R-loop Binding Proteins

Source: R/rlbps.R

A list of annotations for genomic features relevant to R-loops. Both mm10 and hg38 annotations are available.

rlbps(quiet = FALSE)

Arguments

quiet

If TRUE, messages are suppressed. Default: FALSE.

Value

A tbl object. See details.

Details

Source

R-Loop binding proteins (RLBPs) are proteins which were discovered by mass-spectrometry after S9.6 immuno-precipitation (S9.6 is an antibody that binds R-loops). The data were aggregated from three studies which analyzed RLBPs in this manner:

  1. Nadel et al., 2015 - article

  2. Wang et al., 2018 - article

  3. Cristini et al., 2018 - article

The data were downloaded from the supplementary materials of each study and processed using custom R scripts as part of the RLBase-data pipeline. This processing involved normalization of mass-spec abundance calculations and the derivation of a "combined score" for ranking all the proteins.

Structure

geneNameNADEL.2015WANG.2018CRISTINI.2018combinedScore
DDX210.900.9681.87
DHX90.850.06350.8311.74
...............

Columns:

  • geneName

    • The official HGNC symbol of the RLBP

  • NADEL.2015

    • Normalized abundance of protein from Nadel et al., 2015

  • WANG.2018

    • Normalized abundance of protein from Wang et al., 2018

  • CRISTINI.2018

    • Normalized abundance of protein from Cristini et al., 2018

  • combinedScore

    • Sum of normalized abundance across studies.

Examples

rlbpsData <- rlbps()