Ingenuity Pathway Analysis (IPA) | Data Upload workflow

Data Upload definitions

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

Eligible Pathways List

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

Summer IPA Release notes, June 2019

Ingenuity Pathway Analysis (IPA) | Release Notes

Available Canonical Pathways

Ingenuity Pathway Analysis (IPA) | Currently Available Canonical Pathways

Version number or Date of Third Party Databases

Ingenuity Pathway Analysis (IPA)

Identifier and Gene Model Source Versions

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

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.

Analyzed Dataset

How to Overlay Analyses, Datasets, and Lists

Upstream Regulator Analysis

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

Comparison analysis heat map for upstream analysis

MAP-Molecule Activity Predictor

Ingenuity Pathway Analysis (IPA)

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)

Canonical Pathways for a Dataset

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

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)

Comparison analysis heat map for canonical pathways

IPA-Tox Analysis Workflow

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

Ratio Calculations for Pathways

Ingenuity Pathway Analysis (IPA)

IPA Network Generation Algorithm

Ingenuity Pathway Analysis (IPA)

Right Click Menu

Ingenuity Pathway Analysis (IPA)

Graph Preferences

Ingenuity Pathway Analysis (IPA)

Cache

Ingenuity Pathway Analysis (IPA)

BioProfiler

Ingenuity Pathway Analysis (IPA) | Advanced Analytics BioProfiler

Relationship Export

Ingenuity Pathway Analysis (IPA) | Relationship Export

Add My Findings

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

Comparison analysis heat map for causal networks

Ingenuity Pathway Analysis (IPA)

Causal Networks

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

My Findings

Ingenuity Pathway Analysis (IPA) | My Findings

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.

IPA Network Generation Algorithm Whitepaper

Ingenuity Pathway Analysis (IPA) | Whitepaper Link

Running-IPA-on-Windows

Ingenuity Pathway Analysis (IPA) | Running IPA on Windows

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

FAQ - Causal Network Analysis

Ingenuity Pathway Analysis (IPA)

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

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

IPA Legend

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

Accessing and Using Upstream Regulators

Data Source Filter

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)

Human Isoforms View Tutorial

Ingenuity Pathway Analysis (IPA)

Visualize Pathways Tutorial

Ingenuity Pathway Analysis (IPA)

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

Biomarker Analysis

File Format Specification for Uploading Data with Experimental Metadata into IPA

Ingenuity Pathway Analysis (IPA) | Experimental Metadata Specifications

FAQ - Ingenuity Knowledge Base

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

Cell Art

Description of the Cell Art tool of Path Designer

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

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

Grow

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

Connect

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

Mechanistic Networks

Mechanistic Network Viewer

Export All Analysis Results

Export All

Inhibited phosphoproteins

Overlay Analyses, Datasets, and Lists

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

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

Collaboration Workspace CWS

Trim and Keep

Add Molecules and Relationships

Advanced Search

Function and Disease Search

Managing Invitations

Molecules

Gene and Chemical Search

Relationships

Pathways and Tox List Search

Shared With Me

Exporting Molecule Lists

Password Reset

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?

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

SNP Content

Compare Data

Compare data tool

Comparing Biomarkers

How can Functional Analysis help you

IPA-Tox Analysis Overview

Clustering of miRNA in IPA

Printing

Molecule Types Filter

Publication Guidelines

NGS RNA Sequencing

Confidence Level Filter - microRNA

What other tools does IPA work with?

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?

FAQ - microRNA

FAQs on the miRNA targeting relationships in IPA

What kind of data should I have?

How do I add my own custom genes and connections?

Biomarker Definition

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?

Creating a Dataset

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

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.