GO Tools: Term Enrichment

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agriGO

Platform
Online tool
Developer
Bioinformatics Center, China Agricultural University, Beijing, China.
Contact
Zhen Su
Publications
PMID:20435677
License
Free for academic use
GO data updates
weekly (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis. Here, we introduce agriGO, an integrated web-based GO analysis toolkit for the agricultural community, using the advantages of our previous GO enrichment tool (EasyGO), to meet analysis demands from new technologies and research objectives. EasyGO is valuable for its proficiency, and has proved useful in uncovering biological knowledge in massive data sets from high-throughput experiments. For agriGO, the system architecture and website interface were redesigned to improve performance and accessibility. The supported organisms and gene identifiers were substantially expanded (including 38 agricultural species composed of 274 data types). The requirement on user input is more flexible, in that user-defined reference and annotation are accepted. Moreover, a new analysis approach using Gene Set Enrichment Analysis strategy and customizable features is provided. Four tools, SEA (Singular enrichment analysis), PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA), are integrated as a toolkit to meet different demands. We also provide a cross-comparison service so that different data sets can be compared and explored in a visualized way. Lastly, agriGO functions as a GO data repository with search and download functions; agriGO is publicly accessible at http://bioinfo.cau.edu.cn/agriGO/.

  • ontology or annotation browser
  • ontology or annotation visualization
  • database or data warehouse
  • statistical analysis
  • term enrichment
  • text mining

Tool listing last updated 02 June 2010

AmiGO

Platform
Online tool Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
GO Consortium.
Contact
GO Helpdesk
Publications
PMID:19033274
License
Free for academic use
GO data updates
daily
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers
Open Source (OSI) Logo

AmiGO provides an interface to search and browse the ontology and annotation data provided by the GO consortium. Users can search for gene products and view the terms with which they are associated; alternatively, users can search or browse the ontology for GO terms of interest and see term details and gene product annotations. AmiGO also provides a BLAST search engine, which searches the sequences of genes and gene products that have been annotated to a GO term and submitted to the GO Consortium.

AmiGO accesses the GO mySQL database; more information is available from the GO database guide.

  • ontology or annotation browser
  • ontology or annotation search engine
  • ontology or annotation visualization
  • slimmer-type tool
  • term enrichment
  • other analysis

Tool listing last updated 10 October 2010

BiNGO

Platform
Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
Department of Plant Systems Biology, VIB / Ghent University, Ghent, Belgium.
Contact
Steven Maere
Publications
PMID:15972284
License
Free for academic use
GO data updates
no fixed update schedule
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers
Open Source (OSI) Logo

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape's versatile visualization environment to produce an intuitive and customizable visual representation of the results.

  • statistical analysis
  • term enrichment

Tool listing last updated 25 January 2011

Bioconductor

Platform
Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
BioConductor.
Contact
Bioconductor webmaster
License
Free for academic use
GO data updates
every three months (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers
Open Source (OSI) Logo

Bioconductor provides tools for the analysis and comprehension of high-throughput (microarray, sequence, flow, etc.) genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. There are more than core and user-contributed 400 packages. Bioconductor packages the GO ontology into our semi-annual release, with software tools to: query; join with diverse additional gene, microarray, and sequence annotations; incorporate GO into annotation, differential expression, and gene set enrichment work flows; and visualize.

  • ontology or annotation browser
  • ontology or annotation search engine
  • ontology or annotation visualization
  • database or data warehouse
  • software library
  • statistical analysis
  • term enrichment
  • text mining
  • other analysis
  • Flexible integration of GO into statistical analysis and comprehension of high-throughput genetic data.

Tool listing last updated 04 February 2011

Database for Annotation, Visualization and Integrated Discovery (DAVID)

Platform
Online tool
Developer
National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA.
Contact
DAVID bioinformatics team
Publications
PMID:12734009
PMID:19131956
License
Free for academic use
GO data updates
no fixed update schedule
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

Database for Annotation, Visualization and Integrated Discovery (DAVID) now provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes, which are usually derived from high-throughtput experiments, such as micorarray and proteomic studies. By the year of 2010, DAVID tools have been cited in over 2,000 publications.

