pSTIING

Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract pSTIING (Protein, Signaling, Transcriptional Interactions & Inflammation Networks Gateway) is a publicly accessible web-based application and Knowledge Base -- featuring over 65,000 distinct molecular associations (comprising protein-protein, protein-lipid, protein-small molecule interactions and transcriptional regulatory associations), ligand-receptor-cell type information and signal transduction modules.

It has a particular major focus on regulatory networks relevant to chronic inflammation, cell migration and cancer.

pSTIING integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources including:

genomic/proteomic data (e.g. UniGene, RefSeq, HUGO, UniProt/Swiss- Prot/TrEMBL, PDB, InterPro, Pfam), biomolecular interaction data (e.g. BIND, MINT, MIPS, HPRD, Reactome, InAct), transcriptional regulatory elements (e.g. JASPAR, EPD, TRED), signaling modules (e.g. KEGG, STKE, Biocarta, AfCS), human diseases (e.g. OMIM, Pathology Outlines) across human, rat, mouse, fly, worm and yeast.

The web application and interface provide graphical representations of networks allowing users to combine and extend transcriptional regulatory and signaling modules, infer molecular interactions across species and explore networks via protein domains/motifs, gene ontology (GO) annotations and human diseases.

pSTIING also supports the direct cross-correlation of experimental results with interaction information in the Knowledge Base via the CLADIST tool (see below…) associated with pSTIING, which currently analyses and clusters gene expression, proteomic and phenotypic datasets.

This allows the contextual projection of co-expression patterns onto prior network information, facilitating the identification of functional modules in physiologically relevant systems.

Visualizing Interactions, Transcriptional Associations and Extending Pathways -- pSTIING dynamically generates graphical representations of interaction networks and displays maps in both compressed and scalable vector graphics (SVG) formats.

With a suitable SVG viewer plug-in for browsers such as Corel SVG or Adobe SVG viewers, users will be able to zoom in and out, or move (pan) a network map around within the viewing screen.

Nodes represent interacting components (e.g. proteins, macromolecular assemblies, lipids or small molecules) and edges represent interaction or transcriptional regulatory relationships between components.

Linking Transcriptional Associations to Signaling Modules -- In pSTIING, multiple signaling and transcriptional regulatory modules can be displayed in combination, facilitating the identification of important cross-talk points (or hubs) between modules.

Projecting and Mapping Interactions across Species -- pSTIING provides three (3) approaches whereby users can choose to query interaction information across species.

The first uses orthology groupings from Clusters of Orthologous Groups (COG/KOG).

The second approach involves UniRef 50/90 clusters of proteins with at least 50 or 90% identity, respectively.

The third employs a reciprocal best hit approach to map protein interaction information (where available) in model organisms (rat, mouse, fly, worm and yeast) onto human orthologues.

Interaction Networks via Ontology, Motifs, and InterPro Domains -- The inclusion of GO annotation terms and category identifiers into pSTIING facilitates the construction of interaction networks associated with a chosen GO annotation.

It is also possible to explore interaction networks of proteins with similar InterPro domains or motifs. pSTIING supports searches by InterPro accession, InterPro name or regular expression specifying conserved motifs.

Human Disease and Interaction Networks -- A list of diseases was selected from the OMIM morbid map initiative, and the information about proteins whose de-regulation or mutation have association or causal implication in disease was integrated with interaction information in pSTIING.

Linking Gene Expression and Proteomic Experiments to Interaction and Regulatory Networks -- Filtered and normalized datasets from gene expression [including microarrays and massively parallel signature sequencing (MPSS)] and proteomic experiments can be imported into pSTIING via CLADIST, a clustering software tool associated with pSTIING.

pSTIING-CLADIST features various clustering algorithms including hierarchical clustering, k-means and self-organizing maps (SOM) from which users could select the clusters of co-regulated genes or proteins and directly cross-correlate these with molecular interaction and transcriptional information in pSTIING.

This major feature allows the contextual projection of co-expression patterns onto prior network information, facilitating the assembly of protein interaction and transcriptional regulatory networks into functional modules.

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site pSTIING

Price Contact manufacturer.

G6G Abstract Number 20249

G6G Manufacturer Number 101713