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SPARK

Sensor Proteome Alliance for DNA Repair Kinetics

Prof. Debra Toiber's Laboratory

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Read more about SPARK.

Full Networks

Please use this search section to consult the images of the entire SensorID network. Instead of searching for each SensorID protein-interactor, this option retrieves the high-resolution images of the full networks, where each node corresponds to a protein and each edge to a String database curated physical interaction. Two filtering options are available: The type of network to display refers to the node coloring system used, whether it will be based on the structural modules or the annotated nuclear roles. The time point refers to the experimental post-irradiation stage where the networks belong.

Once the two options are selected, the result will display the network of Sirt6ID, Ku80ID, and Mre11ID. Clicking on each image will enlarge the selected images and allow it to be downloaded.

Mre11

Mre11 nonIR5 Structural Modules

Sirt6

Sirt6 nonIR5 Structural Modules

Ku80

Ku80 nonIR5 Structural Modules

This database contains the dynamic interactomes of the DSB-sensor proteins Sirt6, Mre11 and Ku80 through the X-ray damaged DNA repair process

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Please cite as: Garcia-Venzor A, Portillo M, Grupel U, Lurgi M and Toiber D.

SPARK: mapping the sensor Proteome Alliance for Repair Kinetics for Double-Strand Break sensors during DNA damage response.
Choose proteins by their properties

Queried Protein:

    Binding

    Binding Fold Change against noise level in Mre11ID Streptavidin-directed immunoprecipitation experiments.

    Binding Fold Change against noise level in Sirt61ID Streptavidin-directed immunoprecipitation experiments.

    Binding Fold Change against noise level in Ku801ID Streptavidin-directed immunoprecipitation experiments.

    Specificity

    Summarized results of protein classification by OPLS-DA analysis. OPLS-DA was used to classify proteins according to their correlation and covariance with the Sensor protein variable. Levels: S6 (Sirt6 associated), Mre (Mre11 associated), Ku (Ku80 associated), S6&Mre (Sirt6 and Mre11 associated), S6&Ku (Sirt6 and Ku80 associated), Ku&Mre (Ku80 and Mre11 associated), S6&Ku&Mre (Associated with the three sensors), NA (variable that do not contribute to the OPLS-DA model).

    The VIP scores represent the overall contribution of each protein to the OPLS model and are calculated as a weighted sum of the squared correlations of the OPLS-DA components and the Sensor variable. Higher values mean a high contribution of the specific protein to the separation between each Sensor OPLS-DA. VIP. S6&Mre (VIP scores in the Sirt6 versus Mre11 OPLS-DA analysis), S6vsKu (VIP scores in the Sirt6 versus Ku80 OPLS-DA analysis), KuvsMre (VIP scores in the Ku80 versus Mre11 OPLS-DA analysis).

    Venn sets analysis results, that indicate if the protein is specific to one Sensor or shared between two or more sensor proteins at a specific time point. Levels: S6 (Sirt6 associated), Mre (Mre11 associated), Ku (Ku80 associated), S6&Mre (Sirt6 and Mre11 associated), S6&Ku (Sirt6 and Ku80 associated), Ku&Mre (Ku80 and Mre11 associated), S6&Ku&Mre (Associated with the three sensors), NA (The protein is not present at that time point in any sensor protein interactome).

    Venn diagrams
    All nonIR5 IR5' IR30' IR2h IR8h IR24h nonIR24

    Network Metrics and Node Classification

    The number of Protein-Protein Interactions that a specific protein has in the network at a specific time point. It indicates how well connected is the protein during the DNA repair process.

    After modularity analysis of each time point network, the connectivity coefficient (intra-module degree) is calculated as a measure of how well a node (protein) is connected to the nodes (other proteins) on its same module.

    The participation coefficient is close to 1 if the connections (interactions) of a specific node (Protein) are uniformly distributed among all the modules in the network, and close to 0 if it only has connections (interactions) with nodes (proteins) of its module. The participation coefficient indicates if a protein allows the interactions of specific modules among them.

    The module number (a random positive number) indicates the module to which the specific protein belongs. Calculated using rNetcarto modularity analysis algorithm.

    Topological classification of nodes (proteins) based on their connectivity and participation coefficients. Connectors: These are proteins with a high number of interactions (interactions) with proteins belonging to other modules in the network. Central Nodes: These are proteins very well connected with proteins of their module. Peripheral Hubs: These are nodes (proteins) with a low amount of connections (interactions) only within their module. Peripheral: These are proteins with a low degree. Ultra-peripheral: Are proteins very lowly connected.

    Role
      nonIR5 IR5' IR30' IR2h IR8h IR24h nonIR24

    SensorID PPI Networks

    Networks displaying the queried protein, and its neighbors (interacting proteins) in a specific time point. The functional annotation is shown as the color of the node (protein), and the interaction is pointed out as the edge between the two proteins. The size of each node is the scaled Fold Change of that protein in the specific displayed time point.

    Mre11ID

    Sirt6ID

    Ku80ID

    Download data according to annotations:

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