  • term enrichment
  • text mining

Tool listing last updated 11 January 2011

Functional Semantic Similarity Measure between Gene Products (FuSSiMeG)

Platform
Online tool
Developer
Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
Contact
Francisco M Couto
License
Free for academic use
GO data updates
every three months (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) provides a functional similarity measure between two proteins using the semantic similarity between the GO terms annotated with the proteins.

  • statistical analysis
  • term enrichment
  • semantic similarity
  • other analysis

Tool listing last updated 04 June 2010

g:Profiler

Platform
Online tool
Developer
BIIT Group, Institute of Computer Science, University of Tartu, Tartu, Estonia.
Contact
BIIT support
Publications
PMID:17478515
License
Free for academic use
GO data updates
every three months (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

g:Profiler is a public web server for characterising and manipulating gene lists from high-throughput genomic data. g:Profiler has a simple user-friendly web interface with powerful visualisation. g:Profiler currently supports 85 species, including mammals, fungi, plants, insects, etc, from the Ensembl and Ensembl Genomes databases. g:Profiler consists of the following tools:

  • g:GOSt retrieves most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs to a user-specified group of genes, proteins or microarray probes. g:GOSt also allows analysis of ranked or ordered lists of genes, visual browsing of GO graph structure, interactive visualisation of retrieved results, and many other features. Multiple testing corrections are applied to extract only statistically important results.
  • g:Convert allows conversion between gene or protein names, database IDs and microarray probes of more than 100 types. A mix of various IDs may be presented as input; output options include HTML, text and XLS spreadsheet.
  • g:Orth retrieves orthologs for a given set of genes, proteins or probes in a selected organism. Graphical representation also shows orthologs present in all g:Profiler organisms.
  • g:Sorter searches for similar expression profiles to a given gene, protein or probe in a large set of public microarray datasets from the Gene Expression Omnibus (GEO) database.
  • g:Cocoa provides a compact interface for comparing enrichments of multiple gene lists.
  • ontology or annotation visualization
  • statistical analysis
  • slimmer-type tool
  • term enrichment
  • protein interactions
  • functional similarity
  • other analysis
  • coexpression similarity search, Gene ID conversion, network enrichment analysis., orthology mapping, search by genomic locus

Tool listing last updated 26 January 2011

Gene Ontology Browsing Utility (GOBU)

Platform
Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developers
Institute of Information Science, Academia Sinica, Taiwan.
Institute of Plant and Microbial Biology, Academia Sinica, Taiwan.
Contact
Wen-Dar Lin
License
Free for academic use
GO data updates
not applicable (e.g. because users provide data)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers
Open Source (OSI) Logo

Gene Ontology Browsing Utility (GOBU) (GOBU) is a Java-based software program for integrating biological annotation catalogs under an extendable software architecture. Users may interact with the Gene Ontology and user-defined hierarchy data of genes, and then use its plugins to (and not limited to) (1) browse the GO hierarchy with user defined data, (2) browse GO-oriented expression levels in the user data, (3) compute GO enrichment, and/or (4) customize data reporting.
A set of classes and utility functions has been established so that a customized program can be made as a plugin or a command-line tool that programmically manipulate the Gene Ontology and specified user data. See the source code repository for examples.

  • ontology or annotation browser
  • ontology or annotation visualization
  • software library
  • statistical analysis
  • term enrichment

Tool listing last updated 22 April 2011

Gene Ontology For Functional Analysis (GOFFA)

Platform
Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
National Center for Toxicological Research (NCTR), Food and Drug Administration, Jefferson, Arkansas, USA.
Contact
Don Ding
Publications
PMID:17118145
License
Free for academic use
GO data updates
monthly (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

