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IPA-Tox Analysis Workflow


Ingenuity Pathway Analysis (IPA)

Canonical Pathways for a Dataset


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

Collaboration Workspace CWS


Ingenuity Pathway Analysis (IPA)

Biomarker Analysis


Ingenuity Pathway Analysis (IPA)

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)

Data Source Filter


Ingenuity Pathway Analysis (IPA)

MAP-Molecule Activity Predictor


Ingenuity Pathway Analysis (IPA)

Visualize Pathways Tutorial


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.

FAQ - Analysis Match


Ingenuity Pathway Analysis (IPA)

Connect


Grow


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

Publication Guidelines


Ingenuity Pathway Analysis (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

Formatting Your Dataset


Ingenuity Pathway Analysis (IPA)

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


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 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


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


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?


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


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


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


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


PathTracer

Annotations


Importing Pathways


PathTracer


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


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?


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?


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?


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?

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


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

What kind of data should I have?


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?


What species identifiers are accepted for analysis by IPA?

Upstream Regulator Analysis Evidence for Effect


Can I suggest articles and findings to add?


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?


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.