hs_miR: Human microRNA data set

In Krutik6/TimiRGeN: Time sensitive microRNA-mRNA integration, analysis and network generation tool

Human microRNA data set

Description

Differential expression from Human breast cancer cells (MCF-7). Normoxic conditions contrasted against 16H, 32H and 48H under hypoxia. Data was put though limma for DE. hs_miR consists DE results from 189 microRNAs.

Column names are in the following format: timepoint(hours).DEresult (logFC or adjPVal).

The miR names are not using in TimiRGeN friendly nomenclature. Gene names must be changed before use in TimiRGeN analysis. This must be changed before using TimiRGeN. miR gene name changing is explained in section 3.1 of the vignette.

Usage

data("hs_miR")

Format

A data frame of miRNAs put through differential expression with 189 observations on the following 6 variables.

H16.logFC

a numeric vector containing log2FC values of Hypoxia_16_hours/ Normoxic conditions.

H16.adjPVal

a numeric vector containing adjusted P values values of Hypoxia_16_hours/ Normoxic conditions.

H32.logFC

a numeric vector containing log2FC values of Hypoxia_32_hours/ Normoxic conditions.

H32.adjPVal

a numeric vector containing adjusted P values values of Hypoxia_32_hours/ Normoxic conditions

H48.logFC

a numeric vector containing log2FC values of Hypoxia_48_hours/ Normoxic conditions.

H48.adjPVal

a numeric vector containing adjusted P values values of Hypoxia_48_hours/ Normoxic conditions

Source

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47534

References

C. Camps, H. K. Saini, D. R. Mole, H. Choudhry, M. Reczko, J. A. Guerra-Assunção, Y.-M.Tian, F. M. Buffa, A. L. Harris, A. G. Hatzigeorgiou, et al., “Integrated analysis of microrna and mrna expression and association with hif binding reveals the complexity of microrna expression regulation under hypoxia,” Molecular cancer, vol. 13, no. 1, p. 28, 2014.. <https://molecular-cancer.biomedcentral.com/articles/10.1186/1476-4598-13-28>

Examples

data(hs_miR)
## maybe str(hs_miR) ; plot(hs_miR) ...

Krutik6/TimiRGeN documentation built on Jan. 27, 2024, 7:46 p.m.