Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract CellCircuits is an open-access web-based database of molecular network models.

It is also an advanced searchable repository of published network model hypotheses.

Molecular interaction models provide us with a framework for integrating the large-scale data that is now able to be collected at multiple levels of biological info - genes, RNAs, proteins, and small molecules.

CellCircuits contains this type of data (molecular network models/molecular interaction models) and CellCircuits:

1) Bridges the gap between databases of individual pair-wise molecular interactions and databases of validated pathways.

2) Contains functional network hypothesis produced by algorithms that screen molecular interaction networks based on their correspondence with expression or phenotypic data, their internal structure, or their conservation across species.

3) Is searchable using protein/gene names and Gene Ontology terms.

Models are available either as images or in machine-readable formats.

4) Serves as a clearinghouse in which theorists may distribute or revise models in need of validation and experimentalists may search for models or specific hypotheses relevant to their interests.

'Search' the network models in CellCircuits --

1) By gene - Using gene names or aliases [registered by the Gene Ontology (GO) database] (e.g. GCN4).

Models in CellCircuits contain genes from yeast (S. cerevisiae), fly (D. Melanogaster), worm (C. elegans), human (H. sapiens), and the malaria parasite (P. falciparum).

An asterisk (*) is a wild card (e.g. GCN*).

Enter more than one gene, each separated by a space. (e.g. YAP1, SOD1).

2) By Gene Ontology (GO) annotation -

Use GO ID numbers (e.g. GO:0003677).

Use partial or complete GO term names (enclosed in double quotes) (e. g. "DNA binding").

'Advanced Search' the network models in CellCircuits --

1) Publications - Limit the search by publication. All publications are selected by default.

2) Sort - Models are sorted by the number of matching query terms, i.e. gene names, GO term accessions, and/or GO term names. Currently this is the only choice available.

3) Select Species - Hold down the 'Ctrl' key to select/exclude species from your search. All species are selected by default.

4) P-value threshold - All search results are filtered using a P-value cutoff. Valid P-values must be between 0 and 1 and may be entered in decimal or scientific notation (e.g. 0.001 or 1e-3).

NOTE: To find all models containing a specific gene, use a P-value cutoff of 1. Smaller P-values limit the search, yielding fewer search results.

'Advanced Search' Results --

1) Warnings -

Errors and warnings concerning the query are displayed in red. When the query matches a gene synonym, a message similar to this will appear:

[query] matches:

[S], a synonym of G in O. G is shown in results.

Where - S is the gene (S)ynonym matched by query; G is the standard (G)ene symbol of S; G is a gene in an (O)rganism; and G will be shown and highlighted in the results, instead of S.

This message helps interpret the results by alerting you to the standard 'gene names' of synonyms that matched the query.

2) Score - Models are scored by the number of matching query terms (gene names, GO term accessions, and/or GO term names).

When viewing similar models, this score is the number of genes shared between the Query model and the model on each row of the results.

3) Model - Clicking on the 'model thumbnail' displayed gives you a larger picture of the model.

Links below the model thumbnail may include:

[PubMed] - Link to the PubMed abstract;

[legend] - Link to the legend/published-figures for interpreting the model;

[website] - Link to the supplementary website;

[sif] - Text representation of the model in Cytoscape (S)imple (I)nteraction (F)ormat - (see G6G Abstract Number 20092).

4) Matches - Query terms matching the model are highlighted.

5) Show/Hide GO Annotations - Click the tabs to expand or collapse all results for the ontology: Biological Process, Cellular Component, or Molecular Function.

6) View Similar Models - Click to see up to top 20 models that share 3 or more genes with this model.

When viewing similar models, a model score indicates the number of genes shared with the "Query" model. Currently, similarity is only based on shared yeast genes.

7) GO Annotation - The GO annotations for each model are organized into tables which can be expanded or collapsed by clicking on the tabs in the header labeled Biological Process, Molecular function, or Cellular Component.

For each model, the GO annotation tables are grouped first by organism, then by GO ontology.

Within each ontology, the annotations are first sorted by the number of matching query terms, then by the enrichment P-value.

Note: A 'Submit My Data' function is available for all researchers who want to submit their data to the CellCircuits database.

System Requirements



Manufacturer Web Site CellCircuits

Price Contact manufacturer.

G6G Abstract Number 20485

G6G Manufacturer Number 104108