IPA

Applications

  • Target Identification and Validation
  • Biomarker Discovery
  • Drug Mechanism of Action
  • Drug Mechanism of Toxicity
  • Disease Mechanisms

Experimental approaches supported

  • RNA-Seq
  • microarray
  • microRNA
  • mRNA
  • qPCR
  • proteomics
  • genotyping

Identifiers supported in IPA

  • Affymetrix (Exon/Gene Expression, 3' IVT Expression)
  • Affymetrix SNP ID (Genotyping)
  • Agilent (Gene Expression, microRNA)
  • Applied Biosystems (Gene Expression, microRNA)
  • CAS Registry
  • CodeLink
  • dbSNP IDs (including Illumina genotyping arrays with dbSNP ids)
  • Entrez Gene
  • Ensembl
  • GenBank
  • GenPept
  • GI Number
  • HUGO Gene Symbol
  • Human Metabolome Database (HMDB)
  • Illumina (whole-genome & microRNA arrays)
  • International Protein Index
  • KEGG ID
  • miRBase (mature)
  • PubChem CID
  • RefSeq
  • UCSC Human Isoform IDs (hg 18 & hg 19)
  • UniGene
  • UniProt/SwissProt Accession

Species-specific identifierssupported in IPA

  • Human
  • Mouse
  • Rat
  • Canine
  • Additional species supported via ortholog mapping

Ingenuity

Discover the Biology

Interactive pathway analysis of complex 'omics data


Ingenuity Systems creates Intuitive web-based applications for quickly analyzing and accurately interpreting the biological meaning in your genomic data.

Ingenuity offer three products that leverage the Ingenuity Knowledge Base and advanced informatics to get actionable insights from your experiments:

IPA - Ingenuity Pathway Analysis variant analysis

Comprehensive pathway and network analysis of complex 'omics data.

iReport variant analysis

Fastest way to understand gene expression, RNA seq, and real-time PCR data.

Variant Analysis variant analysis

Rapidly find causal variants using a knowledge-driven approach.


IPA - Ingenuity Pathway Analysis

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 of highly structured, detailrich biological and chemical findings.

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 helps you discover hidden causal connections in your data.

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.

  • Understand the relative impact of changes in mRNA, microRNA, protein or metabolite levels in the context of well-characterized pathways.
  • Discover upstream regulators whose predicted activation or inhibition can drive the gene expression changes observed in your dataset.
  • 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.
  • 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
  • Compare affected pathways and predicted phenotypes and upstream regulators across platform, time, dose, or patient population
  • Interpret RNA-Seq data in the context of known biology to quickly narrow in on what is most valuable in your dataset and visualize expression of human splice variants with a novel isoform display tool

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.

  • Analyze metabolomics data (lists of HMDB, CAS, PubChem CID, KEGG identifiers) in the context of dynamic metabolic and signaling pathways.
  • 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.
  • Integrate mRNA, microRNA, SNP, proteomics, and metabolomics data for a complete systems biology approach to understanding disease, biomarker discovery, molecular toxicology, and understanding drug mechanism 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.

  • 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 liver, kidney, or heart.
  • Identify genes, proteins, metabolites that are used in the clinic as biomarkers of drug safety.
  • Understand the relationship between transcript, protein, or metabolite changes and Toxicity Functional Categories, which cover a wide spectrum of well-known drug related injuries and pathologies.
  • Use upstream regulator predictions to better understand the molecular and pathologic effects observed in safety studies. Predictions may involve known toxicants or tool compounds with well known mechanisms of action to provide additional insights.
  • 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:
  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.
  • 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.

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 IPA search results, an existing IPA Network or Canonical Pathway, or an uploaded list of targets or biomarkers. Or upload your own pathways in several supported file formats such as XGMML, BioPax, SBML, or GPML. 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:

  • microRNA-mRNA target networks
  • Transcriptional networks
  • Phosphorylation cascades
  • Protein-Protein or Protein-Promoter Interaction Networks
  • Chemical/Drug effects on proteins

IPA Reagent View

  • 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.
  • Quickly design validation experiments to test hypotheses within specific experimental parameters

Context Filters:

  • Highlight the relationships published within a particular date range.
  • Identify clinical biomarkers in a Network or My Pathway.
  • Narrow in on regulatory events that were demonstrated in a particular cellular context.

Path Explorer tool:

  • Find relevant regulatory paths and physical interactions between genes of interest.
  • 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.

  • Identify all GPCRs known to play a role in obesity.
  • Find all genes implicated in angiogenesis, understand which signaling pathways they participate in, and which are targeted by candidate compounds.
  • Identify all compounds (FDA-approved and clinical candidates) that target prostate cancer genes, or pro-metastatic genes.
  • Quickly identify the subset of disease genes that are used as biomarkers in various clinical applications.

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.

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 PDFs, 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

Content

IPA leverages the Ingenuity® Knowledge Base, a repository of biological interactions and functional annotations created from millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. These modeled relationships, or Findings, include rich contextual details, links to the original article, and are manually reviewed for accuracy. The Ingenuity Knowledge Base provides you with a reliable resource for searching relevant and substantiated knowledge from the literature, and for interpreting experimental results in the context of larger biological systems.

