arabidopsis_interactome — Arabidopsis interactome AI-1 (2011)
- Description
A network of protein-protein interactions of the plant Arabidopsis thaliana, from the Arabidopsis Interactome Mapping Consortium (Dreze et al., 2011), as distributed by the Center for Cancer Systems Biology (CCSB, Dana-Farber Cancer Institute). It combines Arabidopsis Interactome version 1 (AI-1), a binary interaction map obtained with a high-throughput yeast two-hybrid (Y2H) screen of the pairwise combinations of a set of about 8,000 cloned protein-coding genes ("space 1"), with interactions curated from the literature (LCI). Nodes are proteins, identified by their Arabidopsis Genome Initiative (AGI) gene locus, and an undirected edge connects two proteins that interact according to at least one of the sources, which are indicated by edge properties. The network has 11,374 interactions among 4,866 proteins; the 5,664 interactions of the main Y2H screen involve 2,661 proteins. Self-loops are proteins interacting with themselves.
The network has the following properties:
name: the AGI locus of the protein (e.g. "AT1G05410").main_screen(edges): whether the interaction was found in the main AI-1 Y2H screen (AI1_M).repeat_screen(edges): whether the interaction was found in the repeat of the Y2H screen (AI1_R).lci(edges): whether the interaction is reported in the literature, from the curated interaction databases.lci_binary(edges): whether the literature-curated interaction is binary (direct).lci_core(edges): whether the binary literature-curated interaction is supported by at least two publications or two experimental methods.
- Tags
- Biological Protein interactions Unweighted Metadata
- Citation
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- Arabidopsis Interactome Mapping Consortium, "Evidence for network evolution in an Arabidopsis interactome map." Science 333(6042), 601-607 (2011) 10.1126/science.1203877 Sci-Hub
- Upstream URL OK
- https://web.archive.org/web/20150115212311/http://interactome.dfci.harvard.edu/A_thaliana/index.php?page=download
- Networks
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Tip: hover over a column header 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_interactome 4,866 11,374 4.67 9.96 22.76 119.56 -0.18 0.04 14 0.93 Undirected Unipartite name main_screen repeat_screen lci lci_binary lci_core 40 KiB 79 KiB 76 KiB 68 KiB