hqStrNw: STRIND database network of Homo sapiens genes (Example data)

In PCAN: Phenotype Consensus ANalysis (PCAN)

Description

A network of human entrez gene IDs taken from the STRING database.

Format

A data frame of 643683 and 3 columns:

gene1

Entrez gene IDs.

gene2

Entrez gene IDs.

upstream

TRUE if the directionality of the interaction between the 2 genes is known. In this case gene1 is upstream gene 2.

Source

Different ressources were used in June 2 2015:

• http://string-db.org/newstring_download/protein.actions.v10/9606.protein.actions.v10.txt.gz was used to get the network of Ensembl protein IDs. Only interaction with a score greater or equal to 500 were kept.

• BioMart from http://jan2013.archive.ensembl.org/index.html was used to map Ensembl protein IDs to Ensembl gene IDs. Ensembl gene IDs were mapped to Entrez gene IDs using this ressource in addition to ftp://ftp.ncbi.nih.gov/gene/DATA/gene2ensembl.gz

Examples

## Not run: example(hpGeneListComp)

Example output

Loading required package: BiocParallel

PCAN documentation built on Nov. 8, 2020, 6:47 p.m.