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FeaturesiPAVS CurrentView Demos (Green Ready)ReactomePantherNature NCIConsensus
PathDB
KEGGPayaoCellPubisherPathway
Commons

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Pathway data

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Pathway data provenancein house curated + imported from public databasescuratedcruatedcurated + importedimportedcuratedimportedimportedimported

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Curation TypeManual + ExpertINFO_LINKManual + ExpertManualManual + ExpertManualaggregates manually curated pathways drawn in Cell DesignerTool to publish manually curated pathways drawn in CellDesignerimported

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Pathway diagram layoutManualManualManualautomatedautomatedManualsee aboveNObasic network diagram generated automatically

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Integrates pathway information from other public data sourcesCurrently 4 resource + in future several additions INFO_LINKnonenone2 other resource20 public resourcesnonesee aboveNO10 public resources

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Diagram NotationsCellDesigner / SBGN
any native formats like KEGG
INFO_LINKSBGNCellDesigner / SBGNcustom notationcustom notationcustom notationCellDesignerCellDesignerCustom notation

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Automated generation of pathway diagram and layoutingNONOYESYESNONONOYES

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Can allow comparison of pathway information between databasesYESNONONOYESNONONONO

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Integration of data from molecular and interaction databasesUniprot swissprot, tremble, Enzyme database,GO data + links to several othersvia links via linksvia linksvia linksvia linksvia links if the models providevia link if provided by uservia links

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Pathways level annotation with citation to the literatureYESYESYESYESNOYESif model provides or tagged by user
NONO

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Interaction and Molecular level annotation with citations to the literatureYESYESNOYESNONOif model provides or tagged by user
NONO

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Content coverageMetabolic, Signaling, Regulatory pathwaysMetabolic, Signaling, Regulatory pathwaysMetabolic, Signaling, Regulatory pathwaysSignaling, Regulatory pathwaysMetabolic, Signaling, Regulatory pathways and interaction datasetsMetabolic, Signaling, Regulatory pathwaysMetabolic, Signaling, Regulatory pathways and Interaction datasets

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Content distributionFreeFree FreeFreeFreeFree FreeFreeFree

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Pathway data visualizationInteractive predefined and manually layouted easy to follow pathwaysInteractive predefined pathwaysInteractive predefined pathwaysInteractive predefined pathways and dynamically generated interactive network mapsOnly dynamically generated interactive network mapsInteractive predefined pathwaysInteractive predefined pathways provided by usersOnly dynamically generated interactive network maps

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Allows submission of annotation information by user ( tagging the molecules, interactions and pathways)YESDemospecifically designed as social tagging

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Use of standard notation (Systems Biology Graphical Notation)YESYESYESNONONOYESYESNO

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Search and Browse

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Browse pathway content as hierarchical treePathways, Interaction, Molecules, Phenotypes and othersDemoPathways and Interactions

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Search integration with visual mappingYESDemoYESYESYES

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Mind mapping: Options to visually mark the pathway components via search or browse and clicking with meaningful user selected symbols, colors and shapes over several layersYESsame as above

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Advance search with boolean, fuzzy, range search and specific filtersYESDemoYESYESYESYES

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Batch Query to find pathwyasYESDemoYESYESYESYESYES

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Create interaction network dynamically upon searchNONONOYESYESNONONOYES

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comparison of multiple pathwaysYESDEMONONONOPartiallyNONONONO

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Integrated tools for data grouping, organization and comparisonDemo

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Allows upload of molecules form highthroughput experiments like microarray and proteomicsYESYESYESYESYESYESNONONO

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Allows upload of multiple experimental filesYESNOYESNONONONONONO

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Grouping of the Observations in to meaningful analysis setsYESNONONONONONONONO

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Define custom mapping/overlay color settings for individual groupsYESNONONONONONONONO

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Allows SET operations and comparison between groups of data to find intersection and unique data between groupsYESDemoNONONONONONONONO

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Handle duplicates in the uploaded data sets depending on the observation typesYESNONONONONONONONO

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Filter uploaded data based on user set observation thresholdYES

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Handle multiple observation types ( Fold change, Ratio, Log Ratio, Intensity, p-value)YES

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Upload multiple identifier types for molecular listYESYESFew typesFew typesYESSymbolsNONONO

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Data Visualization on the pathwaysDemo

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Overlay Colors on predefined pathwaysYESYESYESYESYESYESNONONO

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Customize Color and shapes to overlay based on observation thresholdYESNONONONONONONONO

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Overlay symbolYESNONONONONONONONO

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Overlay expression data as ChartsYESNONONONONONONONO

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Overlay expression data as heat mapsYESNONONONONONONONO

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Toggle between monochrome and color pathway diagrams for better visualization of overlaysYES NONONONONONONONO

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Advance navigation options ( Recenter, maintain history of visited position, draw region to zoom into) using mouse and key board shotcutsYESsome of the features are unique to iPAVSsome of the features are unique to iPAVSNOsome of the features are unique to iPAVSsome of the features are unique to iPAVSsome of the features are unique to iPAVSNONO

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Overlay data on multiple pathways simultaneously instead of single pathway, facilitating advanced comparisons between pathwaysYESNONONONONONONONO

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Visually compare multiple pathwaysYESDEMONONONOpartiallyNONONONO

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Perform analysis and compare on multiple pathways simultaneouslyYESDEMONONONONONONONONO

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Pathway analysis ( Gene Set Analysis)

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Dynamically choose pathway sets based on various criterias including pathway role, databases, type etcYESNONONONONONONONO

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Support of various analysis algorithms to find statistically enriched pathwaysYESFishersNOYESNONONO

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Design and Architectural Advantages

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Architecture is designed to easily scale to include future analysis algorithmsYES : iPAVS internally uses RServeNONONONONONONONO

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AIOS (all in one screen) design minimizing degrees of separation between relevant informationYES

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Integration of Data resources with Tools for analysis, data management, comparison and visualizationYES: some of the tools are very unique to iPAVSsome of the tools are very unique to iPAVSsome of the tools are very unique to iPAVSsome of the tools are very unique to iPAVSsome of the tools are very unique to iPAVSsome of the tools are very unique to iPAVS

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Employes SVG (scalable vector graphics: a graphics markup for the web ) for Visualization inherently supported by all modern browserYESNONONONOparticallyNONO