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Summer IPA Release notes, June 2020Ingenuity Pathway Analysis (IPA) | Release Notes Version number or Date of Third Party DatabasesIngenuity Pathway Analysis (IPA) Analysis Results TutorialIngenuity Pathway Analysis (IPA) Analysis MatchCore Analysis tab that displays related analyses (among thousands of curated analyses) based on shared pattern of predicted "entities" like Upstream Regulators, Canonical Pathways, etc.) IPA Activity PlotIngenuity Pathway Analysis (IPA) | Plot of the predicted activity of one entity across >65,000 OmicSoft analyses. Entities include Canonical Pathways, Upstream Regulators / Causal Network master regulators, and Diseases and Functions. Available Canonical PathwaysIngenuity Pathway Analysis (IPA) | Currently Available Canonical Pathways Importing PathwaysEligible Pathways ListIngenuity Pathway Analysis (IPA) | Canonical Pathways that are currently eligible for Pathway Activity Analysis Identifier and Gene Model Source VersionsIngenuity Pathway Analysis (IPA) | The versions of the identifier and gene model databases used in IPA currently Batch UploadIngenuity Pathway Analysis (IPA) | How to upload multiple datasets as a batch Downstream Effects Analysis TutorialIngenuity Pathway Analysis (IPA) Accessing and Using Downstream Effects AnalysisIngenuity Pathway Analysis (IPA) My file won’t open/upload correctly. What should I do?My file won’t open/upload correctly. What should I do? Analyzed DatasetHow to Overlay Analyses, Datasets, and Lists NGS RNA SequencingIPA Technical RequirementsIngenuity Pathway Analysis (IPA) | IPA Technical Requirements Formatting Your DatasetIngenuity Pathway Analysis (IPA) Data Upload workflowIngenuity Pathway Analysis (IPA) | Data Upload workflow Canonical Pathways for a DatasetIngenuity Pathway Analysis (IPA) | Canonical Pathways for a Dataset MAP-Molecule Activity PredictorIngenuity Pathway Analysis (IPA) Core, Tox and Metabolomics Comparison AnalysisIngenuity Pathway Analysis (IPA) IPA LegendIngenuity Pathway Analysis (IPA) | Describes the tool bar icons, colors, and more in IPA Search for Genes TutorialIngenuity Pathway Analysis (IPA) Creating a DatasetMolecule ViewIngenuity Pathway Analysis (IPA) | Description of the molecule tab in Core Analysis Accessing and Using Upstream RegulatorsHow many genes are up or down regulated in a pathway?How many genes are up-or-down-regulated in a pathway? Molecule SummaryPreview of basic information about a molecule Running-IPA-on-WindowsIngenuity Pathway Analysis (IPA) | Running IPA on Windows Specialized Features indexIPA Video TutorialsIngenuity Pathway Analysis (IPA) | Summary of available video tutorials for IPA Comparison analysis heat map for canonical pathwaysIngenuity Pathway Analysis (IPA) | Comparison analysis heat map for canonical pathways Project ManagerIngenuity Pathway Analysis (IPA) FAQ - Statistical CalculationIngenuity Pathway Analysis (IPA) My Findings OverviewIngenuity Pathway Analysis (IPA) | How to Format and Upload custom findings data file in IPA Phosphorylation AnalysisCore Analysis of a phosphorylation dataset File Format Specification for Uploading Data with Experimental Metadata into IPAIngenuity Pathway Analysis (IPA) | Experimental Metadata Specifications Canonical Pathways OverviewAn Overview of the Canonical Pathways in IPA IPA-Tox Analysis OverviewHow can I see the pathways related to this analysisHow can I see the pathways related to this analysis? Pathway Activity OverlayIngenuity Pathway Analysis (IPA) | Pathway Activity Overlay (part of Pathway Activity Analysis performed within a core analysis) Can I use more than one identifier type?Ingenuity Pathway Analysis (IPA) | IPA can accept a dataset file that contains more than one identifier type, either in one column or in multiple columns. Overlay Analyses, Datasets, and Listsupload-analyze-your-data-tutorialIngenuity Pathway Analysis (IPA) IsoProfiler FindingsIngenuity Pathway Analysis (IPA) | Examine the detailed relationships between isoforms (splice variants) and known diseases and functions. IsoProfilerIngenuity Pathway Analysis (IPA) | IsoProfiler displays and enables filtering on transcripts & isoforms in your RNA-seq dataset(s) How are networks calculated?How are networks calculated? FAQ - microRNAFAQs on the miRNA targeting relationships in IPA Interpreting the Upstream Regulator ResultsWhat kind of data should I have?What kind of data should I have? Advanced SettingsDescribes the Advanced Settings available to customize a Core Analysis Ratio Calculations for PathwaysIngenuity Pathway Analysis (IPA) Defining the Reference SetMoleculesTox FunctionsAnalyzing Genomic Regions from UCSC Genome BrowserHow Upstream Regulator Analysis Can Help YouIPA-Tox Analysis WorkflowIngenuity Pathway Analysis (IPA) IPA on WindowsRunning IPA on Windows microRNA Target Filter WorkflowWorkflow describing how to use the MicroRNA-Target Filter Path ExplorerPath Explorer Interpreting Functional Analysis ResultsFunction and DiseasePre-Analysis FilteringDescription of the filters available to pre-filter a Core Analysis Core Analysis SetupDescription of how to set up a Core Analysis HighlightObsolete, please see Highlight or Select Highlight or SelectOverlay tool to identify nodes or relationships in networks and pathways and then act upon them Metadata keys used in IPADescription of the existing metadata keys you can use in IPA to annotate your own datasets Introduction to IPA Functional AnalysisShared With OthersData Source FilterIngenuity Pathway Analysis (IPA) Upstream Regulator AnalysisIngenuity Pathway Analysis (IPA) | More info link for URA master table GrowConnectBiomarker AnalysisIngenuity Pathway Analysis (IPA) microRNA Target Filter FAQIngenuity Pathway Analysis (IPA) | FAQs about the microRNA Target Filter What are the guidelines for citing IPA in publications?Running-IPA-on-MacIngenuity Pathway Analysis (IPA) | This article is about running IPA on a Mac. FAQ, Caches and Version of Mac OS and Java Collaboration Workspace CWSIngenuity Pathway Analysis (IPA) Comparison analysis heat map for upstream analysisIngenuity Pathway Analysis (IPA) | Comparison analysis heat map for upstream analysis Upstream Regulators Analysis TutorialIngenuity Pathway Analysis (IPA) Visualize Pathways TutorialIngenuity Pathway Analysis (IPA) FAQ - Analysis MatchIngenuity Pathway Analysis (IPA) Publication GuidelinesIngenuity Pathway Analysis (IPA) FAQ - Ingenuity Knowledge BaseCore, Tox and Metabolomic AnalysesIngenuity Pathway Analysis (IPA) FAQs on HumanCyc DatabaseIngenuity Pathway Analysis (IPA) | FAQs on HumanCyc Database Data Upload definitionsIngenuity Pathway Analysis (IPA) | Definitions for the Data Upload workflow Listing of NetworksIngenuity Pathway Analysis (IPA) | Listing of Networks Isoforms ViewIngenuity Pathway Analysis (IPA) | Isoform view on Gene Views Comparison analysis heat map for Diseases and FunctionsIngenuity Pathway Analysis (IPA) | Comparison Analysis heat map for Disease and Functions How to Chart Diseases and Functions Comparison Data in ExcelIngenuity Pathway Analysis (IPA) Spotfire Integration with IPAIngenuity Pathway Analysis (IPA) How to Chart Comparison Analysis Using ExcelIngenuity Pathway Analysis (IPA) IPA Network Generation AlgorithmIngenuity Pathway Analysis (IPA) Right Click MenuIngenuity Pathway Analysis (IPA) CacheIngenuity Pathway Analysis (IPA) Graph PreferencesIngenuity Pathway Analysis (IPA) Causal NetworksIngenuity Pathway Analysis (IPA) | Advanced Analytics - Generate virtual upstream regulators which are networks of regulators Relationship ExportIngenuity Pathway Analysis (IPA) | Relationship Export My FindingsIngenuity Pathway Analysis (IPA) | My Findings Add My FindingsIngenuity Pathway Analysis (IPA) | Add My Findings from the Build Tool BioProfilerIngenuity Pathway Analysis (IPA) | Advanced Analytics BioProfiler Comparison analysis heat map for causal networksIngenuity Pathway Analysis (IPA) IPA Network Generation Algorithm WhitepaperIngenuity Pathway Analysis (IPA) | Whitepaper Link Application PreferencesIngenuity Pathway Analysis (IPA) IPA installerIngenuity Pathway Analysis (IPA) | How to use the IPA client installer FAQ - Causal Network AnalysisIngenuity Pathway Analysis (IPA) IPA Toolbar MenusIngenuity Pathway Analysis (IPA) IPA GlossaryIngenuity Pathway Analysis (IPA) Dataset and Analysis SearchIngenuity