ARNIE is an online database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network

This online tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters using the drop-down menus. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.

• Construction of a large extracellular protein interaction network and its resolution by spatiotemporal expression profiling.

  Martin S, Söllner C, Charoensawan V, Adryan B, Thisse B, Thisse C, Teichmann S and Wright GJ

  Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB101HH, United Kingdom.

  Extracellular interactions involving both secreted and membrane-tethered receptor proteins are essential to initiate signaling pathways that orchestrate cellular behaviors within biological systems. Because of the biochemical properties of these proteins and their interactions, identifying novel extracellular interactions remains experimentally challenging. To address this, we have recently developed an assay, AVEXIS (avidity-based extracellular interaction screen) to detect low affinity extracellular interactions on a large scale and have begun to construct interaction networks between zebrafish receptors belonging to the immunoglobulin and leucine-rich repeat protein families to identify novel signaling pathways important for early development. Here, we expanded our zebrafish protein library to include other domain families and many more secreted proteins and performed our largest screen to date totaling 16,544 potential unique interactions. We report 111 interactions of which 96 are novel and include the first documented extracellular ligands for 15 proteins. By including 77 interactions from previous screens, we assembled an expanded network of 188 extracellular interactions between 92 proteins and used it to show that secreted proteins have twice as many interaction partners as membrane-tethered receptors and that the connectivity of the extracellular network behaves as a power law. To try to understand the functional role of these interactions, we determined new expression patterns for 164 genes within our clone library by using whole embryo in situ hybridization at five key stages of zebrafish embryonic development. These expression data were integrated with the binding network to reveal where each interaction was likely to function within the embryo and were used to resolve the static interaction network into dynamic tissue- and stage-specific subnetworks within the developing zebrafish embryo. All these data were organized into a freely accessible on-line database called ARNIE (AVEXIS Receptor Network with Integrated Expression; www.sanger.ac.uk/arnie) and provide a valuable resource of new extracellular signaling interactions for developmental biology.

  Funded by: Medical Research Council; Wellcome Trust: 077108/Z/05/Z

  Molecular & cellular proteomics : MCP 2010;9;12;2654-65

  PUBMED: 20802085; PMC: 3101854; DOI: 10.1074/mcp.M110.004119

[Genome Research Limited]

Network

Zebrafish orthologous table

Orthologous genes are provided for six animal species.

Orthologous genes were identified using Ensembl compara and OrthoMCL (see Methods). Orthologs in each species are grouped into clusters of paralogs and ordered alphabetically. Labelled in blue are the genes which have expression images publicly, which can be obtained through FlyBase (fly), BDGP (fly), MGD (mouse), MEPD (Medaka), Aniseed (ciona) and WormBase (worm).

Zebrafish Paralogues tables

Additional paralogous genes and domain architecture for all 92 extracellular proteins are provided.

ZFIN protein names are organised into 62 paralogous clusters. The best full length peptide matches to reference protein library (Ensembl, Refseq, etc) are provided. Pfam and Superfamily domain architecture, and intracellular motifs for each full length protein sequence is also available for reference. All columns are ordered corresponding to the ZFIN protein names in the first column, except for paralogous genes, which are ordered alphabetically.

Zebrafish gene by gene orthologues

Orthologs for each of 92 extracellular proteins, obtained using Ensembl compara and OrthoMCL.

Orthologous gene ids, gene names and total number of orthologs found are provided in gene-by-gene format.