Ingenuity Pathways Analysis (IPA®)
Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools, Cross-Omics>Biomarker Discovery/Analysis/Tools and Genomics>Gene Expression Analysis/Profiling/Tools
Abstract IPA is an all-in-one, web-based software application that enables you to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays; metabolomics, proteomics, and RNA-Seq experiments; and small-scale experiments that generate gene and chemical lists.
With IPA you can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of your experimental systems.
IPA’s data analysis and search capabilities help you understand the significance of your data, specific target, or candidate biomarker in the context of larger biological or chemical systems, backed by the Ingenuity® Knowledge Base - (see G6G Abstract Number 20018U) of highly structured, detail-rich biological and chemical Findings.
IPA Data Analysis & Interpretation --
IPA’s Data Analysis and Interpretation unlocks the insights buried in experimental data by quickly identifying relationships, mechanisms, functions, and pathways of relevance, allowing you to move beyond statistical analysis, to novel biological insights, testable hypotheses, and validation experiments.
IPA Core Analysis - delivers a rapid assessment of the signaling and metabolic pathways, molecular networks, and biological processes that are most significantly perturbed in a dataset of interest. With it you can:
1) Understand the relative impact of changes in mRNA, microRNA, protein or metabolite levels in the context of well-characterized pathways.
2) Identify the cellular and disease phenotypes most significant to a set of genes, and understand how those genes impact that phenotype, i.e. whether they increase or decrease a biological process.
3) Optimize visualization and biological context of analyses with Context and Network Size parameters.
4) Construct networks of interaction and regulatory events focused on your genes and proteins of interest, or narrow in on analysis results most closely aligned with your experimental model.
5) Compare affected pathways and phenotypes across platform, time, dose, or patient population.
6) Interpret RNA-Seq data in the context of known biology to quickly narrow in on what is most valuable in your dataset.
IPA - Metabolomics® - overcomes the metabolomics data analysis challenge by providing the critical context necessary to gain biological insight into cell physiology and metabolism from metabolite data. With it you can:
1) Analyze metabolomics data (lists of HMDB, CAS, PubChem CID, KEGG identifiers) in the context of dynamic metabolic and signaling pathways.
2) Understand which biological processes and phenotypes your metabolites are involved in and what regulates their synthesis, as well as the metabolite subcellular location and detection in biofluids.
3) Integrate mRNA, microRNA, SNP, proteomics, and metabolomics data for a complete ‘systems biology’ approach to understanding disease, biomarker discovery, molecular toxicology, and understanding drug mechanisms of action.
IPA - Tox® - delivers a focused toxicity and safety assessment of candidate compounds, and provides a more complete understanding of pharmacological response, drug mechanism of action, and mechanism of toxicity. With it you can:
1) Determine whether compound-induced changes in transcript or protein levels are significantly associated with Toxicity Lists. These lists describe adaptive, defensive, or reparative responses to xenobiotic insult and can be used to understand biological responses in the liver, kidney, or heart.
2) Identify genes, proteins, metabolites that are used in the clinic as biomarkers of drug safety.
3) Understand the relationship between transcripts, protein, or metabolite changes and Toxicity Functional Categories, which cover a wide spectrum of well-known drug related injuries and pathologies.
4) Integrate Toxicity Functional Analysis results with Toxicity Lists Analysis insights to link experimental data to clinical pathology endpoints and support mechanistic hypothesis generation.
IPA - Biomarker® - identifies the most promising and relevant biomarker candidates within experimental datasets.
The Biomarker Filter capability rapidly prioritizes biomarker candidates based on biological characteristics most relevant to a discovery study. With it you can:
1) Identify genes, mRNA, proteins and metabolites that are being used in the clinic as biomarkers of disease diagnosis and prognosis, disease progression, markers of drug efficacy and safety, and patient response to therapy.
2) Determine if proteins are detected in over 10 bodily fluids including blood, bronchoalveolar lavage fluid, CSF, PBMCs, saliva, and urine.
3) Filter by expression patterns in 30 normal tissues as well as the NCI-60 panel of cell lines and over 30 primary immune cell types and cell lines.
The Biomarker Comparison feature generates lists of candidate markers that are unique to one treatment or patient sample or common across all treatments and patients.
IPA - MicroRNA Target Filter - combines filtering tools and microRNA-mRNA content to provide insight into the biological effects of microRNAs.