Gene Ontology For Functional Analysis (GOFFA) is a tool developed for ArrayTrack that takes a list of genes and identifies terms in Gene Ontology associated with those genes. GOFFA provides tools to view/access the following:
* GO term hierarchy
* Full listing of GO terms annotated with the genes associated with a given term
* Fisher's exact test p-value providing the probability of identifying that many genes for a given term by chance alone
* Relative enrichment factor (E-value) giving the enrichment of a GO term for genes in the submitted list relative to the frequency of genes assigned to that term from the full set of GOFFA annotated genes for a particular species

  • ontology or annotation browser
  • ontology or annotation search engine
  • ontology or annotation visualization
  • database or data warehouse
  • term enrichment
  • text mining

Tool listing last updated 26 September 2011

GeneMANIA

Platform
Online tool Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
GeneMania team: Bader and Morris labs, University of Toronto, Toronto, Canada.
Contact
GeneMANIA team
Publications
PMID:20576703
PMID:20926419
License
Free for academic use
GO data updates
every three months (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers
Open Source (OSI) Logo

GeneMANIA helps you predict the function of your favourite genes and gene sets.
GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input.
If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets.
GeneMANIA also performs Gene Ontology term enrichment of the query list along with the returned gene list.
GeneMANIA is also accessible via a Cytoscape plugin, designed for power users.
GeneMANIA is actively developed at the University of Toronto, in the Donnelly Centre for Cellular and Biomolecular Research, in the labs of Gary Bader and Quaid Morris, with input from an independent scientific advisory board. GeneMANIA development was funded by Genome Canada, through the Ontario Genomics Institute (2007-OGI-TD-05).

  • database or data warehouse
  • software library
  • statistical analysis
  • term enrichment
  • other analysis
  • an interaction browser and GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest., GeneMANIA is also a gene recommendation system

Tool listing last updated 13 January 2011

GeneMerge

Platform
Online tool Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
Castillo-Davis Laboratory, University of Maryland, Maryland, USA.
Contact
Dr. Cristian Castillo-Davis
Publications
PMID:12724301
License
Free for academic use
GO data updates
every three months (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers
Open Source (OSI) Logo

GeneMerge is a web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. GeneMerge uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries.

  • statistical analysis
  • slimmer-type tool
  • term enrichment
  • text mining
  • false discovery rate and Bonferroni correction

Tool listing last updated 14 January 2011

Generic GO Term Finder

Platform
Online tool Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA.
Contact
Mark Schroeder
License
Free for academic use
GO data updates
daily
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

The Generic GO Term Finder finds the significant GO terms shared among a list of genes from your organism of choice, displaying the results in a table and as a graph (showing the terms and their ancestry). The user may optionally provide background information or a custom gene association file or filter evidence codes. This tool is capable of batch processing multiple queries at once.

  • ontology or annotation visualization
  • term enrichment

Tool listing last updated 19 February 2011

Generic GO Term Mapper

Platform
Online tool Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA.
Contact
Mark Schroeder
License
Free for academic use
GO data updates
daily
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

The Generic GO Term Mapper finds the GO terms shared among a list of genes from your organism of choice within a slim ontology, allowing them to be binned into broader categories. The user may optionally provide a custom gene association file or slim ontology, or a custom list of slim terms.

  • slimmer-type tool
  • term enrichment

Tool listing last updated 19 February 2011

GeneTools

Platform
Online tool
Developer
Norwegian University of Science and Technology, Trondheim, Norway.
Contact
Vidar Beisvag
Publications
PMID:17062145
License
Free for academic use
GO data updates
no fixed update schedule
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

GeneTools is a collection of web-based tools that brings together information from a broad range of resources, and provides this in a manner particularly useful for genome-wide analyses. Today, the two main tools connected to this database are the NMC Annotation Database V2.0 and eGOn V2.0 (explore Gene Ontology).

