collectri — CollecTRI human transcriptional regulation (2023)

Description

The human gene regulatory network of CollecTRI ("Collection of Transcriptional Regulatory Interactions"), compiled by Müller-Dott et al. from twelve resources of transcription factor (TF) to target gene interactions: the text-mining resource ExTRI, the curated databases HTRI, TRRUST, TFactS, GOA, IntAct, SIGNOR, CytReg and GEREDB, the curations of NTNU and of Pavlidis et al. (2021), and the highest-confidence interactions of DoRothEA. 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 $j$.

There are two networks:

regulons: the authors' signed regulons (43,175 interactions), in which each interaction is an activation or a repression. The sign was taken from the resources when available, otherwise from the TF's known role as activator or repressor, and otherwise set to activation by default. Two sources (AP1 and NFKB) are protein complexes rather than single TFs.
source: all TF-target pairs of the integrated resources (48,681 pairs), from the authors' source table, before the filtering and the assignment of signs.

Self-loops are autoregulation. The regulons for mouse and rat distributed with the tools of the authors are translated from the human ones by orthology, and are not included here.

The networks have the following properties:

(Node) name: the gene symbol of the gene (e.g. MYC).
(Edge) sign (edges, regulons only): the mode of regulation, +1 for activation and -1 for repression.
(Edge) sign_decision (edges, regulons only): how the sign was decided (PMID: from the literature evidence in the resources; regulon: from the role of the TF; default activation).
(Edge) resources (edges): the resources in which the interaction is found, separated by ;.
(Edge) references (edges, regulons only): the PubMed identifiers of the publications supporting the interaction, separated by ;.
(Edge) extri_confidence (edges, source only): the confidence of the text-mined interaction in ExTRI (High or Low); empty if not in ExTRI.

Tags

Biological Gene regulation Signed Unweighted Metadata

Added

2026-10-27

Citation

S. Müller-Dott, E. Tsirvouli, M. Vazquez, R. O. Ramirez Flores, P. Badia-i-Mompel, R. Fallegger, D. Türei, A. Lægreid, J. Saez-Rodriguez, "Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities." Nucleic Acids Research 51, 10934-10949 (2023) 10.1093/nar/gkad841 Sci-Hub

Upstream URL OK

https://github.com/saezlab/CollecTRI
https://doi.org/10.5281/zenodo.8192729

Upstream license

CC BY 4.0, https://creativecommons.org/licenses/by/4.0/

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
regulons	6,957	43,175	6.21	44.56	87.99	4.44	-0.22	0.05	7	1.00	Directed	Unipartite	name	sign sign_decision resources references	518 KiB	691 KiB	674 KiB	659 KiB
source	7,792	48,681	6.25	46.39	93.13	6.47	-0.21	0.05	8	1.00	Directed	Unipartite	name	resources extri_confidence	270 KiB	454 KiB	449 KiB	357 KiB

Ridiculograms^*

^* These are automatically generated force-directed visualizations, and can be quite meaningless for networks both big and small. They should not be taken seriously as sources of scientific insight. See here for a discussion.