yeast_interactome_ccsb — Yeast binary interactomes, CCSB (2008)

Description

Networks of protein-protein interactions of the budding yeast Saccharomyces cerevisiae, as distributed by the Center for Cancer Systems Biology (CCSB, Dana-Farber Cancer Institute) together with the high-quality binary interactome map of Yu et al. (2008). In all networks, nodes are proteins (identified by their genes) and an undirected edge connects two proteins that interact. Self-loops are proteins interacting with themselves.

ccsb_yi1: CCSB-YI1, the binary interactions found by Yu et al. with a high-throughput yeast two-hybrid (Y2H) screen of the pairwise combinations of about 6,000 yeast proteins, each verified by retesting (1,809 interactions among 1,278 proteins).
ito_core: the "core" set of the Y2H screen of Ito et al. (2001), i.e. the interactions found three or more times (843 interactions among 813 proteins).
uetz_screen: the interactions of the large-scale library screen of Uetz et al. (2000) (691 interactions among 806 proteins; the source page states 437 proteins).
y2h_union: the union of ccsb_yi1, ito_core and uetz_screen (2,930 interactions among 2,018 proteins).
lc_multiple: literature-curated interactions from Reguly et al. (2006), restricted to those supported by at least two publications (2,925 interactions).
binary_gs: the binary gold standard set of Yu et al., high-confidence binary interactions used as reference to benchmark the screens (1,318 interactions).

Other data sets of the CCSB Interactome Database are in the entries collins_yeast (the yeast co-complex associations of Collins et al., from the same page), interactome_vidal (the first human binary map CCSB-HI1/HI-I-05), human_interactome_2014 (the human maps HI-II-14 and Lit-BM-13) and celegans_interactomes (the C. elegans interactome networks).

The networks have the following property:

name: the systematic ORF name (e.g. "YLR291C") or standard gene name of the protein, as given in the source files.

Tags

Biological Protein interactions Unweighted

Citation

H. Yu, P. Braun, M. A. Yıldırım, I. Lemmens, K. Venkatesan, J. Sahalie, et al., "High-quality binary protein interaction map of the yeast interactome network." Science 322(5898), 104-110 (2008) 10.1126/science.1158684 Sci-Hub
T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, Y. Sakaki, "A comprehensive two-hybrid analysis to explore the yeast protein interactome." Proceedings of the National Academy of Sciences 98(8), 4569-4574 (2001) 10.1073/pnas.061034498 Sci-Hub
P. Uetz, L. Giot, G. Cagney, T. A. Mansfield, R. S. Judson, J. R. Knight, et al., "A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae." Nature 403(6770), 623-627 (2000) 10.1038/35001009 Sci-Hub
T. Reguly, A. Breitkreutz, L. Boucher, B.-J. Breitkreutz, G. C. Hon, C. L. Myers, et al., "Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae." Journal of Biology 5(4), 11 (2006) 10.1186/jbiol36 Sci-Hub

Upstream URL OK

https://web.archive.org/web/20110818144057/http://interactome.dfci.harvard.edu/S_cerevisiae/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

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	gt	GraphML	GML	csv
ccsb_yi1	1,278	1,809	2.83	4.82	9.86	183.30	-0.07	0.02	14	0.75	Undirected	Unipartite	name	9 KiB	15 KiB	14 KiB	13 KiB
ito_core	813	843	2.07	2.99	6.02	117.71	-0.07	0.02	16	0.52	Undirected	Unipartite	name	5 KiB	8 KiB	8 KiB	8 KiB
uetz_screen	806	691	1.71	1.42	2.49	198.36	-0.02	0.02	22	0.33	Undirected	Unipartite	name	5 KiB	8 KiB	7 KiB	8 KiB
y2h_union	2,018	2,930	2.90	4.88	11.19	44.03	-0.04	0.02	14	0.82	Undirected	Unipartite	name	13 KiB	22 KiB	21 KiB	21 KiB
lc_multiple	1,536	2,925	3.81	4.21	14.82	381.35	0.09	0.35	19	0.79	Undirected	Unipartite	name	12 KiB	20 KiB	19 KiB	18 KiB
binary_gs	1,090	1,318	2.42	2.31	6.69	251.55	0.04	0.30	20	0.28	Undirected	Unipartite	name	7 KiB	11 KiB	10 KiB	11 KiB