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Eligible Pathways ListCanonical Pathways (signaling) that are currently eligible for Pathway Activity Analysis Ratio Calculations for PathwaysIngenuity Pathway Analysis (IPA) IPA Network Generation AlgorithmIngenuity Pathway Analysis (IPA) Right Click MenuIngenuity Pathway Analysis (IPA) Graph PreferencesIngenuity Pathway Analysis (IPA) CacheIngenuity Pathway Analysis (IPA) BioProfilerIngenuity Pathway Analysis (IPA) | Advanced Analytics BioProfiler Relationship ExportIngenuity Pathway Analysis (IPA) | Relationship Export Add My FindingsIngenuity Pathway Analysis (IPA) | Add My Findings from the Build Tool Comparison analysis heat map for causal networksIngenuity Pathway Analysis (IPA) Causal NetworksIngenuity Pathway Analysis (IPA) | Advanced Analytics - Generate virtual upstream regulators which are networks of regulators My FindingsIngenuity Pathway Analysis (IPA) | My Findings Application PreferencesIngenuity Pathway Analysis (IPA) IsoProfiler FindingsIngenuity Pathway Analysis (IPA) | Examine the detailed relationships between isoforms (splice variants) and known diseases and functions. IPA Network Generation Algorithm WhitepaperIngenuity Pathway Analysis (IPA) | Whitepaper Link Running-IPA-on-WindowsIngenuity Pathway Analysis (IPA) | Running IPA on Windows 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 IPA installerIngenuity Pathway Analysis (IPA) | How to use the IPA client installer IsoProfilerIngenuity Pathway Analysis (IPA) | IsoProfiler displays and enables filtering on transcripts & isoforms in your RNA-seq dataset(s) FAQ - Causal Network AnalysisIngenuity Pathway Analysis (IPA) My Findings OverviewIngenuity Pathway Analysis (IPA) | How to Format and Upload custom findings data file in IPA FAQ - Statistical CalculationIngenuity Pathway Analysis (IPA) IPA Technical RequirementsIngenuity Pathway Analysis (IPA) | IPA Technical Requirements Project ManagerIngenuity Pathway Analysis (IPA) IPA GlossaryIngenuity Pathway Analysis (IPA) Spotfire Integration with IPAIngenuity Pathway Analysis (IPA) IPA Toolbar MenusIngenuity Pathway Analysis (IPA) Dataset and Analysis SearchIngenuity Pathway Analysis (IPA) | Search Project Manager for Analysis and Dataset IPA LegendIngenuity Pathway Analysis (IPA) | Describes the tool bar icons, colors, and more in IPA Accessing and Using Upstream RegulatorsCanonical Pathways for a DatasetCanonical Pathways for a Dataset Isoforms ViewIsoform view on Gene Views Available Canonical PathwaysIngenuity Pathway Analysis (IPA) | Currently Available Canonical Pathways Identifier and Gene Model Source VersionsThe versions of the identifier and gene model databases used in IPA currently Winter IPA Release notes, December 2018Summary of Release Notes Upstream Regulator AnalysisMore info link for URA master table Formatting Your DatasetIngenuity Pathway Analysis (IPA) Upstream Regulators Analysis TutorialIngenuity Pathway Analysis (IPA) Search for Genes TutorialIngenuity Pathway Analysis (IPA) Upload and Analyze Example Data TutorialIngenuity Pathway Analysis (IPA) Data Source FilterCan I use more than one identifier type?A dataset file may contain more than one of the identifier type. If your dataset file has more than one identifier type, select all appropriate identifier types found in the dataset file from the dropdown menu. Human Isoforms View TutorialIngenuity Pathway Analysis (IPA) microRNA Target Filter FAQFAQs about the microRNA Target Filter Visualize Pathways TutorialIngenuity Pathway Analysis (IPA) Data Upload workflowIngenuity Pathway Analysis (IPA) | Data Upload workflow Downstream Effects Analysis TutorialIngenuity Pathway Analysis (IPA) upload-analyze-your-data-tutorialIngenuity Pathway Analysis (IPA) Filtered and Annotated DatasetsIngenuity Pathway Analysis (IPA) FAQs on HumanCyc DatabaseFAQs on HumanCyc Database Biomarker AnalysisFile Format Specification for Uploading Data with Experimental Metadata into IPAIngenuity Pathway Analysis (IPA) | Experimental Metadata Specifications FAQ - Ingenuity Knowledge BaseBatch UploadIngenuity Pathway Analysis (IPA) | How to upload multiple datasets as a batch IPA-Tox Analysis WorkflowMAP-Molecule Activity PredictorAnalysis Results TutorialIngenuity Pathway Analysis (IPA) Data Upload definitionsIngenuity Pathway Analysis (IPA) | Definitions for the Data Upload workflow Molecule ViewDescription of the molecule tab in Core Analysis Listing of NetworksListing of Networks Accessing and Using Downstream Effects AnalysisVersion number or Date of Third Party DatabasesAnalysis 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. How can I see the pathways related to this analysisHow can I see the pathways related to this analysis? FAQ - Analysis MatchDefining the Reference SetIngenuity Pathway Analysis (IPA) Pathway Activity OverlayPathway Activity Overlay (part of Pathway Activity Analysis performed within a core analysis) Reference set array platformsReference Set Array platforms in IPA Pathway and Network Explorer ToolbarList AnalysisRegulator EffectsRegulator Effects Advanced SettingsDescribes the Advanced Settings available to customize a Core Analysis Legend ToolDescribes