3/6/2023 0 Comments Cytoscape 2.8 user manual![]() The basic question answered by these tests is the following : PiNGO currently provides two statistical tests, borrowed from BiNGO, to assess functional enrichment in a set of genes. This may serve as an indicator of the usefulness of the network for studying cold stress (note that you only assess the recall or sensitivity of the network-based predictions here, not the precision). Use case 2: You want to check how many known ‘response to cold stress’ genes are predicted to be involved in ‘response to cold stress’ on the basis of an input network. Additionally, you’re not interested in genes that are known to be involved in ‘response to other organism’ (51707). You’re only interested in transcription factors (3700) and signal transducers (4871) that are not already annotated to the ‘response to cold stress’ category. Use case 1: You want to find candidate genes in your network that are associated with some process, say ‘response to cold stress’ (70417). You should only paste numbers in the GO category boxes, not the GO:00. The GO category ID for a term can be found with tools like AMIGO. ![]() ![]() Target GO categories: GO categories for which you want to predict candidate genes Start GO categories: the existing GO annotations a candidate gene should haveįilter GO categories: existing GO annotations a candidate gene should not have Start, Filter and Target GO categories and use cases Header lines are not necessary, but if they’re there, they should start with ‘#’.Ģ. edge weights) can be present but are not taken into account in the current version of PiNGO. Separating genes with regular spaces will not work. Each line represents an edge in the network going from gene x to gene y (edge direction does not matter). PiNGO accepts custom networks in a tab-delimited text file format with at least two columns, e.g. To get a taste of the basic user interface, please take a look at the tutorial section. This manual aims to explain the inner workings, and potential pitfalls, of PiNGO in more detail. extensive results in tab-delimited text file format.Multiple testing correction using Bonferroni (FWER) or Benjamini&Hochberg (FDR) correction.Hypergeometric or binomial test for enrichment analysis. ![]() Customizable annotations, ontologies and reference sets, not limited to GO.Limit your candidate gene search to genes already annotated to specific GO categories, or to genes not annotated to certain GO categories, or both.PiNGO also takes full advantage of Cytoscape's versatile visualization environment. The main advantage of PiNGO is its flexibility. Networks can either be selected from the Cytoscape interface or uploaded from file. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO is a Java-based tool to find unknown genes in a molecular network that are significantly associated with user-defined target Gene Ontology (GO) categories. After installing Cytoscape, install BiNGO (2.42 or higher) and PiNGO using the Cytoscape Plugins Manager (under Plugins menu). If not already installed on your computer, download and install the Java 2 Runtime Environment, version 1.6.0 or higher.Ģ. PiNGO 1.11 is compatible with Cytoscape version 2.8, not with earlier versions. PiNGO is a plugin for the Cytoscape platform.
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