common_genes: Genes shared between six expression platforms

In tidyestimate: A Tidy Implementation of 'ESTIMATE'

Genes shared between six expression platforms

Description

As the ESTIMATE model was trained on a specific set of genes, only those within this dataset should be included before running estimate_scores.

These are the genes common to 6 platforms:

- Affymetrix HG-U133Plus2.0

- Affymetrix HT-HG-U133A

- Affymetrix Human X3P

- Agilent 4x44K (G4112F)

- Agilent G4502A

- Illumina HiSeq RNA sequence

The Entrez IDs for the original 10412 genes were matched to HGNC symbols using biomaRt. Duplicates and blank entries were filtered. As some have now been discovered to be pseudogenes or have been deprecated, 22 genes (at time of writing, June 2021) that were in the ESTIMATE package do not exist here.

As one gene can have multiple synonyms/aliases, and there is only one alias per line, the number of rows in the data frame (26339) does not reflect the number of unique genes in the dataset (10391).

Usage

common_genes

Format

A data frame with 26339 rows and 3 variables:

entrezgene_id

Entrez id of the gene

hgnc_symbol

Human Genome Organisation (HUGO) Gene Nomenclature Committee symbol

external_synonym

A synonym/alias a given gene may go by or previously went by

Details

The ESTIMATE model was trained on a set of genes shared between six expression profiling platforms. Those genes are listed in this dataset.

Source

https://r-forge.r-project.org/scm/viewvc.php/pkg/estimate/data/common_genes.RData?root=estimate&view=log

tidyestimate documentation built on Aug. 21, 2023, 9:08 a.m.