NOA (abbreviated to Network Ontology Analysis) is a freely available collection of Gene Ontology tools aiming to analyze functions of gene network instead of gene list. Network rewiring facilitates the function changes between conditions even with the same gene list. Therefore, it is necessary to annotate the specific function of networks by considering the fundamental roles of interactions from the viewpoint of systems biology. NOA is such a novel functional enrichment analysis method capable to handle both dynamic and static networks. The application of NOA in biological networks shows that NOA can not only capture changing functions in rewiring networks but also find more relevant and specific functions in traditional static networks.
NOA as a freely accessible webserver is a collection of web tools for whole-net NOA, sub-net NOA, whole-net GLM, and sub-net GLM. For whole-net methods, users can input either a gene list or a gene network, i.e. a link list according to pasting in the text box or uploading a data file from local disk, then the webserver will return the resulting rank of related GO terms by whole-net GLM for a gene list and both whole-net NOA and whole-net GLM for a network. Differently, for sub-net methods, in addition to the input of test gene list or test gene network, reference gene list or reference network is also necessary. It is worth to mention that reference set is required to contain test set due to the definition of reference set. Two parameters, species and cutoff for p-value, are required to be chosen after inputting data. Until now NOA support four types of species including Homo sapiens, Mus musculus, Rattus norvegicus, and Saccharomyces cerevisiae. The output of NOA is a ranked GO ID list of significant terms of biological processes (BP), cellular components (CC), and molecular functions (MF), additional with corresponding value of G, R, T, O in formula (1), p-values, corrected p-values, and related genes or links. Top ten GO terms are directly shown in a resulting table and the whole rank of significant terms can be downloaded via a hyperlink below the web page.
NOA is implement based on Java and it can get the result in a few seconds for most networks.
Homo sapiens: Uniprot ID and Gene Symbol.
Mus musculus: MGI ID and Gene Symbol.
Rattus norvegicus: RGD ID and Gene Symbol.
Saccharomyces cerevisiae: SGD ID and Gene Symbol.
There are 8 examples in the following.
(Examples: AD-i, AD-m, AD-s, aging, cellcycle, cellcycle-TF, sporulation, sporulation-TF)
AD-i, AD-s, AD-m is the different stages network from human Alzheimer's disease.
Cellycle, cellycle-TF and sporulation, sporulation-TF are the different stages in the yeast TF cooperation networks.
Aging is an aging network from human.
All the detail can be found in our paper and supplementary material.
Reference:Jiguang Wang, Qiang Huang, Zhi-Ping Liu, Yong Wang, Ling-Yun Wu, Luonan Chen, and Xiang-Sun Zhang. NOA: a novel Network Ontology Analysis method. Nucleic Acids Research, doi: 10.1093/nar/gkr251, 2011.