Table 6.
Software tools.
| Gene Ontology (GO) Analysis Tools |
Full name | Comments | Cost | Visualization | Knowledgebase | Website | Ref |
|---|---|---|---|---|---|---|---|
| MAPPFinder | MicroArray Pathway Profiles Finder | View data in the context of Gene Ontology (GO) and GenMAPP biological pathways. | Free | Y | GO | www.genmapp.org/MAPPFinder.html | [10] |
| GoMiner | - | Tool to classify gene onto the Gene Ontology(GO) hierarchy framework. | Free | Y | GO | discover.nci.nih.gov/gominer | [8] |
| EASE | Expression Analysis Systematic Explorer | Statistical tool to analyze gene list by GO. | Free | Y | GO | david.abcc.ncifcrf.gov | [65] |
| Onto-Express | - | Analyze the list of genes into GO hierarchy. | Free | Y | GO | vortex.cs.wayne.edu/Projects.html #Onto-Express | [11] |
| GoSurfer | - | Analyze gene list using GO and visualize them as a hierarchical tree. | Free | Y | GO | bioinformatics.bioen.uiuc.edu/gos urfer | [109] |
| FatiGO | Fast Assignment and Transference of Information | Web-based tool to analyze and compare GO terms in 2 sets of gene list. | Free | Y | GO | fatigo.bioinfo.cipf.es | [110] |
|
| |||||||
| Pathway Analysis Tools | Full name | Comments | Cost | Visualization | Knowledgebase | Website | Ref |
|
| |||||||
| PathwayExplorer | - | Web-based tool to visualize data on publicly available biological pathways. | Free | KEGG, Biocarta, GenMAPP | KEGG, Biocarta, GenMAPP | pathwayexplorer.genome.tugraz.at | [68] |
| WholePathwayScope | - | Pathway-based analysis tool to visualize BioCarta, KEGG, and GO term relationships. | Free | KEGG, Biocarta, GO | KEGG, Biocarta, GO | www.abcc.ncifcrf.gov/wps/wps_index.php | [67] |
| PathwayExpress | - | Analyze the list of genes in the context of KEGG pathways. | Free | KEGG | KEGG | vortex.cs.wayne.edu/Projects.html #Onto-Express | [12] |
| Pathway Processor | - | Visualization and statistical analysis | Free | KEGG | KEGG | sysbio.harvard.edu/csb | [66] |
| Reactome Skypainter | - | Tool to calculate statistical significance of affected pathways and visualize pathways. | Free | Skypainter maps | Reactome | www.reactome.org/cgi-bin/skypainter2?DB=gk_current | [62] |
| Oncomine | - | Cancer profiling database and provides web-based tools to analyze data. | Free | Scalable Vector Graphics (SVG) | KEGG, BioCarta, HRD, SOURCE | www.oncomine.org | [111] |
| DAVID | Database for Annotation, Visualization and Integrated Discovery | Offers various functional annotation tools to analyze gene list. | Free | DAVID Pathway Viewer | BioCarta, KEGG | david.abcc.ncifcrf.gov/home.jsp | [112] |
| GenePattern | A platform for integrative genomics | Tools for statistical analysis of data. | Free | heatmaps and other tools. | Multiple tools. | www.broad.mit.edu/cancer/software/genepattern | [113] |
| VisANT | Visualization and analysis tool for biological networks and pathways | A web-based application for the predicted functional links between genes and proteins analysis of biological networks and pathways. | Free | nodes and edges | Predictome, MIPS, BIND | visant.bu.edu | [114] |
| FatiGO+ | Fast Assignment and Transference of Information | Compare distributions of GO or KEGG pathways between two groups of genes. | Free | KEGG | KEGG | babelomics.bioinfo.cipf.es/fatigopl us/cgi-bin/fatigoplus.cgi | [115] |
| PathwayStudio/PathwayAssist | - | Pathway analysis software. | License | Y | Manual curation | www.ariadnegenomics.com/products/pathway | [116] |
| Ingenuity Pathways Analysis | - | Pathway analysis software. | License | Y | Manual curation | www.ingenuity.com/products/pathways_analysis.html | N/A |
| MetaCore | - | Pathway analysis software. | License | Y | Manual curation | www.genego.com | N/A |
| PathArt | - | Pathway analysis software. | License | Y | Manual curation | jubilantbiosys.com/ppa.htm | N/A |
|
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| Visualization Tools | Full name | Comments | Cost | Visualization | Knowledgebase | Website | Ref |
|
| |||||||
| Cytoscape | - | Visualize molecular interactions and integrate gene expression profiles into pathways. | Free | Y | Retrieved from various databases. | www.cytoscape.org | [60] |
| GenMAPP | Gene Microarray Pathway Profiler | Visualize gene expression and genomic data on biological pathway maps. | Free | Y | Retrieved from various databases. | www.genmapp.org | [61] |
| Osprey | - | Graphical representation from Gene Ontology annotated interaction data by The GRID. | Y | The GRID | biodata.mshri.on.ca/osprey/servlet/Index | [117] | |
| CellDesigner | - | Software to draw pathways. | Y | Panther Classification System | www.celldesigner.org | [118] | |
| PathwayArchitect | - | Software for building pathways from databases or from own interaction data. | License | Y | - | www.stratagene.com/tradeshows/feature.aspx?fpId=90 | N/A |