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Isoforms View


Isoform view on Gene Views

Available Canonical Pathways


Ingenuity Pathway Analysis (IPA) | Currently Available Canonical Pathways

Identifier and Gene Model Source Versions


The versions of the identifier and gene model databases used in IPA currently

Winter IPA Release notes, December 2018


Summary of Release Notes

Upstream Regulator Analysis


More info link for URA master table

Formatting Your Dataset


Ingenuity Pathway Analysis (IPA)

Upstream Regulators Analysis Tutorial


Ingenuity Pathway Analysis (IPA)

Search for Genes Tutorial


Ingenuity Pathway Analysis (IPA)

Upload and Analyze Example Data Tutorial


Ingenuity Pathway Analysis (IPA)

Data Source Filter


Can 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 Tutorial


Ingenuity Pathway Analysis (IPA)

microRNA Target Filter FAQ


FAQs about the microRNA Target Filter

Visualize Pathways Tutorial


Ingenuity Pathway Analysis (IPA)

Data Upload workflow


Ingenuity Pathway Analysis (IPA) | Data Upload workflow

Downstream Effects Analysis Tutorial


Ingenuity Pathway Analysis (IPA)

upload-analyze-your-data-tutorial


Ingenuity Pathway Analysis (IPA)

Filtered and Annotated Datasets


Ingenuity Pathway Analysis (IPA)

FAQs on HumanCyc Database


FAQs on HumanCyc Database

Biomarker Analysis


File Format Specification for Uploading Data with Experimental Metadata into IPA


Ingenuity Pathway Analysis (IPA) | Experimental Metadata Specifications

FAQ - Ingenuity Knowledge Base


FAQ - Causal Network Analysis


Batch Upload


Ingenuity Pathway Analysis (IPA) | How to upload multiple datasets as a batch

IPA-Tox Analysis Workflow


MAP-Molecule Activity Predictor


Analysis Results Tutorial


Ingenuity Pathway Analysis (IPA)

Data Upload definitions


Ingenuity Pathway Analysis (IPA) | Definitions for the Data Upload workflow

IPA Technical Requirements


IPA Technical Requirements

Molecule View


Description of the molecule tab in Core Analysis

Listing of Networks


Listing of Networks

Accessing and Using Downstream Effects Analysis


Version number or Date of Third Party Databases


Analysis Match


Core 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 analysis


How can I see the pathways related to this analysis?

FAQ - Analysis Match


FAQ - Statistical Calculation


Defining the Reference Set


Ingenuity Pathway Analysis (IPA)

My Findings Overview


How to Format and Upload custom findings data file in IPA

Canonical Pathways for a Dataset


Canonical Pathways for a Dataset

Pathway Activity Overlay


Pathway Activity Overlay (part of Pathway Activity Analysis performed within a core analysis)

Running-IPA-on-Mac


This article is about running IPA on a Mac. FAQ, Caches and Version of Mac OS and Java

Reference set array platforms


Reference Set Array platforms in IPA

Pathway and Network Explorer Toolbar


IPA Legend


Describes the tool bar icons, colors, and more in IPA

List Analysis


Regulator Effects


Regulator Effects

Accessing and Using Upstream Regulators


Advanced Settings


Describes the Advanced Settings available to customize a Core Analysis

Legend Tool


Describes how to add a legend to a Path Designer pathway

Interpreting the Upstream Regulator Results


Ingenuity Knowledge Base


How 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 Pathways


Canonical Pathways Overview


An Overview of the Canonical Pathways in IPA

Interpreting Functional Analysis Results


Shared With Others


Cell Art


Description of the Cell Art tool of Path Designer

Eligible Pathways List


Canonical Pathways that are currently eligible for Pathway Activity Analysis

Introduction to IPA Functional Analysis


Overlapping Network


An overview of Overlapping Networks

Network Explorer Tool


Networks View

Analysis Summary Page


Analysis Summary Page

Reviewing Mapped Identifiers


Comparison analysis heat map for canonical pathways


Comparison analysis heat map for canonical pathways

Pathway Filtering


Description of the filters used in Build tools

Metadata keys used in IPA


Description of the existing metadata keys you can use in IPA to annotate your own datasets

Highlight or Select


Overlay tool to identify nodes or relationships in networks and pathways and then act upon them

Highlight


Obsolete, please see Highlight or Select

Core Analysis Setup


Description of how to set up a Core Analysis

Pre-Analysis Filtering


Description of the filters available to pre-filter a Core Analysis

Exporting References


How can I share data with others?


How can I share data with others?