The NMC Annotation Database V2.0 provides information from UniGene, EntrezGene, SwissProt and Gene Ontology (GO). Major features are:

  • Single search/Batch search, extraction of data for single or batches of genes.
  • Manage reporter lists: in folders and share selected lists with other users.
  • Manual GO Annotation: add your own Gene Ontology (GO) annotations to genes of interest.
  • Export: to Excel, text or XML format.

eGOn V2.0 facilitates interpretation of GO annotation. GO terms are retrieved in batch modus from EntrezGene and the GO database and displayed in the GO directed acyclic hierarchical graph (DAG). Essential features of eGOn V2.0 are:

  • Visualization: gene annotations are visualized in the GO DAG or as a table view. The granularity of the GO DAG can be edited freely by the user.
  • Filtering: GO annotations can be filtered on evidence codes.
  • Include user defined GO annotations: previously added to the Annotation database.
  • Statistical analysis: Several gene lists are analyzed simultaneously to compare the distribution of the annotated genes over the GO hierarchy.

Statistical tests are implemented to allow the user to compute GO annotation dissimilarity within or between gene lists.

  • Connection to Annotation database: Links to Annotation database gene and protein information are offered directly from the GO DAG or in exported data.
  • Export: GO DAG information, statistical results and gene and protein information can be exported in excel, text or XML format.
  • ontology or annotation browser
  • ontology or annotation search engine
  • ontology or annotation visualization
  • database or data warehouse
  • statistical analysis
  • term enrichment

Tool listing last updated 18 January 2011

Genomic Regions Enrichment of Annotations Tool (GREAT)

Platform
Online tool
Developer
Bejerano Lab, Stanford University, Stanford, California, USA.
Contact
GREAT users mailing list
Publications
PMID:20436461
License
Free for academic use
GO data updates
no fixed update schedule

We developed the Genomic Regions Enrichment of Annotations Tool (GREAT) to analyze the functional significance of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets.

  • term enrichment

Tool listing last updated 01 May 2010

GoBean

Platform
Windows compatible Mac OS X compatible Linux compatible
Developer
Gachon University of Medicine and Science, Incheon, South Korea.
Contact
Ungsik Yu
License
Free for academic use
GO data updates
no fixed update schedule
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

Features of GoBean:
Graphical comparison of multiple enrichment analysis results
Versatile filter facility for focused analysis of enrichment results
Effective exploitation of the graphical/hierarchical structure of GO
Evidence code based association filtering
Supports local ontology obo file and gene association files
Supports late enrichment methods and multiple testing corrections
Built-in ID conversion for popular species using Ensembl biomart service

  • term enrichment

Tool listing last updated 10 October 2011

GOrilla

Platform
Online tool
Developers
Technion Laboratory of Computational Biology, Haifa, Israel.
Agilent Labs Tel-Aviv, Tel-Aviv, Israel.
Contact
Roy Navon
Publications
PMID:19192299
License
Free for academic use
GO data updates
weekly (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

GOrilla is a web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. These are determined in a data driven manner. GOrilla employs a flexible threshold statistical approach to discover GO terms that are significantly enriched at the top of a ranked gene list. The tool supports several input formats: gene symbol, gene and protein RefSeq, Uniprot, Unigene and Ensembl. Supported organisms include: human, mouse, rat, yeast, zebrafish, D. melanogaster, C. elegans and A. thaliana. The input to GOrilla is either a ranked gene list or target and background sets. The graphical output shows the results in the context of the GO DAG.

  • ontology or annotation visualization
  • statistical analysis
  • term enrichment

Tool listing last updated 17 August 2010

GraphWeb

Platform
Online tool
Developer
BIIT Group, Institute of Computer Science, University of Tartu, Tartu, Estonia.
Contact
Laur Tooming
Publications
PMID:18460544
License
Free for academic use
GO data updates
every three months (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers
Open Source (OSI) Logo

GraphWeb allows the detection of modules from biological, heterogeneous and multi-species networks, and the interpretation of detected modules using Gene Ontology, cis-regulatory motifs and biological pathways.