With it you can:
1) Identify mRNA targets for microRNAs using predicted microRNA-mRNA binding relationships from TargetScan, plus experimentally validated relationships from TarBase.
2) Reduce the number of steps to confidently identify targets by examining microRNA-mRNA pairings, exploring the related biological context of these relationships, and filtering mRNA targets based on relevant biological characteristics, all within a single tool.
3) Easily prioritize mRNA target interactions based on the confidence level of interaction predictions, source, or role/presence of species, diseases, tissues, pathways, cell lines, molecular types, and more.
IPA Search & Exploration of Biological and Chemical Knowledge --
IPA’s Search and Explore allows you to generate targeted search results, and act on those results to create biological models representing your experimental systems.
My Pathways: For building custom pathway and gene or chemical list libraries.
Start with gene lists from the IPA search results, an existing IPA Network or Canonical Pathway, or an uploaded list of targets or biomarkers. Then use the Build tools to identify upstream activators and inhibitors or downstream targets of those genes, layer in additional biological information or experimental data, and build event-specific pathways such as:
- a) microRNA-mRNA target networks;
- b) Transcriptional networks;
- c) Phosphorylation cascades;
- d) Protein-protein or protein-promoter interaction networks; and
- e) Chemical/Drug effects on proteins.
IPA Reagent View (beta) -
1) Easily locate reagents information for genes and proteins in your experimental system, and link to vendor websites for more information or to place an order.
2) Quickly design validation experiments to test hypotheses within specific experimental parameters.
Context Filters -
1) Highlight the relationships published within a particular date range.
2) Identify clinical biomarkers in a Network or My Pathway.
3) Narrow in on regulatory events that were demonstrated in a particular cellular context.
Path Explorer tool -
1) Find relevant regulatory paths and physical interactions between genes of interest.
2) Identify shortest literature-supported paths between drugs or genes associated with a disease or toxicity phenotype.
Gene, Chemical, & Pathway Search - Generate and compare targeted lists of genes, druggable proteins, biomarkers, and chemicals. With it you can:
1) Identify all GPCRs known to play a role in obesity.
2) Find all genes implicated in angiogenesis, understand which signaling pathways they participate in, and which are targeted by candidate compounds.
3) Identify all compounds (FDA-approved and clinical candidates) that target prostate cancer genes, or pro-metastatic genes.
4) Quickly identify the subset of disease genes that are used as biomarkers in various clinical applications.
IPA Communication & Collaboration Tools --
IPA provides a central place to analyze molecular data, generate testable hypotheses, and build and visualize molecular models of experimental systems. Update models with recent insights and generate custom, interactive reports to communicate and share insights with colleagues.
IPA Professional Dynamic Reports - Helpful summaries of relevant information.
Understand the broader biological and therapeutic relevance of a particular pathway, gene or molecule list (including uploaded proprietary lists), or analysis result by generating reports with detailed summaries and tables including pathway descriptions, top related biological processes, drugs that target pathway members, and targets in the pathway.
These dynamic reports enable faster decision making and hypothesis generation, allow for accurate versioning, and can be saved and exported as a fully interactive PDF, so you can easily share insights and link back to the underlying knowledge in IPA.
Path Designer - The easy-to-use pathway design and publishing tool.
Transform your networks and pathways in IPA into publication-quality pathway graphics rich with color, customized text and fonts, species-specific nomenclature, biological icons, organelles, and custom backgrounds. Path Designer pathways are fully interactive and supported by the high quality content stored in IPA.
You can also send colleagues professional pathway reports with links to Path Designer pathways. Path Designer lets you complete your entire workflow -- from data analysis to publication and rapid communication of insights to colleagues -- within IPA.
Sharing and Collaborative Workspace - Tools to facilitate research collaboration and sharing.
IPA provides easy, flexible options for sharing biological information with colleagues. You can invite selected individuals to share particular datasets, analyses, or pathways with you, or you can utilize customized Collaboration Workspaces to share projects with specific team members within or across institutions or consortia.
- Ingenuity Systems, Inc.
- 1700 Seaport Blvd. Third Floor
- Redwood City, CA 94063
- Tel: 650.381.5100
- Fax: 650.381.5190
- Email: email@example.com
Manufacturer Web Site Ingenuity Pathway Analysis
Price Contact manufacturer.
G6G Abstract Number 20017U
G6G Manufacturer Number 101440