genetic_multiplex — Multiplex genetic interactions (2014)

Description

Multiplex networks of genetic and protein interactions in several organisms, assembled by M. De Domenico and collaborators. Nodes are genes (or their protein products), identified by their gene symbols, and each layer corresponds to a different type of interaction.

Most networks were extracted from BioGRID (Biological General Repository for Interaction Datasets, version 3.2.108 of 1 January 2014), a curated database of genetic and protein interactions from high-throughput data sets and focused studies in the literature. These are directed multiplex networks with up to seven layers, named according to BioGRID's interaction types: direct interaction, physical association, association, colocalization, and additive, suppressive and synthetic genetic interactions defined by inequality. An edge connects two genes that have an interaction of the type of its layer; the direction of the edges follows the order of the two genes in the data, and its meaning is not documented. Not every organism has every layer, and the numbering of the layers differs between organisms (see the graph property layer_key). The organisms are: Arabidopsis thaliana (Arabidopsis), Bos taurus (Bos_Multiplex_Genetic), Candida albicans (Candida), Caenorhabditis elegans (Celegans), Danio rerio (DanioRerio), Drosophila melanogaster (Drosophila), Gallus gallus (Gallus), Hepatitis C virus (HepatitusCVirus), Homo sapiens (Homo), human herpesvirus 4 (HumanHerpes4), HIV-1 (HumanHIV1), Mus musculus (Mus), Oryctolagus cuniculus (Oryctolagus), Plasmodium falciparum (Plasmodium), Rattus norvegicus (Rattus), Saccharomyces cerevisiae (Sacchcere), Schizosaccharomyces pombe (Sacchpomb) and Xenopus laevis (Xenopus).

The network YeastLandscape is different: it is based on the genetic interaction map of Saccharomyces cerevisiae of Costanzo et al. (Science 327, 425-431, 2010), obtained with synthetic genetic array experiments. It has four layers: positive and negative genetic interactions, and positive and negative correlations between the genetic interaction profiles of genes. Unlike the other networks, it is undirected. It contains all pairs present in the original data set (pairs listed twice, in both orientations with the same value, are included only once), without any threshold applied, so the edges should be filtered by their weight value before use.

The networks have the following properties:

(Node) name and nodeLabel: the gene symbol.
(Edge) layer (edges): the interaction type (layer); the graph property layer_key maps the layer numbers to their names.
(Edge) weight (edges): always 1, except in YeastLandscape, where it is the genetic interaction score (interaction layers) or the Pearson correlation coefficient between interaction profiles (correlation layers).

Tags

Biological Gene regulation Protein interactions Unweighted Multilayer

Added

2020-08-11

Citation

M. De Domenico, M. A. Porter, & A. Arenas. "MuxViz: a tool for multilayer analysis and visualization of networks". Journal of Complex Networks, cnu038. (2014). 10.1093/comnet/cnu038 Sci-Hub

Upstream URL OK

https://manliodedomenico.com/data.php

Upstream license

Open Data Commons Open Database License (ODbL), https://opendatacommons.org/licenses/odbl/

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
Arabidopsis	6,980	18,655	2.67	18.85	21.49	83.73	-0.08	0.03	14	0.96	Directed	Unipartite	name nodeLabel	weight layer	163 KiB	248 KiB	247 KiB	205 KiB
Bos_Multiplex_Genetic	325	322	0.99	2.28	2.56	73.00	-0.24	0.03	12	0.20	Directed	Unipartite	name nodeLabel	weight layer	8 KiB	11 KiB	11 KiB	8 KiB
Candida	367	398	1.08	11.88	3.28	66.85	-0.45	0.00	7	0.83	Directed	Unipartite	name nodeLabel	weight layer	8 KiB	12 KiB	12 KiB	9 KiB
Celegans	3,879	8,182	2.11	13.26	25.60	31.64	-0.14	0.03	13	0.95	Directed	Unipartite	name nodeLabel	weight layer	90 KiB	134 KiB	133 KiB	109 KiB
Drosophila	8,215	43,367	5.28	17.27	46.06	26.69	0.06	0.15	10	0.99	Directed	Unipartite	name nodeLabel	weight layer	238 KiB	395 KiB	384 KiB	324 KiB
DanioRerio	155	188	1.21	2.50	3.63	28.73	0.09	0.16	6	0.20	Directed	Unipartite	name nodeLabel	weight layer	4 KiB	6 KiB	6 KiB	4 KiB
Gallus	313	389	1.24	9.58	5.23	21.46	-0.44	0.01	8	0.65	Directed	Unipartite	name nodeLabel	weight layer	7 KiB	11 KiB	11 KiB	8 KiB
HepatitusCVirus	105	137	1.30	13.10	1.00	0.05	-0.99	0.00	2	0.98	Directed	Bipartite	name nodeLabel	weight layer	3 KiB	4 KiB	4 KiB	3 KiB
Homo	18,222	170,899	9.38	100.44	122.68	14.20	-0.06	0.03	9	1.00	Directed	Unipartite	name nodeLabel	weight layer	627 KiB	1.1 MiB	1.1 MiB	927 KiB
HumanHerpes4	216	259	1.20	11.05	1.60	228.28	-0.52	0.00	7	0.88	Directed	Unipartite	name nodeLabel	weight layer	5 KiB	8 KiB	7 KiB	6 KiB
HumanHIV1	1,005	1,355	1.35	16.35	8.60	26.39	-0.65	0.00	5	1.00	Directed	Unipartite	name nodeLabel	weight layer	21 KiB	32 KiB	31 KiB	24 KiB
Mus	7,747	19,843	2.56	14.41	31.94	59.36	-0.18	0.03	16	0.96	Directed	Unipartite	name nodeLabel	weight layer	186 KiB	284 KiB	281 KiB	227 KiB
Oryctolagus	144	144	1.00	6.52	1.81	0.03	-0.44	0.01	2	0.55	Directed	Unipartite	name nodeLabel	weight layer	4 KiB	5 KiB	5 KiB	4 KiB
Plasmodium	1,203	2,522	2.10	6.05	11.37	12.72	0.01	0.03	10	0.96	Directed	Unipartite	name nodeLabel	weight layer	27 KiB	40 KiB	39 KiB	33 KiB
Rattus	2,640	4,268	1.62	18.11	13.66	85.57	-0.16	0.01	13	0.89	Directed	Unipartite	name nodeLabel	weight layer	59 KiB	88 KiB	87 KiB	70 KiB
Sacchcere	6,570	282,755	43.04	141.24	207.99	4.94	-0.08	0.15	6	1.00	Directed	Unipartite	name nodeLabel	weight layer	514 KiB	1.2 MiB	1.1 MiB	961 KiB
Sacchpomb	4,092	63,677	15.56	64.69	108.20	17.30	-0.23	0.11	8	1.00	Directed	Unipartite	name nodeLabel	weight layer	165 KiB	337 KiB	311 KiB	267 KiB
Xenopus	461	620	1.34	3.43	4.30	115.21	-0.14	0.12	14	0.57	Directed	Unipartite	name nodeLabel	weight layer	11 KiB	16 KiB	16 KiB	12 KiB
YeastLandscape	4,458	8,473,997	1900.85	818.52	3913.37	1.12	-0.01	0.93	2	1.00	Directed	Unipartite	name nodeLabel	weight layer	14.4 MiB	51.3 MiB	46.7 MiB	33.6 MiB

Ridiculograms^*

Bos_Multiplex_Genetic drawing — Bos_Multiplex_Genetic

HepatitusCVirus drawing — HepatitusCVirus

^* 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.