Ingenuity Pathway Analysis (IPA)

Canonical Pathways for a Dataset

Ingenuity Pathway Analysis (IPA) | Canonical Pathways for a Dataset

Comparison analysis heat map for upstream analysis

Ingenuity Pathway Analysis (IPA) | Comparison analysis heat map for upstream analysis

Upstream Regulators Analysis Tutorial

Ingenuity Pathway Analysis (IPA)

MAP-Molecule Activity Predictor

Ingenuity Pathway Analysis (IPA)

Fall IPA Release notes, September 2019

Ingenuity Pathway Analysis (IPA) | Release Notes

Version number or Date of Third Party Databases

Ingenuity Pathway Analysis (IPA)

Eligible Pathways List

Ingenuity Pathway Analysis (IPA) | Canonical Pathways (signaling) that are currently eligible for Pathway Activity Analysis

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.

Available Canonical Pathways

Ingenuity Pathway Analysis (IPA) | Currently Available Canonical Pathways

IPA Legend

Ingenuity Pathway Analysis (IPA) | Describes the tool bar icons, colors, and more in IPA

FAQ - Ingenuity Knowledge Base

Comparison analysis heat map for canonical pathways

Ingenuity Pathway Analysis (IPA) | Comparison analysis heat map for canonical pathways

Core, Tox and Metabolomic Analyses

Ingenuity Pathway Analysis (IPA)

FAQs on HumanCyc Database

Ingenuity Pathway Analysis (IPA) | FAQs on HumanCyc Database

Data Upload workflow

Ingenuity Pathway Analysis (IPA) | Data Upload workflow

Data Upload definitions

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

Identifier and Gene Model Source Versions

Ingenuity Pathway Analysis (IPA) | The versions of the identifier and gene model databases used in IPA currently

Analyzed Dataset

How to Overlay Analyses, Datasets, and Lists

Upstream Regulator Analysis

Ingenuity Pathway Analysis (IPA) | More info link for URA master table

Molecule View

Ingenuity Pathway Analysis (IPA) | Description of the molecule tab in Core Analysis

Listing of Networks

Ingenuity Pathway Analysis (IPA) | Listing of Networks

Core, Tox and Metabolomic Comparison Analysis

Ingenuity Pathway Analysis (IPA)

Accessing and Using Downstream Effects Analysis

Ingenuity Pathway Analysis (IPA)

microRNA Target Filter FAQ

Ingenuity Pathway Analysis (IPA) | FAQs about the microRNA Target Filter

IPA Video Tutorials

Ingenuity Pathway Analysis (IPA) | Summary of available video tutorials for IPA

Pathway Activity Overlay

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

Isoforms View

Ingenuity Pathway Analysis (IPA) | Isoform view on Gene Views

Can I use more than one identifier type?

Ingenuity Pathway Analysis (IPA) | 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.

Comparison analysis heat map for Diseases and Functions

Ingenuity Pathway Analysis (IPA) | Comparison Analysis heat map for Disease and Functions

How to Chart Diseases and Functions Comparison Data in Excel

Ingenuity Pathway Analysis (IPA)

FAQ - Statistical Calculation

Ingenuity Pathway Analysis (IPA)

Spotfire Integration with IPA

Ingenuity Pathway Analysis (IPA)

How to Chart Comparison Analysis Using Excel

Ingenuity Pathway Analysis (IPA)

Running-IPA-on-Mac

Ingenuity Pathway Analysis (IPA) | This article is about running IPA on a Mac. FAQ, Caches and Version of Mac OS and Java

IPA Network Generation Algorithm

Ingenuity Pathway Analysis (IPA)

Right Click Menu

Ingenuity Pathway Analysis (IPA)

Cache

Ingenuity Pathway Analysis (IPA)

Ratio Calculations for Pathways

Ingenuity Pathway Analysis (IPA)

Graph Preferences

Ingenuity Pathway Analysis (IPA)

