10 Best Gene Ontology Tools and Software

Gene Ontology is a significant sub-set of Bioinformatical analysis on genes of varied living sources or the genetic materials. It refers to assigning relevant biological terms to the genes and viewing the relationships in the form of interconnected graphs.

Gene Ontology is a term that comprises three broad biological aspects- cellular component, molecular functions, and biological processes. There are many gene ontology tools available that help in identifying the GO terms associated with a gene or protein.

Some of the best gene ontology tools are free to use as public web- browsers. Some are downloadable on local machines for offline usage.

What are The Best Gene Ontology Tools and Software

It is perplexing to choose one tool or a group of tools for performing gene ontology tasks. Each day developers are modifying the most used and cited tools for improving accuracies and performance with reduction in false positives.

According to us, the best gene ontology software and tools are the ones that are favoured by the science community for significant science projects. Highly cited and critically acclaimed tools must be opted for research.

Given below is a list of the Best Gene Ontology Tools & Software available for free that you can choose from.

1. DAVID

DAVID is a Database for Annotation, Visualization, and Integrated Discovery. An accessible program on the web that integrated functional and genomic annotation with interesting graphical representations.

It assists in the interpretation of genome-scale datasets by facilitating conversion of biological data into meaningful biological information. The lists of predicted genes identifiers are annotated rapidly, summarized intuitively for the users into categorical data.

Generation of list of interacting proteins, gene-disease associations, protein functional domains and motifs identification, and more are the outputs of DAVID tool. More than 51k citations with average daily usage of approx.

KEY FEATURES

  • Identification of enriched biological themes, Gene Ontology terms
  • Identification of function related gene groups
  • Redundant annotation terms clustered into groups
  • Visualization of genes on BioCarta and KEGG pathway database

2. GOrilla

GOrilla is a Gene Ontology enrichment analysis and visualization tool available on web-based application, identifies enriched Gene Ontology terms in ranked lists of genes without specifying the target and background sets of data.

The tool employs flexible threshold statistical approach for GO terms discovery. Computes exact p-value for the enriched observations taking threshold for multiple testing into account without simulations.

Output of the analysis is visualized as hierarchical structure that reflects clear relations between different enriched Gene Ontology terms. Flexibility in customization of input and results settings.

KEY FEATURES

  • Multiple parameters for adjusting input values for the sequences
  • Input file is a ranked list of genes and protein names
  • Choice for the type of ontology- process, function and component
  • Advance parameters such as type of output format

3. QuickGO

QuickGO is a web-based tool for Gene Ontology and GO Annotations. It provides easy browsing of the GO and associated electronic and manual GO annotations given by GO Consortium annotation groups. It can be installed on local machines too.

A popular gene ontology tool for many years with great range of facilities including heavy size file downloads of GO annotation data. It can be filtered by assigning different parameters to the settings option.

Multiple advance features makes it worth. Simple search to view information is feasible. Results are ranked well. There are total nine parameters to filter annotation files for download- specific protein, evidence codes, qualifier data, GO terms and more.

KEY FEATURES

  • Interface is built using JavaScript, Ajax and HTML
  • Optimized and streamlined set of files used for large queries and data extractions
  • Imports protein descriptions and taxonomic hierarchies form UniProtKB
  • Updated information to ensure all latest data is fed to public

4. GeneGO MetaCore

GeneGO MetaCore accelerates the pace of biological research by providing high-quality biological systems data. It includes integrated pathways and network analysis for multi-omics data. Mainly developed for data mining and pathway analysis.

Efficient in analyzing high-throughput experimental data for pathways, networks and maps. An ideal software for pathway analysis applications. It identifies pathways and networks for the lists of genes, proteins, transcripts or compounds.

Allows real time data mining- multiple data points, time-series, conditions, and more. For studies based on diseases, apply filters on disease, tissue, functional processes, and sub-cellular localization.

KEY FEATURES

  • Easy to use workflow wizards for uploading data, analysis and interpretation
  • Visualization and cross-validation of different data types- Gene Expression data, microarray data, and more.
  • Choice for network creating algorithms and multiple filters for optimal results
  • Total control over settings such as- colors, data sets, choice of ranges

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5. GOnet

GOnet is a bioinformatics tool for interactive gene ontology analysis. It is an open-source web application that takes a list of genes and proteins as input and generates GO term annotation analysis for human or mouse data.

The tool is capable of producing convertible data formats and interactive visualization of the Gene Ontology results. Allows the users to explore genes and GO terms for depiction of natural hierarchy of the terms and retains relationships between genes and proteins.