  • ontology or annotation visualization
  • statistical analysis
  • term enrichment
  • protein interactions
  • Gene ID conversion; orthology mapping; network visualisation; graph clustering

Tool listing last updated 26 January 2011

High-Throughput GoMiner

Platform
Online tool Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
Genomics and Bioinformatics Group, NIH National Cancer Institute, Bethesda, Maryland, USA.
Contact
Barry Zeeberg
Publications
PMID:12702209
PMID:15998470
License
Free for academic use
GO data updates
no fixed update schedule
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interpretation of the results from a single microarray (or other high-throughput experimental platform), using a graphical user interface. Although that version can be used to examine the results from a number of microarrays one at a time, that is a rather tedious task, and original GoMiner includes no apparatus for obtaining a global picture of results from an experiment that consists of multiple microarrays. We wanted to provide a computational resource that automates the analysis of multiple microarrays and then integrates the results across all of them in useful exportable output files and visualizations.
High-Throughput GoMiner, has those capabilities and a number of others: It (i) efficiently performs the computationally-intensive task of automated batch processing of an arbitrary number of microarrays, (ii) produces a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories, (iii) integrates the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories, (iv) provides a fast form of 'false discovery rate' multiple comparisons calculation, and (v) provides annotations and visualizations for relating transcription factor binding sites to genes and GO categories.
High-Throughput GoMiner achieves the desired goal of providing a computational resource that automates the analysis of multiple microarrays and integrates results across all of the microarrays. High-Throughput GoMiner will be useful in a wide range of applications, including the study of time-courses, evaluation of multiple drug treatments, comparison of multiple gene knock-outs or knock-downs, and screening of large numbers of chemical derivatives generated from a promising lead compound.

  • term enrichment

Tool listing last updated 03 June 2010

Network Ontology Analysis (NOA)

Platform
Online tool
Developers
Operations Research and Bioinformatics Group, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China.
Systems Science and Key Laboratory of Systems Biology, Chinese Academy of Sciences, Beijing, China.
Contact
Jiguang Wang
Publications
PMID:21543451
License
Free for academic use
GO data updates
no fixed update schedule
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers
Open Source (OSI) Logo

Network Ontology Analysis (NOA) (abbreviated to NOA) 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.

  • ontology or annotation browser
  • statistical analysis
  • term enrichment

Tool listing last updated 19 July 2011

Onto-Express (OE)

Platform
Online tool
Developer
Intelligent Systems and Bioinformatics Laboratory, Wayne State University, Detroit, Michigan, USA.
Contact
Dr. Sorin Draghici
Publications
PMID:11829497
PMID:12620386
PMID:15215428
License
Free for academic use
GO data updates
every three months (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially regulated in the condition under study. Independently of the methods used to select these genes, the common task faced by any researcher is to translate these lists of genes into a better understanding of the biological phenomena involved. Currently, this is done through a tedious combination of searches through the literature and a number of public databases. We developed Onto-Express (OE) as a novel tool able to automatically translate such lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. We demonstrated the validity and the utility of this comprehensive global analysis of gene function by analyzing two breast cancer data sets from two separate laboratories. OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms (Draghici et.al, Genomics, 81(2), 2003). Other results obtained with Onto-Express can be found in Khatri et.al., Genomics. 79(2), 2002.

  • ontology or annotation browser
  • ontology or annotation search engine
  • ontology or annotation visualization
  • database or data warehouse
  • statistical analysis
  • term enrichment
  • other analysis
  • custom level of abstraction of the Gene Ontology

Tool listing last updated 29 June 2010

Onto-Express To Go (OE2GO)

Platform
Online tool Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
Intelligent Systems and Bioinformatics Laboratory, Wayne State University, Detroit, Michigan, USA.
Contact
Dr. Sorin Draghici
Publications
PMID:17584796
License
Free for academic use
GO data updates
every three months (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

Onto-Express is a web-based tool in the Onto-Tools suite that performs automated function profiling for a list of differentially expressed genes. However, Onto-Express does not support functional profiling for the organisms that do not have annotations in public domain, or use of custom (i.e. user-defined) ontologies. This limitation is also true for most of the other existing tools for functional profiling (10), which means that researchers working with uncommon organisms and/or new annotations or ontologies may be forced to construct such profiles manually. Onto-Express To Go (OE2GO) is a new tool added to the Onto-Tools ensemble to address these issues. OE2GO is built on top of OE to leverage its existing functionality. In OE2GO, the users now have an option to use either the Onto-Tools database as a source of functional annotations or provide their own annotations in a separate file. Currently, OE2GO supports annotation file in the Gene Ontology format.

