NOA performs Gene Ontology enrichment analysis on networks. NOA performs both gene set and interaction-based enrichment analysis, on one or more networks. The algorithm works by first annotating the network (nodes and interactions) with GO terms, followed enrichment analysis.
The NOA algorithm was first implemented by Jiguang Wang, et al. Please contact us with any feedback, questions or comments.

NOA is supported by the National Resource for Network Biology (P41 GM103504).

To install, place the following jar files in the plugins directory of your Cytoscape installation:
Note that NOA requires the CyThesaurus plugin, version 1.3.1 or higher:
Technical documentation
The NOA algorithm workflow is explained in the below graphics. Click to enlarge.

Single network mode

NOA workflow, single

Batch mode

NOA workflow, batch
Running NOA - Single Mode
  1. Select a network to load under File>Import Network (Multiple File Types). The network can be in any of the Cytoscape supported network file formats.
  2. Download sample file: galFiltered.sif (8KB)
  3. Start NOA by selecting Plugins>NOA.
  4. NOA Interface Single
The NOA interface is divided into three sections; Input, Retrieve GO Annotations and Set Parameters:
  1. Select either Edge-based or Node-based algorithm.
  2. Select to run analysis on either the Whole network or a Selected sub network. NOA will display the number of nodes or edges in the selected sub network.
  3. Select a Reference network for over-representation. This can be either the Whole network or a Clique.
Retrieve GO Annotations
  1. Under Species, select the appropriate species for your data.
  2. If this is the first time running NOA, you will see a message to download necessary databases. Click Download to continue. NOA will download the necessary database for your data. It is only necessary to download datbases once per species.
  3. Once database download is complete, NOA will prompt you to annotate your network with GO annotations. Verify that the correct Identifier attribute and Type of identifier are selected.
  4. In addition, you will also be able to select which GO annotation to use:
  5. Click Annotate to continue. You can save the annotated network as a session file for future use. You can also re-annotate the network with the latest annotations from GO at any time by clicking Re-annotate.
Set Parameters
  1. In the Set Parameters section you can choose several parameters that will directly affect the results of NOA:
    • Edge annotation:
    • Correction method: Method to use for multiple testing correction.
    • Statistical method: Method to sue for over-representation.
    • P-value threshold: P-value threshold for results.
  2. Click Run to start NOA.
Navigating the results
NOA results will be displayed as a results table of GO terms relevant to the network, listed by descending P-value. The results table is shown below next to the original network. NOA Results Single The table includes the following information:
  • GO ID: The identifier assigned by the Gene Ontology
  • Type: Gene Ontology type, either Biological Process (BP), Cellular Component (CC) or Molecular Function (MF).
  • P-value: The resulting P-value as calcualted based on the statistical method selected.
  • Test: Number of nodes/edges in the network associated with the GO term and the total number of nodes/edges in the network. For example, if 8 out of 362 network nodes are found in the GO term, the Sample column displays 8/362.
  • Reference: Number of nodes/edges in the network associated with the entire GO hierarchy and the total number of nodes/edges in the hierarchy. For example, if 15 out of 54615 network nodes are found in the hierarchy, the Population column displays 15/54615.
  • Description: Description of GO term from the ontology.
  • Associated nodes/edges: List of nodes/edges associated with the GO term. Selecting any GO term in the results table will select the associated nodes/edges in the network.
To save the results as a spreadsheet, click Save and select a location and file name. This will save the results as a comma-separated spreadsheet. The results table is interactive, clicking on a GO term highlights the corresponding edges and nodes in the network. Double-clicking a GO term opens a browser displaying the detailed information for that GO term at the Gene Ontology website. In addition to the results table, the results are also displayed as an overview network. Nodes correspond to GO terms, and are colored based on the corresponding p-value, with brightly colored indicating a lower p-value. Node size indicated the number of nodes and edges in the analyzed network with that annotation, and the thickness of edges between nodes indicates the number of overlapping genes between the two GO terms. Overview network
Running NOA - Batch Mode
  1. Start NOA by selecting Plugins>NOA.
  2. NOA Interface Batch
The NOA batch mode interface is similar to the single mode interface, and is divided into three sections; Input, Retrieve GO Annotations and Set Parameters:
Selecting Input parameters for batch mode is similar to single mode, except that a batch input file must be specified under Test network. The batch network file must conform to the following formatting:
  • The beginning of each network is specified by a closing angle bracket (>) followed by the network name, for example ">Net1".
  • Each network is specified in sif format.
For the purposes of this manual, use the sample file disease_gene.noa (4KB). This file contains human data, annotated with HGNC IDs. Select the Node-based algorithm, and All networks as the reference network.
Retrieve GO Annotations
Retrieving GO annotations for a batch analysis is identical to single analysis mode, except that the Identifier attribute does not need to be specified, since NOA uses identifiers directly from the batch network file.
Set Parameters
Setting analysis parameters is also identical to single mode.
Navigating the results
NOA results will be displayed as a results table of GO terms relevant to the input networks. For batch mode, results are provided in two different ways, Results, formatted like the results from single mode, and Overlap results , listed by subnetwork in order of descending P-value. NOA Results Batch The table includes the same information as for single mode, with one additional column for Network ID, the individual network name from the input file.
For overlap results, a list of GO terms found to be associated with more than one network is displayed. NOA Results Batch Overlap NOA also includes a heatmap view of the results. The heatmap results can be saved as individual image files and comma-separated spreadsheets for each of the three branches of GO. NOA Results Batch Heatmap