The interactive output graph allows to re-arrange genes and GO term annotations to optimally represent the interpretation of discovered functional classification pattern. Depending on the number of nodes visualized, different layouts can be opted.

KEY FEATURES

  • Input includes a list of genes and proteins from the specific organism
  • Analysis of three domains can be obtained separately as output graph
  • Default output format is Interactive graph, CSV, machine-readable text file also
  • Supports multiple export options for downstream analysis

6. GOATOOLS

GOATOOLS Is a python-based library that allows latest ontology and annotations for genes enrichment. It organises results for clarity and easier interpretation using GOATOOLS grouping methods.

It processes over and under representation of certain gene ontology terms based on Fisher’s exact test. It includes multiple test corrections from stats models. It processes the obo-formatted file from Gene Ontology website.

The data structure is a directed acyclic graph that allows easy traversing from leaf to root. Easily read the gene ontology association files such as GAF, GPAD, NCBIs gene2go file and id2gos formats. The GO terms can be grouped for easy viewing.

KEY FEATURES

  • Identify ancestors or parents for a GO term with or without optional relationships
  • Get details about a GO IDs parents, plot GO hierarchies
  • Easy mapping of GO terms with multiple associations to GO terms to GOslim terms.
  • Get descendants count and information content for a list of GO terms

7. GOLEM

GOLEM is a gene ontology local exploration map, visualisation and analysis tool for Gene ontology graph generation. It is an open source and freely available both as an application and on the web browser.

GOLEM lets the user to dynamically expand and focus the local Graphic structures of the gene ontology hierarchy in the neighbourhood of any chosen term. It supports rapid analysis of input gene list to find enriched gene ontology terms.

Users are permitted to utilise local gene ontology and annotations file without the internet connection. They can also access the most recent ontology and annotation information from the web pages of gene ontology.

KEY FEATURES

  • Allows dynamic expansion of GO graph
  • Loads the local annotation files for analysis
  • Works with local files in the absence of internet connection
  • Allows gene enrichment analysis and dynamic visualisation

8. AmiGO

AmiGO is a widely used open source software tool for biologist looking forward to visualise the local directed acyclic graph structure of the GO hierarchy. It allows users to query, search, and visualise ontologies.

The GO Consortium provides access to the data used on this website. Very well structured and controlled vocabularies for description of gene and their products. It executes BLAST search, GO slimmer tools, GO online SQL environment, and user help guide.

Allows advance interactive search for the GO data for annotations, products, terms by employing powerful search algorithm and filters. GOOSE feature allows to query the legacy GO database with SQL.

KEY FEATURES

  • Detail description for gene annotated to the term
  • Complete details of the gene products
  • Simple search tools for gene products
  • Browsing option is an alternative to search terms and gene products to explore GO

9. GOEAST

GOEAST is a bioinformatics software toolkit that provides visualisation and comprehensive gene ontology analysis for high throughput experimental data. Microarray hybridisation experiments data are mostly analysed.

Available on web server for free use as it is open source. The main goal is to identify enriched GO terms for a list of genes using appropriate statistical algorithms. It generates interactive graphs that exhibit relationships among GO terms and GO hierarchy.

It also prepares separate graft for each of the GO categories namely biological process, molecular function, and cellular component. It permits to compare results from multiple experiments using multi – GOEAST tool.

KEY FEATURES

  • Supports non-microarray data also
  • Allows correct format of gene list as input
  • Multi-GOEAST is combination of different colours used in individual analysis
  • Publication already graphical results of high-quality

10. GOFFA

GOFFA is a gene ontology for functional analysis tool. A popular tool used for ranking of GO terms in order of prevalence for a list of input genes.

Allows the user to interactively select the GO terms as per the significance and specific complexity within hierarchal structure. It offers five interactive functions namely preview, terms view, genes view, GO Path, and GO TreePrune for GO data analysis.

GO path and GO TreePrune are unique in features. Based on statistical analysis, GO path displays ranks that order GOFFA tree paths. The GO TreePrune provides visualisation of reduced GO terms based on statistical cut-offs.

KEY FEATURES

  • Interesting depiction of most relevant biological functions
  • Gene expression results from various sources
  • Fruitful in identification of new discoveries and hypothesis
  • High-quality images, graphs and results available

In this article, we have thrown light on the biologically significant best gene ontology tools for functional enrichment of genes. Each of the GO tool is freely available for use, or either through academic license.

Full exploration of these software can help in building gene-disease relationships and discovery of novel ideas for therapeutics.

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