Natalie Clark). Adipose: Cheehoon Ahn. Provenance in data-raw/PTMSEA/README.md.

See also

CAMERA_RESULTS, plot_enrich_heatmap, PTMSEA_INPUT