Pathway Analysis (IPA) | Search Project Manager for Analysis and Dataset Upload and Analyze Example Data TutorialIngenuity Pathway Analysis (IPA) Human Isoforms View TutorialIngenuity Pathway Analysis (IPA) Filtered and Annotated DatasetsIngenuity Pathway Analysis (IPA) Reference set array platformsReference Set Array platforms in IPA Pathway and Network Explorer ToolbarList AnalysisRegulator EffectsRegulator Effects Legend ToolDescribes how to add a legend to a Path Designer pathway Ingenuity Knowledge BaseHow can I find research papers on a given topic?How can I find research papers on a given topic? Overlapping Canonical PathwaysCell ArtDescription of the Cell Art tool of Path Designer Overlapping NetworkAn overview of Overlapping Networks Network Explorer ToolNetworks View Analysis Summary PageAnalysis Summary Page Reviewing Mapped IdentifiersPathway FilteringDescription of the filters used in Build tools Node Overlay filterDescribes the filter that is used in certain overlay and build tools Exporting ReferencesHow can I share data with others?How can I share data with others? Exporting ImagesCuffdiff file importUploading Cuffdiff RNA-Seq files as datasets in IPA Exploring Upstream Regulators Results in a PathwayFunctional Categories DefinitionsView/Edit PreferencesGene ViewPathway ReportDisease or Function ViewMechanistic NetworksMechanistic Networks ChemViewExport All Analysis ResultsExport All Mechanistic Network ViewerInhibited phosphoproteinsVariant gain loss and ACMG classificationImporting and using variant loss/gain and ACMG classification datasets Core Analysis TypesDescription of the types of Core Analysis types you can run in IPA High Resolution IPA LegendHigh Resolution Images of IPA Legend Batch AnalysisHow to run multiple analysis as a batch Grow to Diseases and FunctionsGrow to Diseases and Functions PathTracerPathTracer Layout OptionsChoose different ways to arrange nodes on a network or a my pathway AnnotationsPathTracerPathTracer Advanced SearchTrim and KeepAdd Molecules and RelationshipsManaging InvitationsGene and Chemical SearchFunction and Disease SearchPathways and Tox List SearchShared With MeRelationshipsPassword ResetPassword Reset Gene View, Disease or Function View, Chem ViewGene view Disease or Function view Chem view Filter PreferencesExporting Molecule ListsCanonical PathwayCanonical Pathways for ComparisonsTox ListsMy Pathway (Tool)Creating and Saving My ListsUsing ListsBest Practice - Expression Data AnalysisRelationship Types FilterSpecies FilterBiofluids FilterTissue and Cell Line FilterDisease FilterLine and Relationship ToolPublication Date Range FilterDrugBiomarker FilterBackgroundMy ListText ToolMolecules in Path DesignerPath Designer Workflow OverviewTox ListWhat can I do with the search results?What can I do with the search results? BiomarkersDifferences between the search tabsWhat’s the difference between the search tabs? Searching for pathways associated with a geneHow do I search for pathways associated with a gene? Emailing Interactive PathwaysSNP ContentCompare DataCompare data tool Comparing BiomarkersHow can Functional Analysis help youPrintingMolecule Types FilterClustering of miRNA in IPACan I do an analysis with a list of genes only?Can I do an analysis with a list of genes only? My PathwaysOverview of MY Pathways Confidence Level Filter - microRNAWhat other tools does IPA work with?What other tools does IPA work with? How do I add my own custom genes and connections?How do I add my own custom genes and connections? What species identifiers are accepted for analysis by IPA?What species identifiers are accepted for analysis by IPA? Biomarker DefinitionDownstream Effect Analysis: Evidence for EffectMore info link for Downstream Effect Analysis Evidence for Effect Can I suggest articles and findings to add?Can I suggest articles and findings to add? Upstream Regulator Analysis Evidence for EffectPlease select one of the sub categories under Uploading and Analyzing DataA comprehensive set of feature descriptions is available in the sub categories under Uploading and Analyzing Data. Select the topic you are interested in and the list of available articles will appear in this space. |