hqStrNw


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


Phenotypes comparison based on a pathway consensus
approach. Assess the relationship between candidate genes and a
set of phenotypes based on additional genes related to the
candidate (e.g. Pathways or network neighbors).

Matthew Page

PCAN

Phenotype Consensus ANalysis (PCAN)

hqStrNw function

A data frame of 643683 and 3 columns:
<dl>
<dt>gene1</dt><dd>Entrez gene IDs.</dd> <dt>gene2</dt><dd>Entrez gene IDs.</dd> <dt>upstream</dt><dd>TRUE if the directionality of the interaction
between the 2 genes is known. In this case gene1 is upstream gene 2.</dd> </dl>

Format

Different ressources were used in June 2 2015: <ul>
<li>
<a href="http://string-db.org/newstring_download/protein.actions.v10/9606.protein.actions.v10.txt.gz">http://string-db.org/newstring_download/protein.actions.v10/9606.protein.actions.v10.txt.gz</a>
was used to get the network of Ensembl protein IDs.
Only interaction with a score greater or equal to 500 were kept.
</li>
<li>BioMart from <a href="http://jan2013.archive.ensembl.org/index.html">http://jan2013.archive.ensembl.org/index.html</a>
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
<a href="/link/ftp%3A%2F%2Fftp.ncbi.nih.gov%2Fgene%2FDATA%2Fgene2ensembl.gz?package=PCAN&version=1.0.2" data-mini-rdoc="PCAN::ftp://ftp.ncbi.nih.gov/gene/DATA/gene2ensembl.gz">ftp://ftp.ncbi.nih.gov/gene/DATA/gene2ensembl.gz</a>
</li>
</ul> 

Source

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

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

Description

Arguments

Format

Source

Examples