GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins

BACKGROUND: A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aiming at exploring and analysing such graphs. This paper describes GenoLink, a software platform for the graphical querying and exploration of graphs. RESULTS: GenoLink provides a generic framework for representing and querying data graphs. This framework provides a graph data structure, a graph query engine, allowing to retrieve sub-graphs from the entire data graph, and several graphical interfaces to express such queries and to further explore their results. A query consists in a graph pattern with constraints attached to the vertices and edges. A query result is the set of all sub-graphs of the entire data graph that are isomorphic to the pattern and satisfy the constraints. The graph data structure does not rely upon any particular data model but can dynamically accommodate for any user-supplied data model. However, for genomic and post-genomic applications, we provide a default data model and several parsers for the most popular data sources. GenoLink does not require any programming skill since all operations on graphs and the analysis of the results can be carried out graphically through several dedicated graphical interfaces. CONCLUSION: GenoLink is a generic and interactive tool allowing biologists to graphically explore various sources of information. GenoLink is distributed either as a standalone application or as a component of the Genostar/Iogma platform. Both distributions are free for academic research and teaching purposes and can be requested at [email protected]. A commercial licence form can be obtained for profit company at [email protected]. See also

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins-3

<p><b>Copyright information:</b></p><p>Taken from "GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins"</p><p>BMC Bioinformatics 2006;7():21-21.</p><p>Published online 17 Jan 2006</p><p>PMCID:PMC1382257.</p><p>Copyright © 2006 Durand et al; licensee BioMed Central Ltd.</p>ided with GenoLink. Classes are indicated by boxes (white arrows indicate inheritance) and association names are indicated in italics. For clarity, class and association attributes have not been indicated (an example is shown to the right part of the figure, with the Polypeptide class). The complete diagram is distributed with the GenoLink software documentation. (b) An example of data graph based on this data model. It represents a portion of the genome of the bacterium strain 26695 (NCBI RefSeq entry no. NC000915); IRO, ILO, ICF, IIG, HPA, CD and HPIW stand for edges that are instances of associations: IsRepliconOf, IsLocatedOn, IsCodingFor, IsInGeneOrtholog, HasPolypeptideAnnotation, ContainsDomain and HasPhysicalInteractionWith. The entire data graph for this genome actually contains 3197 vertices (1 Organism, 1 Replicon, 1576 ProteinGenes, 43 RNAGenes, 1576 Polypeptides) and 4664 edges (1 IsRepliconOf, 1619 IsLocatedOn, 1576 IsCodingFor and 1468 HasPhysicalInteractionWith). The dashed box displays the attributes for the Polypeptide ureB. COG, EC and IPR data are from the COG database [21], the Enzyme Commission database [24], and the InterPro database [23], respectively. Protein-protein interactions are public data available from Hybrigenics [30] and distributed with GenoLink

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins-5

<p><b>Copyright information:</b></p><p>Taken from "GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins"</p><p>BMC Bioinformatics 2006;7():21-21.</p><p>Published online 17 Jan 2006</p><p>PMCID:PMC1382257.</p><p>Copyright © 2006 Durand et al; licensee BioMed Central Ltd.</p>orresponds to a result sub-graph. Each column's header contains two lines: the first one indicates the label of a vertex from the query graph (see Figure 5); the second line indicates the name of an attribute of this vertex (the user can select which attributes to display: in this example only the "Name" attributes have been selected)

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins-2

<p><b>Copyright information:</b></p><p>Taken from "GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins"</p><p>BMC Bioinformatics 2006;7():21-21.</p><p>Published online 17 Jan 2006</p><p>PMCID:PMC1382257.</p><p>Copyright © 2006 Durand et al; licensee BioMed Central Ltd.</p> protein-protein interactions where at least one of the two proteins has an annotated known function (Name !: "hypothetical"). (b) The GQL script describing the same query. GQL reserved keywords are indicated in bold. In the declaration of variable , the expression located to the right of the 'where' clause is a local constraint (here: the name must not contain ). In the declaration of , the expression located to the right of the 'where' clause is the global constraint (here: the two names must be different). (c) Result obtained by executing this query against the data graph shown in Figure 4b. When applied to the entire strain 26695 data set, this query yields 896 different answers

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins-6

<p><b>Copyright information:</b></p><p>Taken from "GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins"</p><p>BMC Bioinformatics 2006;7():21-21.</p><p>Published online 17 Jan 2006</p><p>PMCID:PMC1382257.</p><p>Copyright © 2006 Durand et al; licensee BioMed Central Ltd.</p> it. This snapshot shows an example of result sub-graph corresponding to the Query Q7 (Table 1 [see ] and Figure 5). The edge linking the two Polypeptides corresponds to a physical interaction (HPIW). The red crosshair on the top-right of some vertices denotes that they are linked to some others that are not currently shown. These vertices may therefore be further expanded to gain more information about the full data graph. In this example, this operation has been performed on vertices holA and holB (from ) in order to display the corresponding Polypeptides (DNA polymerase III) that were not part of the query (see Figure 5)

Functional Proteomics Mapping of a Human Signaling Pathway

Access to the human genome facilitates extensive functional proteomics studies. Here, we present an integrated approach combining large-scale protein interaction mapping, exploration of the interaction network, and cellular functional assays performed on newly identified proteins involved in a human signaling pathway. As a proof of principle, we studied the Smad signaling system, which is regulated by members of the transforming growth factor β (TGFβ) superfamily. We used two-hybrid screening to map Smad signaling protein–protein interactions and to establish a network of 755 interactions, involving 591 proteins, 179 of which were poorly or not annotated. The exploration of such complex interaction databases is improved by the use of PIMRider, a dedicated navigation tool accessible through the Web. The biological meaning of this network is illustrated by the presence of 18 known Smad-associated proteins. Functional assays performed in mammalian cells including siRNA knock-down experiments identified eight novel proteins involved in Smad signaling, thus validating this integrated functional proteomics approach

Abnormal CNO abundances in magnetic cataclysmic variables

International audienc

Abnormal CNO abundances in magnetic cataclysmic variables

International audienc