lincs.kd: LINCS L1000 Knockdown Example Dataset

In BayesKnockdown: BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Description

Example knockdown dataset from the National Institute of Health (NIH) Library of Integrated Network-based Cellular Signatures (LINCS) program (http://lincsproject.org).

Usage

data("lincs.kd")

Format

The data is a 21x27 matrix. Each row is the expression level of a different gene across 27 knockdown experiments.

Details

This data is from the National Institute of Health (NIH) Library of Integrated Network-based Cellular Signatures (LINCS) program (htpp://lincsproject.org). The aim of this program is to generate genetic and molecular signatures of cells in response to various perturbations. To support this endeavor, many large datasets have been made available, including proteomic and imaging data.

The data is from knockdown experiments targeting gene PPARG in cell line A375. The first row is the expression levels of PPARG in 27 different experiments, while the other rows are a subset of the measured genes in the same experiments. The data has been normalized to account for differences in the experimental settings, as described in Young, et al. (2016).

Value

matrix

Source

http://lincscloud.org

References

Duan, Q., et al. (2014), LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Research, gku476

Examples

data(lincs.kd)

Example output

BayesKnockdown documentation built on Nov. 8, 2020, 5:48 p.m.