IsoProfiler


IsoProfiler displays and enables filtering on transcripts & isoforms in your RNA-seq dataset(s)

Exporting Images


Cuffdiff file import


Uploading Cuffdiff RNA-Seq files as datasets in IPA

IPA installer


How to use the IPA client installer

Application Preferences


Exploring Upstream Regulators Results in a Pathway


Grow


Function and Disease


Specialized Features index


IPA on Windows


Running IPA on Windows

What are the guidelines for citing IPA in publications?


Running-IPA-on-Windows


Running IPA on Windows

microRNA Target Filter Workflow


Workflow describing how to use the MicroRNA-Target Filter

Connect


Path Explorer


Path Explorer

Analyzing Genomic Regions from UCSC Genome Browser


How Upstream Regulator Analysis Can Help You


Functional Categories Definitions


Disease or Function View


View/Edit Preferences


Pathway Report


Gene View


ChemView


IPA Network Generation Algorithm Whitepaper


Whitepaper Link

Mechanistic Networks


Mechanistic Networks

Mechanistic Network Viewer


Export All Analysis Results


Export All

Inhibited phosphoproteins


IsoProfiler Findings


Examine the detailed relationships between isoforms (splice variants) and known diseases and functions.

BioProfiler


Advanced Analytics BioProfiler

Core Analysis Types


Description of the types of Core Analysis types you can run in IPA

Variant gain loss and ACMG classification


Importing and using variant loss/gain and ACMG classification datasets

Overlay Analyses, Datasets, and Lists


High Resolution IPA Legend


High Resolution Images of IPA Legend

Batch Analysis


How to run multiple analysis as a batch

My Findings


My Findings

Dataset and Analysis Search


Search Project Manager for Analysis and Dataset

Comparison analysis heat map for Diseases and Functions


Comparison Analysis heat map for Disease and Functions

Causal Networks


Advanced Analytics - Generate virtual upstream regulators which are networks of regulators

Add My Findings


Add My Findings from the Build Tool

Comparison analysis heat map for upstream analysis


Comparison analysis heat map for upstream analysis

Grow to Diseases and Functions


Grow to Diseases and Functions

Comparison analysis heat map for causal networks


Molecule Summary


Preview of basic information about a molecule

Layout Options


Choose different ways to arrange nodes on a network or a my pathway

PathTracer


PathTracer

PathTracer


PathTracer

Relationship Export


Relationship Export

Annotations


Importing Pathways


Collaboration Workspace CWS


Trim and Keep


Add Molecules and Relationships


Advanced Search


Function and Disease Search


Managing Invitations


Molecules


Ratio Calculations for Pathways


Gene and Chemical Search


Cache


Pathways and Tox List Search


Shared With Me


Relationships


IPA Toolbar Menus


Project Manager


Exporting Molecule Lists


Password Reset


Password Reset

Graph Preferences


Filter Preferences


Canonical Pathway


Gene View, Disease or Function View, Chem View


Gene view Disease or Function view Chem view

Tox Lists


Canonical Pathways for Comparisons


Using Lists


Best Practice - Expression Data Analysis


Creating and Saving My Lists


My Pathway (Tool)


Species Filter


Relationship Types Filter


Biofluids Filter


Tox Functions


Line and Relationship Tool


Tissue and Cell Line Filter


Publication Date Range Filter


Disease Filter


Biomarker Filter


Drug


Background


Text Tool


My List


Path Designer Workflow Overview


Molecules in Path Designer


What can I do with the search results?


What can I do with the search results?

Core, Tox and Metabolomic Analyses


Tox List


Biomarkers


Differences between the search tabs


What’s the difference between the search tabs?

Searching for pathways associated with a gene


How do I search for pathways associated with a gene?

Emailing Interactive Pathways


Right Click Menu


SNP Content


Compare Data


Compare data tool

Analyzed Dataset


How to Overlay Analyses, Datasets, and Lists

Comparing Biomarkers


How can Functional Analysis help you


IPA Network Generation Algorithm


IPA-Tox Analysis Overview


Clustering of miRNA in IPA


Printing


Molecule Types Filter


Spotfire Integration with IPA


Publication Guidelines


NGS RNA Sequencing


Confidence Level Filter - microRNA


What 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 Pathways


Overview 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 - microRNA


FAQs 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 Definition


What species identifiers are accepted for analysis by IPA?


What species identifiers are accepted for analysis by IPA?

Downstream Effect Analysis: Evidence for Effect


More info link for Downstream Effect Analysis Evidence for Effect

Upstream Regulator Analysis Evidence for Effect


Can I suggest articles and findings to add?


Can I suggest articles and findings to add?

Creating a Dataset


My 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 Analysis


Please select one of the sub categories under Uploading and Analyzing Data


A 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.

IPA Glossary