Causal Networks

Ingenuity Pathway Analysis (IPA) | Advanced Analytics - Generate virtual upstream regulators which are networks of regulators

Relationship Export

Ingenuity Pathway Analysis (IPA) | Relationship Export

My Findings

Ingenuity Pathway Analysis (IPA) | My Findings

Add My Findings

Ingenuity Pathway Analysis (IPA) | Add My Findings from the Build Tool

BioProfiler

Ingenuity Pathway Analysis (IPA) | Advanced Analytics BioProfiler

Comparison analysis heat map for causal networks

Ingenuity Pathway Analysis (IPA)

IPA Network Generation Algorithm Whitepaper

Ingenuity Pathway Analysis (IPA) | Whitepaper Link

Running-IPA-on-Windows

Ingenuity Pathway Analysis (IPA) | Running IPA on Windows

Application Preferences

Ingenuity Pathway Analysis (IPA)

IsoProfiler Findings

Ingenuity Pathway Analysis (IPA) | Examine the detailed relationships between isoforms (splice variants) and known diseases and functions.

IsoProfiler

Ingenuity Pathway Analysis (IPA) | IsoProfiler displays and enables filtering on transcripts & isoforms in your RNA-seq dataset(s)

IPA installer

Ingenuity Pathway Analysis (IPA) | How to use the IPA client installer

My Findings Overview

Ingenuity Pathway Analysis (IPA) | How to Format and Upload custom findings data file in IPA

IPA Technical Requirements

Ingenuity Pathway Analysis (IPA) | IPA Technical Requirements

FAQ - Causal Network Analysis

Ingenuity Pathway Analysis (IPA)

Project Manager

Ingenuity Pathway Analysis (IPA)

IPA Glossary

Ingenuity Pathway Analysis (IPA)

IPA Toolbar Menus

Ingenuity Pathway Analysis (IPA)

Dataset and Analysis Search

Ingenuity Pathway Analysis (IPA) | Search Project Manager for Analysis and Dataset

Accessing and Using Upstream Regulators

License Errors: What does "The server does not have a license for this product" mean?

CLC Genomics Workbench

License Errors: What does "Unknown License-ID" mean?

CLC Genomics Workbench

License Errors: What does "Error code: LMX_FILE_READ_ERROR" mean?

CLC Genomics Workbench

License Errors: What does "The license is not valid..." mean?

CLC Genomics Workbench

License Errors: What does "Version not covered by license" mean?

CLC Genomics Workbench

Search for Genes Tutorial

Ingenuity Pathway Analysis (IPA)

Upload and Analyze Example Data Tutorial

Ingenuity Pathway Analysis (IPA)

Human Isoforms View Tutorial

Ingenuity Pathway Analysis (IPA)

Filtered and Annotated Datasets

Ingenuity Pathway Analysis (IPA)

upload-analyze-your-data-tutorial

Ingenuity Pathway Analysis (IPA)

Downstream Effects Analysis Tutorial

Ingenuity Pathway Analysis (IPA)

File Format Specification for Uploading Data with Experimental Metadata into IPA

Ingenuity Pathway Analysis (IPA) | Experimental Metadata Specifications

Batch Upload

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

Analysis Results Tutorial

Ingenuity Pathway Analysis (IPA)

How can I see the pathways related to this analysis

How can I see the pathways related to this analysis?

Defining the Reference Set

Ingenuity Pathway Analysis (IPA)

Reference set array platforms

Reference Set Array platforms in IPA

Pathway and Network Explorer Toolbar

List Analysis

Regulator Effects

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 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

License Errors: What does LMX_NOT_NETWORK_FEATURE in the Workbench mean?

CLC Genomics Workbench

License Errors: What does "The requested license order is not available for the specified Host ID" mean?

CLC Genomics Workbench

License Errors: What does "Unable to connect to license server" mean?

