celegans_interactomes — C. elegans interactomes (2009)

Description

Networks of protein–protein interactions and other functional relationships between genes of the nematode Caenorhabditis elegans, from the study of N. Simonis and collaborators at the Center for Cancer Systems Biology (Dana-Farber Cancer Institute), which produced an empirically controlled, high-quality map of the C. elegans interactome. Nodes are genes (proteins), identified by their C. elegans sequence names (e.g. AC7.2), and an undirected edge connects two genes that are related in the corresponding source (a physical interaction between their proteins, a genetic interaction, correlated expression or similar phenotypes, see below). There are ten networks:

• wi2004: protein interactions from the first high-throughput yeast two-hybrid (Y2H) map of Li et al. (2004);
• wi2007: protein interactions from the new Y2H screens of Simonis et al. (Worm Interactome version 2007);
• BPmaps: Y2H interactions from earlier smaller-scale "biological process maps" focused on specific processes;
• WI8: the union of wi2004, wi2007 and BPmaps;
• LCI: literature-curated interactions supported by small-scale experiments;
• Interolog: interactions predicted from interactions between orthologous proteins in other species;
• Genetic: genetic interactions;
• Microarray: pairs of genes with highly correlated expression profiles in microarray experiments;
• Phenotypes: pairs of genes with similar phenotypic profiles (e.g. in RNAi experiments);
• IntegratedNetwork: the union of all of the above sources.

The networks have the following properties:

• Nodes: name, the gene's sequence name.
• Edges (Microarray): pcc, the Pearson correlation coefficient of the expression profiles of the two genes.
• Edges (Phenotypes): phenotypes, the phenotypic similarity score of the two genes.
• Edges (WI8): wi2004, wi2007 and bpmaps, the status of the interaction in each of the three source data sets (e.g. core or noncore; empty if the interaction is not in the data set).
• Edges (IntegratedNetwork): wi8, lci, interologs and genetic, whether the edge is present in the corresponding source network; phenotypes and coexpression, the phenotypic similarity score and the expression correlation of the two genes (NaN if not available).

The networks come from the C. elegans download page of the CCSB Interactome Database, whose other data sets are in the entries yeast_interactome_ccsb and collins_yeast (yeast) and interactome_vidal and human_interactome_2014 (human).

Tags

Biological Protein interactions Unweighted

Citation

• N. Simonis et al., "Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network." Nature Methods 6(1), 47-54 (2009) 10.1038/nmeth.1279 Sci-Hub

Upstream URL OK

https://web.archive.org/web/20240123025943/http://interactome.dfci.harvard.edu/C_elegans/index.php?page=download

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

Show all columns

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
wi2007	1,496	1,816	2.43	4.48	7.86	93.32	-0.17	0.02	16	0.74	Undirected	Unipartite	name		33 KiB	44 KiB	44 KiB	36 KiB
wi2004	1,237	1,735	2.81	5.27	8.82	55.47	-0.18	0.02	14	0.88	Undirected	Unipartite	name		27 KiB	36 KiB	36 KiB	29 KiB
BPmaps	537	554	2.06	2.58	3.29	96.79	-0.25	0.02	18	0.64	Undirected	Unipartite	name		12 KiB	16 KiB	16 KiB	13 KiB
LCI	431	438	2.03	4.74	5.62	187.61	-0.16	0.04	11	0.27	Undirected	Unipartite	name		10 KiB	13 KiB	13 KiB	10 KiB
Microarray	2,436	136,930	112.42	167.11	358.18	2133.71	-0.07	0.52	21	0.96	Undirected	Unipartite	name		131 KiB	474 KiB	473 KiB	365 KiB
Phenotypes	912	22,738	49.86	47.35	93.61	4.27	-0.03	0.35	5	0.97	Undirected	Unipartite	name		38 KiB	85 KiB	85 KiB	69 KiB
Interolog	2,724	14,322	10.52	20.23	71.43	139.68	-0.01	0.44	15	0.87	Undirected	Unipartite	name		65 KiB	106 KiB	105 KiB	89 KiB
Genetic	759	1,593	4.20	5.15	10.46	53.09	-0.03	0.19	13	0.90	Undirected	Unipartite	name		18 KiB	24 KiB	23 KiB	19 KiB
WI8	2,528	3,864	3.06	5.78	11.43	40.08	-0.14	0.02	14	0.88	Undirected	Unipartite	name		56 KiB	77 KiB	77 KiB	61 KiB
IntegratedNetwork	6,176	178,151	57.69	123.63	361.03	114.24	0.16	0.47	12	0.97	Undirected	Unipartite	name		257 KiB	744 KiB	705 KiB	554 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.