data_nfkb: Data from experiment with NFkB pathway

In SLEMI: Statistical Learning Based Estimation of Mutual Information

Data from experiment with NFkB pathway

Description

In the paper describing methodological aspects of our algorithm we present the analysis of information transmission in NfkB pathway upon the stimulation of TNF-\alpha. Experimental data from this experiment in the form of single-cell time series are attached to the package as a data.frame object and can be accessed using 'data_nfkb' variable. Each row of ‘data_nfkb' represents a single observation of a cell. Column ’signal' indicates the level of TNF-\alpha stimulation for a given cell, while columns 'response_T', gives the normalised ratio of nuclear and cytoplasmic transcription factor as described in Supplementary Methods of the corresponding publication. In the CRAN version of the package we included only a subset of the data (5 time measurements). For the full datasets, please access GitHub pages.

Usage

data_nfkb

Format

A data frame with 15632 rows and 6 variables:

signal

Level of TNFa stimulation

response_0

The concentration of normalised NfkB transcription factor, measured at time 0

response_3

The concentration of normalised NfkB transcription factor, measured at time 3

response_21

The concentration of normalised NfkB transcription factor, measured at time 21

response_90

The concentration of normalised NfkB transcription factor, measured at time 90

response_120

The concentration of normalised NfkB transcription factor, measured at time 120

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Details

For each concentration, there are at least 1000 single-cell observation (with the exception of 0.5ng stimulation, where the number of identified cells is almost 900)

Source

in-house experimental data

SLEMI documentation built on Nov. 20, 2023, 1:06 a.m.