trrust — TRRUST transcriptional regulatory networks (2018)

Description

Human and mouse transcriptional regulatory networks from TRRUST ("Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining"), version 2, compiled by Han et al. by text mining of PubMed abstracts for sentences describing transcriptional regulation, followed by manual curation of the candidate interactions. Nodes are genes (identified by their gene symbols), and a directed edge $(i, j)$ indicates that the transcription factor $i$ regulates the expression of gene $j$, with the mode of regulation (activation or repression) when it is known.

There are two networks, human (8,427 regulatory links) and mouse (6,490 links), from the release of 16 April 2018. A pair of genes for which both activation and repression are reported (or a known and an unknown mode) is connected by one edge per mode, as listed in the source (9,396 edges for human, 7,057 for mouse).

The networks have the following properties:

name: the gene symbol of the gene (e.g. AATF).
regulation (edges): the mode of regulation (Activation, Repression or Unknown).
sign (edges): the mode of regulation as a number, +1 for activation, -1 for repression and 0 if unknown.
pmids (edges): the PubMed identifiers of the publications describing the regulation, separated by ;.

Tags

Biological Gene regulation Signed Unweighted Multigraph Metadata

Citation

H. Han et al., "TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions." Nucleic Acids Research 46, D380-D386 (2018) 10.1093/nar/gkx1013 Sci-Hub

Upstream URL OK

https://www.grnpedia.org/trrust/

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
human	2,862	9,396	3.28	21.30	31.97	18.62	-0.17	0.04	9	0.98	Directed	Unipartite	name	regulation sign pmids	73 KiB	102 KiB	100 KiB	93 KiB
mouse	2,456	7,057	2.87	14.42	22.81	17.57	-0.13	0.04	10	0.98	Directed	Unipartite	name	regulation sign pmids	47 KiB	74 KiB	73 KiB	67 KiB