Unparalleled Structure and Contextual Details
Ingenuity structures all of the biological and chemical content in the Ingenuity Knowledge Base using the Ingenuity® Ontology. By structuring the content, we enable computation and inferencing, ensure semantic and linguistic consistency, and support the integration and mapping of content from multiple sources. Unlike other ontologies, the Ingenuity Ontology is comprehensive. This level of detail helps us capture relevant contextual details from the literature such as species specificity, cell type/tissue context, site and type of mutations, direction of change, post-translational modification sites, epigenetic modifications, and experimental methods used. These contextual details are what make our Findings different from other solutions that only report on simple "A to B" relationships. Ingenuity Findings ensure that you can access knowledge and generate hypotheses that are highly relevant to your specific experimental system.

Expert Review Process for Trusted Information
All information in the Ingenuity Knowledge Base is manually reviewed by experts for accuracy and detail, and follows strict quality control processes.

Broad and Timely Content
The Ingenuity Knowledge Base is updated weekly to include information published as recently as the prior week. It is the largest knowledge base of its kind, including modeled relationships between proteins, genes, complexes, cells, tissues, drugs, pathways, and diseases. It includes information from a wide range of published biomedical literature, textbooks, reviews, internally curated knowledge (such as pathways), and a variety of trusted third party sources and databases.

Dowload the IPA datasheet


iReport

Ingenuity iReport for Isoform-level Human RNA-Seq Data - The easiest way to understand the meaning of your gene expression data

Interpretation of RNA-Seq data can be a daunting task. The biological story inherent in the data can be difficult to read when facing a spreadsheet of transcript names and expression values. Ingenuity® iReport™ for Isoform-level Human RNA-Seq Data eliminates the obstacles between data and biological insight by providing an easy, accurate biological interpretation tool for RNA-Seq data. iReport delivers a unique combination of interactive visual tools that help you quickly identify compelling genes, molecular interactions, pathways, diseases, and processes relevant to your experiment, resulting in a deeper biological understanding of your samples and a more efficient way to rapidly translate an experimental dataset into actionable biological insights.

Isoform-level Human RNA-Seq Data

With the release of the Isoform iReport bench scientists are now able to quickly move forward with RNA-Seq data, identify differentially expressed isoforms between condition and control samples, and interpret the impact of expression changes in the context of biological processes, disease and cellular phenotypes, and molecular interactions.

  • Easily narrow in on genes in your RNA-Seq samples that have multiple differentially expressed isoforms
  • Visualize your RNA-Seq data in the context of Isoform View, which displays alternatively spliced transcripts and details of their chromosomal locus, predicted protein domains, and encoded protein isoforms
  • Compile targeted bibliographies with experimental evidence linking your differentially expressed isoforms to biological processes, diseases, and molecular interactions

Narrowing in on the most interesting cases

The Isoform Icon is used throughout iReport to identify genes that are known to have more than one isoform, according to the RefSeq gene model. Sorting gene tables in iReport by this icon quickly identifies cases where more than one transcript for a gene is found to be differentially expressed between your condition and control samples.

Backing up your insights with evidence from the Ingenuity Knowledge Base

All of the evidence linking your differentially expressed transcripts to the biological results in iReport comes from the Ingenuity Knowledge Base. Use the publication filters in iReport to quickly compile lists of original research articles with experimental evidence that establish functional roles for specific isoforms in biological processes, diseases, and molecular interactions.

How do I get started?

Isoform iReport currently supports analysis of human RNA-Seq data in cuffdiff format.

To get started go to www.ingenuity.com/getireport

Click on the Upload Your Data button, fill out a short form, then on the upload page choose the RNA-Seq Cuffdiff Output option under the File Type drop down list and upload the following files:

  • gene_exp.diff
  • isoform_exp.diff
  • isoforms.fpkm_tracking

Download the iReport datasheet


Variant Analysis

Identify causal variants from human resequencing data in just minutes.

Ingenuity® Variant Analysis™ combines analytical tools and integrated content to help you rapidly identify a short list of compelling variants using selection criteria based both upon published biological evidence and your own knowledge of disease biology.

FOR: Researchers who need to identify causal variants from human resequencing data.

HOW: Drill down on biologically relevant variants based on information in the Ingenuity® Knowledge Base, including primary literature on human mutations in patients with particular diseases or abnormal phenotypes.

Interactive Filtering to Prioritize Variants:

  • Quickly select for uncommon variants anywhere in the genome that likely cause loss or gain of function
  • Identify variants that impact symptoms, pathways, processes, and genes implicated in drug response or disease progression
  • Interactively adjust variant selection criteria in real-time
  • Apply genetic selection criteria appropriate for your study design, from one to hundreds of samples

Integrated Evidence for Fast, Accurate Results:

  • Nearly 4 million manually-curated findings from the literature, including effects of mutations on human disease and phenotypes
  • Mutation content from databases including COSMIC and OMIM
  • Known and inferred effects on protein function resulting from variants in coding and regulatory regions, copy number variation, and fusions
  • Cancer disease models that enable rapid causally-consistent identification of driver variants.

Download the Variant Analysis datasheet


About Ingenuity Systems

Ingenuity Systems is a leading provider of biomedical information solutions for the exploration, interpretation, and analysis of life science information. Ingenuity's products and services have one common goal - to help life science researchers generate maximum value from all types of biological and chemical knowledge. All Ingenuity products leverage the Ingenuity Knowledge Base, the largest database of its kind, which houses biological and chemical relationships extracted from the scientific literature. Today, Ingenuity's solutions are used by thousands of researchers and clinicians at hundreds of leading pharmaceutical, biotechnology, and academic research institutions worldwide. Ingenuity was founded in 1998 and is headquartered in Redwood City, California..

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