how to add a legend to a Path Designer pathway Interpreting the Upstream Regulator ResultsIngenuity Knowledge BaseHow are networks calculated?How are networks calculated? How can I find research papers on a given topic?How can I find research papers on a given topic? Overlapping Canonical PathwaysCanonical Pathways OverviewAn Overview of the Canonical Pathways in IPA Interpreting Functional Analysis ResultsShared With OthersCell ArtDescription of the Cell Art tool of Path Designer Introduction to IPA Functional AnalysisOverlapping NetworkAn overview of Overlapping Networks Network Explorer ToolNetworks View Analysis Summary PageAnalysis Summary Page Reviewing Mapped IdentifiersComparison analysis heat map for canonical pathwaysComparison analysis heat map for canonical pathways Pathway FilteringDescription of the filters used in Build tools Metadata keys used in IPADescription of the existing metadata keys you can use in IPA to annotate your own datasets Highlight or SelectOverlay tool to identify nodes or relationships in networks and pathways and then act upon them HighlightObsolete, please see Highlight or Select Core Analysis SetupDescription of how to set up a Core Analysis Pre-Analysis FilteringDescription of the filters available to pre-filter a Core Analysis 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 PathwayGrowFunction and DiseaseSpecialized Features indexIPA on WindowsRunning IPA on Windows What are the guidelines for citing IPA in publications?microRNA Target Filter WorkflowWorkflow describing how to use the MicroRNA-Target Filter ConnectPath ExplorerPath Explorer Analyzing Genomic Regions from UCSC Genome BrowserHow Upstream Regulator Analysis Can Help YouFunctional Categories DefinitionsDisease or Function ViewView/Edit PreferencesPathway ReportGene ViewChemViewMechanistic NetworksMechanistic Networks Mechanistic Network ViewerExport All Analysis ResultsExport All Inhibited phosphoproteinsOverlay Analyses, Datasets, and ListsCore Analysis TypesDescription of the types of Core Analysis types you can run in IPA Variant gain loss and ACMG classificationImporting and using variant loss/gain and ACMG classification datasets High Resolution IPA LegendHigh Resolution Images of IPA Legend Batch AnalysisHow to run multiple analysis as a batch Comparison analysis heat map for Diseases and FunctionsComparison Analysis heat map for Disease and Functions Grow to Diseases and FunctionsGrow to Diseases and Functions Comparison analysis heat map for upstream analysisComparison analysis heat map for upstream analysis Molecule SummaryPreview of basic information about a molecule Layout OptionsChoose different ways to arrange nodes on a network or a my pathway PathTracerPathTracer PathTracerPathTracer AnnotationsImporting PathwaysCollaboration Workspace CWSTrim and KeepAdd Molecules and RelationshipsAdvanced SearchFunction and Disease SearchManaging InvitationsMoleculesGene and Chemical SearchRelationshipsPathways and Tox List SearchShared With MeExporting Molecule ListsPassword ResetPassword Reset Filter PreferencesCanonical PathwayGene View, Disease or Function View, Chem ViewGene view Disease or Function view Chem view Tox ListsCanonical Pathways for ComparisonsUsing ListsBest Practice - Expression Data AnalysisCreating and Saving My ListsMy Pathway (Tool)Species FilterRelationship Types FilterBiofluids FilterTox FunctionsLine and Relationship ToolTissue and Cell Line FilterPublication Date Range FilterDisease FilterBiomarker FilterDrugBackgroundText ToolMy ListPath Designer Workflow OverviewMolecules in Path DesignerWhat can I do with the search results?What can I do with the search results? Core, Tox and Metabolomic AnalysesTox ListBiomarkersDifferences 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 Analyzed DatasetHow to Overlay Analyses, Datasets, and Lists Comparing BiomarkersHow can Functional Analysis help youIPA-Tox Analysis OverviewClustering of miRNA in IPAPrintingMolecule Types FilterPublication GuidelinesNGS RNA SequencingConfidence Level Filter - microRNAWhat other tools does IPA work with?What other tools does IPA work with? Can 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 How many genes are up or down regulated in a pathway?How many genes are up or down regulated in a pathway? FAQ - microRNAFAQs on the miRNA targeting relationships in IPA What kind of data should I have?What kind of data should I have? How do I add my own custom genes and connections?How do I add my own custom genes and connections? Biomarker DefinitionWhat species identifiers are accepted for analysis by IPA?What species identifiers are accepted for analysis by IPA? Downstream Effect Analysis: Evidence for EffectMore info link for Downstream Effect Analysis Evidence for Effect Upstream Regulator Analysis Evidence for EffectCan I suggest articles and findings to add?Can I suggest articles and findings to add? Creating a DatasetMy file won’t open/upload correctly. What should I do?My file won’t open/upload correctly. What should I do? Core, Tox and Metabolomic Comparison AnalysisPlease 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. 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