GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

By Bing Zhang, D. Schmoyer, Stefan Kirov, Jay Snoddy. BMC Bioinformatics, 2004

491 citations recorded by the source corpus.

BackgroundMicroarray and other high-throughput technologies are producing large sets of interesting genes that are difficult to analyze directly. Bioinformatics tools are needed to interpret the functional information in the gene sets.ResultsWe have created a web-based tool for data analysis and data visualization for sets of genes called GOTree Machine (GOTM). This tool was originally intended to analyze sets of co-regulated genes identified from microarray analysis but is adaptable for use with other gene sets from other high-throughput analyses. GOTree Machine generates a GOTree, a tree-like structure to navigate the Gene Ontology Directed Acyclic Graph for input gene sets. This system provides user friendly data navigation and visualization. Statistical analysis helps users to identify the most important Gene Ontology categories for the input gene sets and suggests biological areas that warrant further study. GOTree Machine is available online at http://genereg.ornl.gov/gotm/.ConclusionGOTree Machine has a broad application in functional genomic, proteomic and other high-throughput methods that generate large sets of interesting genes; its primary purpose is to help users sort for interesting patterns in gene sets.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b79ff82502b35738c16b42a47b7f23334fab99c8

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Citations in the corpus

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists (2009, unknown): “A few tools visualize the results of enrichment analysis in the DAG structure, including the downloadable version of GoMiner [3], the CytoScape plug-in BiNGO [5], GOLEM [8], GOEAST [9] and GOTM [10].”
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists (2007, background): “A number of publicly available bioinformatics tools have addressed the first three points above, including, but not limited to, GoMiner, DAVID, EASE, GOstat, Onto-express, GoToolBox, FatiGO, GOSSIP, GFINDer, GOBar, and so on [1-25].”
GOToolBox: functional analysis of gene datasets based on Gene Ontology (2004, result): “As far as the output types are concerned, several programs propose a tabulated output file with terms ranked according to their P-values, (with the exception of GoMiner [15] and GOTM [16], therefore precluding the interpretation of the results in these cases).”
WebGestalt: an integrated system for exploring gene sets in various biological contexts (2005, methodology): “The GO Tree is based on our published tool GO Tree Machine, which was described in detail in (9).”
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists (2008, unknown): “For example, tools such as GOToolBox (18), GOstat (14), GoMiner (10), FatiGO (13) and GOTM (24), use the total genes in the genome as a global reference background.”
Ontological analysis of gene expression data: current tools, limitations, and open problems (2005, methodology): “The web-based services provide the experimental biologists a convenient solution by avoiding the problems usually associated with a local installation of a program (Zhang et al., 2004).”
BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks (2005, unknown): “2004; Zhang et al., 2004).”
Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function (2005, methodology): “category representation analysis using the Gene Ontology Tree Machin”
GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists (2007, methodology): “In order to explain the 'protein phosphorylation' category in the context of the phenotypic feature of the gene cluster, Zhang and colleagues [19] remarked that, 'spermatozoa undergo a series of changes before and during egg binding to acquire the ability to fuse with the oocyte.”
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis (2008, background): “Among the few available GO analysis tools with graphical output (12,19,20,23,28), only EasyGO has similar functions, but it is limited to several plants and farm animals (28).”
Analyzing gene expression data in terms of gene sets: methodological issues (2007, unknown): “Contact: j.j.goeman@lumc.nl”