  • ontology or annotation browser
  • ontology or annotation search engine
  • ontology or annotation visualization
  • statistical analysis
  • term enrichment
  • other analysis
  • custom annotations, custom level of abstraction

Tool listing last updated 29 June 2010

PiNGO

Platform
Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
Department of Plant Systems Biology, VIB / Ghent University, Ghent, Belgium.
Contact
Steven Maere
License
Free for academic use
GO data updates
no fixed update schedule
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers
Open Source (OSI) Logo

PiNGO is a Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file.

  • ontology or annotation search engine
  • statistical analysis
  • term enrichment
  • functional similarity
  • functional prediction

Tool listing last updated 25 January 2011

ProteInOn

Platform
Online tool
Developer
Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
Contact
Catia Pesquita
License
Free for academic use
GO data updates
every three months (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

ProteInOn calculates semantic similarity between GO terms or proteins annotated with GO terms. It also calculates term enrichment of protein sets, by applying a term representativity score, and gives additional information on protein interactions.

  • statistical analysis
  • term enrichment
  • protein interactions
  • semantic similarity
  • other analysis

Tool listing last updated 14 July 2010

Short Time-series Expression Miner (STEM)

Platform
Windows compatible Mac OS X compatible Linux compatible Unix compatible
Developer
Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
Contact
Jason Ernst
Publications
PMID:15961453
PMID:16597342
License
Free for academic use
GO data updates
no fixed update schedule
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers
Open Source (OSI) Logo

The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data (eight time points or less). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database and supports GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category, identifying which temporal expression profiles were enriched for these genes.

  • statistical analysis
  • term enrichment

Tool listing last updated 01 January 2011

StRAnGER

Platform
Online tool
Developer
Metabolic Engineering and Bioinformatics Group, Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
Contact
Panagiotis Moulos
License
Free for academic use
GO data updates
monthly (or more frequently)
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

StRAnGER (Statistical Ranking of ANotated Genomic Experimental Results) is a web application for the automated statistical analysis of annotated gene profiling experiments, exploiting controlled biological vocabularies, like the Gene Ontology or the KEGG pathways terms. Starting from annotated lists of differentially expressed genes StRAnGER repartitions and reorders the initial distribution of terms to define a new distribution of elements where each element pools terms holding the same enrichment score. The elements are then prioritized according to StRAnGER's algorithm and, by applying bootstrapping techniques, a corrected measure of the statistical significance of these elements is derived, enabling the selection of terms mapped to these elements, unambiguously associated with respective significant gene sets. Besides their high statistical score, another selection criterion for the terms is the number of their members, something that incurs a biological prioritization in line with a Systems Biology context.

  • ontology or annotation visualization
  • statistical analysis
  • term enrichment

Tool listing last updated 26 January 2011

ToppGene Suite

Platform
Online tool
Developer
Cincinnati Childrens Hospital Medical Center, Cincinnati, Ohio, USA.
Contact
Anil Jegga
Publications
PMID:19465376
License
Free for academic use
GO data updates
no fixed update schedule
GO data used
  • terms
  • definitions and comments
  • synonyms
  • cross-references
  • relationships
  • subsets or GO slims
  • gene product data
  • taxon
  • evidence codes
  • references
  • qualifiers

ToppGene Suite is a one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations. The similarity scores from individual features are combined into an overall score using statistical meta-analysis. A P-value of each annotation of a test gene is derived by random sampling of the whole genome.

  • database or data warehouse
  • slimmer-type tool
  • term enrichment
  • protein interactions
  • functional similarity
  • other analysis
  • disease gene ranking based on functional annotation similarity

Tool listing last updated 21 January 2011