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Ingenuity Pathway Analysis (IPA)

For modeling, analyzing, and understanding complex 'omics data
  • Analysis of gene expression/miRNA/SNP microarray data
  • Deeper understanding of metabolomics, proteomics, and RNAseq data
  • Identification of upstream regulators
  • Insight into molecular and chemical interactions and cellular phenotypes
  • Discoveries about disease processes
IPA is an all-in-one, web-based software application that enables analysis, integration, and understanding of data from gene expression, miRNA, and SNP microarrays, as well as metabolomics, proteomics, and RNAseq experiments. IPA can also be used for analysis of small-scale experiments that generate gene and chemical lists. IPA allows searches for targeted information on genes, proteins, chemicals, and drugs, and building of interactive models of experimental systems. Data analysis and search capabilities help in understanding the significance of data, specific targets, or candidate biomarkers in the context of larger biological or chemical systems. The software is backed by the Ingenuity Knowledge Base of highly structured, detail-rich biological and chemical findings.
Cat No./ID: 830003
IPA 1-Month, 1-Dataset NUL
For new academic users who have one dataset and would like to try Ingenuity Pathway Analysis for an extended trial.
Cat No./ID: 830011
IPA Advanced Analytics, 25 Datasets LNUL
For new academic users who have a limited amount of data to analyze.  This Named User License has the full capabilities of Ingenuity Pathway Analysis for one year, but for a limited number of datasets.
The Ingenuity Pathway Analysis (IPA) is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.
Performance
A wealth of analysis capabilities in IPA
Causal Network Analysis
Causal Network Analysis comprehensively identifies upstream molecules that control the expression of the genes in datasets. Expanding beyond direct or single-hop relationships between the upstream regulator and the target molecules in the dataset, Causal Network Analysis uncovers networks of regulators that connect to the dataset targets. Focus on the networks that are of highest relevance by scoring the resulting causal networks against molecules, diseases, or functions of interest.
 
Comparison Analysis
Comparison Analysis provides quick visualization of canonical pathway score trends across dose, time, or other factors using the Comparison Analysis heat map. Prioritize by score, hierarchical cluster, or trend.
 
BioProfiler
A disease or phenotype can be rapidly profiled by understanding its associated genes and compounds. Identify genes known to be causally relevant as potential targets or identify targets of toxicity, associated known drugs, biomarkers, and pathways.
 
Upstream Regulator Analysis
This analysis predicts upstream molecules, including miRNA and transcription factors, that may be causing observed gene expression changes.
 
Mechanistic Networks
Mechanistic Networks automatically generate plausible signaling cascades, describing potential mechanisms of action that lead to observed gene expression changes.
 
Downstream Effects Analysis
Gene expression results are used to identify whether significant downstream biological processes are increased or decreased.
 
Pathway Analysis, Canonical Pathways, Overlapping Pathways, Pathway Import, and scoring
These analyses are used to determine the most significantly affected pathways.
 
Comparison Analysis
Comparison Analysis determines the most significant pathways, upstream regulators, diseases, biological functions, and more, across time points, dose, or other conditions.
 
Network Analysis
Build and explore transcriptional networks, miRNA–mRNA target networks, phosphorylation cascades, and protein–protein or protein–DNA interaction networks. Identify regulatory events that lead from signaling events to transcriptional effects. Understand toxicity responses by exploring connections between drugs or targets and related genes or chemicals. Edit and expand networks based on the molecular relationships most relevant to the project.
 
microRNA Target Filter
This filter reduces the number of steps it takes to confidently, quickly, and easily identify mRNA targets by allowing examination of miRNA–mRNA pairings, exploration of related biological context, and filtering based on relevant biological information as well as the expression information. The microRNA Target Filter provides insights into the biological effects of miRNAs, using experimentally validated interactions from TarBase and miRecords, as well as predicted miRNA–mRNA interactions from TargetScan. Additionally, Ingenuity IPA includes a large number of miRNA-related findings from the peer-reviewed literature.
 
Toxicity Lists and Toxicity Functions
Toxicity Functions and Toxicity Lists link experimental data to clinical pathology endpoints, enable understanding of pharmacological response, and support mechanism-of-action and mechanism-of-toxicity hypothesis generation.
 
Molecule Activity Predictor (MAP)
MAP enables interrogation of sub-networks and canonical pathways and hypothesis generation by selecting a molecule of interest, indicating up or down regulation, and simulating directional consequences of downstream molecules and the inferred activity upstream in the network or pathway.
 
Isoform View
Using Isoform view, the biological implications of high-throughput RNAseq data become clear. Significantly regulated isoforms in your experiment can be identified and their potential impact determined using information about functional protein domains and isoform-specific literature.
 
Gene and ChemView
Search and explore capabilities in Ingenuity IPA provide access to the most current findings on genes, drugs, chemicals, protein families, normal cellular and disease processes, and signaling and metabolic pathways.
 
Biomarker Filter
This filter rapidly identifies the best biomarker candidates based on biological characteristics most relevant to the discovery study.
 
Path Designer
Path Designer transforms networks and pathways into publication-quality pathway graphics rich with color, customized text and fonts, biological icons, organelles, and custom backgrounds. Expand and explore pathways using the high-quality content stored in Ingenuity IPA.
Principle
Unparalled database knowledge
IPA leverages the Ingenuity Knowledge Base, a repository of expertly curated biological interactions and functional annotations created from millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. These modeled relationships include rich details, links to the original article, and are reviewed for accuracy by Ph.D. scientists. The curated content in the Knowledge Base is structured into an ontology that allows for contextual information, computation by the applications, and synonym resolution to ensure consistency across concepts. These features make the Ingenuity Knowledge Base distinctive and unparalleled by any other database.
Applications
IPA helps to uncover the discovery behind the data in:
  • Transcriptomics
  • Biomarker discovery
  • miRNA research
  • Toxicogenomics
  • Metabolomics
  • Drug repositioning
  • Proteomics
  • Causal network analysis

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