readMarkers: Load a file with known markers linked to apoptosis or...

In tnaake/apoptosisQuantification: Assessment of apoptosis and necroptosus unsing proteomics

Description

The function readMarkers loads a data set with markers linked to apoptosis or necroptosis.

The returned tibble contains three columns:

• feature: name of the marker,

• change: maximum/minimum fold change from the time-course experiment (maximum absolute value is taken),

• significant_n: number of significant time-points.

Classical necrotic markers include lactate deydrogenase (LDH), high-mobility group B1 (HMGB1), myoglobin, enolase, and 14-3-3 proteins. Commonly, a protein release is observed during apoptosis and necroptosis for human myeloid/lymphoma cell lines and human primary macrophage cells as observed time course experiments (cf. Tanzer et al., 2020).

Usage

readMarkers(type = c("apoptosis", "necroptosis"), fc = 2, n = 1)

Arguments

type	character, "apoptosis" or "necroptosis"
fc	numeric(1), threshold for fold change (default 2), e.g. if set to 2, the features are retained that have absolute fold changes greater or equal to fc
n	numeric, threshold for number of significant time points (default 1), e.g. if set to 1, the features are retained that have at least 1 significant time point

Details

The function loads the Supplementary Table S1 from Tanzer et al. (2020).

In the data set of Tanzer et al. (2020), the following abbreviations are used:

• TNF: tumor necrosis factor (TNF-mediated apoptosis),

• SM: birinapant (inhibition of cIAPs using small molecules called Smac mimetics),

• IDN: caspase inhibitor IDUN-6556 (IDN-6556, used in induction of necroptosis),

• TNF application: leads to production of cytokines (no induction of apoptosis or necroptosis),

• TNF+SM application: inducton of apptosis,

• TNF+SM+IDN-6556 application: induction of necroptosis.

The time points 1 h, 3 h, 5 h, and 7 h are taken into account for defining the markers. For apoptosis, the time points 9 h, 12.5 h and 15 h are removed prior to filtering the data set.

Value

tibble

References

Tanzer et al. (2020): Quantitative and Dynamic Catalogs of Proteins Released during Apoptotic and Necroptotic Cell Death. Cell Reports, 30, 1260-1270.e5. 10.1016/j.celrep.2019.12.079.

Examples

## "apoptosis"
readMarkers(type = "apoptosis", fc = 2, n = 1)

## "nectroptosis"
readMarkers(type = "necroptosis", fc = 2, n = 2)

tnaake/apoptosisQuantification documentation built on Feb. 20, 2022, 5:37 p.m.