CLC Genomics Workbench

License Errors: What does "Your license has expired" mean?

CLC Genomics Workbench

License Errors: What does "XF Error: Rejected actively from license server!" mean?

CLC Genomics Workbench

License Errors: What does "The License Web-Service could not be contacted. Unknown host: secure.clcbio.com" mean?

CLC Genomics Workbench

License Errors: What does "No more licenses available" mean (network license)?

CLC Genomics Workbench

License Errors: What does "Your license can not be used on a Terminal Server" mean (with static license)?

CLC Genomics Workbench

License Errors: What does "No valid application license could be found" mean after the jobs are submitted to the grid?

CLC Genomics Workbench

Cell Art

Description of the Cell Art tool of Path Designer

How can I keep the input sample name in the extracted consensus sequences from mappings?

CLC Genomics Workbench

Introduction to IPA Functional Analysis

Overlapping Network

An overview of Overlapping Networks

Network Explorer Tool

Networks View

Analysis Summary Page

Reviewing Mapped Identifiers

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

Node Overlay filter

Describes the filter that is used in certain overlay and build tools

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?

Exporting Images

Cuffdiff file import

Uploading Cuffdiff RNA-Seq files as datasets in IPA

Exploring Upstream Regulators Results in a Pathway

Function and Disease

Specialized Features index

IPA on Windows

Running IPA on Windows

What are the guidelines for citing IPA in publications?

microRNA Target Filter Workflow

Workflow describing how to use the MicroRNA-Target Filter

Path Explorer

Analyzing Genomic Regions from UCSC Genome Browser

How Upstream Regulator Analysis Can Help You

Functional Categories Definitions

View/Edit Preferences

Gene View

Pathway Report

Disease or Function View

Mechanistic Networks

ChemView

Export All Analysis Results

Export All

Mechanistic Network Viewer

Inhibited phosphoproteins

Variant gain loss and ACMG classification

Importing and using variant loss/gain and ACMG classification datasets

Core Analysis Types

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

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

Grow to Diseases and Functions

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

Annotations

Importing Pathways

PathTracer

Advanced Search

Trim and Keep

Add Molecules and Relationships

Managing Invitations

Molecules

Gene and Chemical Search

Function and Disease Search

Pathways and Tox List Search

Shared With Me

Relationships

Password Reset

Gene View, Disease or Function View, Chem View

Gene view Disease or Function view Chem view

Filter Preferences

Exporting Molecule Lists

Canonical Pathway

Canonical Pathways for Comparisons

Tox Lists

My Pathway (Tool)

Creating and Saving My Lists

Using Lists

Best Practice - Expression Data Analysis

Relationship Types Filter

Tox Functions

Species Filter

Biofluids Filter

Tissue and Cell Line Filter

Disease Filter

Line and Relationship Tool

Publication Date Range Filter

Drug

Biomarker Filter

Background

My List

Text Tool

Molecules in Path Designer

Path Designer Workflow Overview

Tox List

What can I do with the search results?

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

SNP Content

Compare Data

Compare data tool

Comparing Biomarkers

IPA-Tox Analysis Overview

How can Functional Analysis help you

Printing

Molecule Types Filter

NGS RNA Sequencing

Clustering of miRNA in IPA

Can I do an analysis with a list of genes only?

My Pathways

Overview of MY Pathways

Confidence Level Filter - microRNA

What other tools does IPA work with?

How do I add my own custom genes and connections?

How many genes are up or down regulated in a pathway?

What kind of data should I have?

FAQ - microRNA

FAQs on the miRNA targeting relationships in IPA

What species identifiers are accepted for analysis by IPA?

Upstream Regulator Analysis Evidence for Effect

Can I suggest articles and findings to add?

Downstream Effect Analysis: Evidence for Effect

More info link for Downstream Effect Analysis Evidence for Effect

Biomarker Definition

My file won’t open/upload correctly. What should I do?

Creating a Dataset

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.