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Category Cross-Omics>Pathway Analysis/Tools Abstract Ingenuity Pathways Analysis 5.5 (IPA) is an advanced pathway analysis system solution. You can use IPA to model, analyze and understand the complex biological systems at the core of your research. IPA leverages one of the worlds largest and highest quality knowledge bases of biological networks, advanced algorithms and an easy-to-use software interface to provide you with the insights and confidence to make better and faster decisions at every step of your research. IPA is available as a web-delivered, hosted, or deployed solution. Products features/capabilities include: Search - Use Search to - 1) Look for information on genes and chemicals, their impact on diseases and cellular processes, and their role in pathways; 2) Build interactive pathways representing the key genes, chemicals, and processes in experimental systems of interest; 3) Validate experimental assumptions; 3) Get up to speed quickly, and stay current in a new research area; 4) Understand the biological effects of chemicals. With the new, expanded chemical content of IPA, you can search for genes or chemicals that are - 1) Localized to a specific cell compartment; 2) Targeted by FDA approved drugs or clinical candidates; 3) Involved in a particular disease or process; 4) Members of a specific protein or chemical family; 5) Most relevant by running combinations of searches to rapidly generate lists of genes with biological characteristics. ChemView - ChemView provides access to chemical content describing therapeutic information, target protein, toxicity, bioavailability, LD50, PK/PD, metabolism, CAS number, synonyms (including systematic name and brand names for drugs), chemical formula, and SMILES notation. You can - 1) Utilize the chemical content to build pathways and working models representing compound mechanism of toxicity and mechanism of action; 2) Include chemicals when generating networks and analyzing datasets; 3) Add chemicals to custom pathways. Dynamic Signaling & Metabolic Pathways - You can use IPA’s extensive library of well-characterized signaling and metabolic pathways as a starting point for exploration and a bridge between novel discovery and known biology. You can layer in novel insights, drugs, and ‘omics data; You can also - 1) Explore beyond the boundaries of well-characterized signaling and metabolic pathways to incorporate the molecular relationships that are the most relevant to the experimental system being studied; 2) Customize pathways using IPA’s extensive molecular interaction content; 3) Understand chemical effects on genes; find upstream activators, and downstream transcriptional targets of pathways; 4) Drill down to the supporting evidence from the scientific literature; 5) Layer in expression, proteomic, and copy number data. My Pathways & Lists - You can build custom libraries of pathways representing mechanism of action and mechanism of toxicity. Create custom, literature-supported signaling pathways with proteins of interest. Store collections of custom pathways and lists for subsequent IPA Core, IPA-Tox, or IPA-Biomarker analyses. You can use the Grow and Connect tools to edit and expand networks based on the molecular relationships most relevant to the project - including 1) Transcriptional networks; 2) Phosphorylation cascades; 3) Protein-Protein of Protein-DNA Interaction Networks; 4) Chemical effects on proteins. You can use Search results as building blocks for custom pathways to - 1) Identify cross-talk between biological processes and pathways; 2) Understand whether gene lists and signatures are tightly connected. Path Explorer - Can be used to - 1) Find relevant regulatory paths and physical interactions between genes of interest; 2) Find biological paths that connect one set of genes to another; 3) Identify regulatory events that lead from signaling events to transcriptional effects. Analyze and Interpret Data - IPA helps you derive maximum benefit from data generated by various large-scale technologies, including gene expression and SNP microarrays and proteomics experiments, and small-scale experiments that generate gene lists. With IPA, you can understand the biological impact due to time and dose effects, and identify key mechanistic differences between various patient populations. IPA Core Analysis - IPA delivers a rapid assessment of the signaling and metabolic pathways, molecular networks, and biological processes that are most significantly perturbed in the dataset of interest. The key components of the IPA Core Analysis are - 1) Signaling and Metabolic Pathways Analysis; 2) Cellular and Disease Process Analysis; 3) Molecular Network Analysis. These capabilities enable you to - a) Analyze data in the context of molecular mechanisms; b) Relate molecular events to higher-order cellular and disease processes; c) Understand the relevance to organismal physiology and pathophysiology; d) Visualize time course and dose response effects; e) Interpret and integrate data from multiple platforms (e.g., genomics, proteomics, genotyping) and with mixed identifiers. IPA-Tox Analysis - IPA-Tox uses Toxicity Functions in combination with Toxicity Lists to link experimental data to clinical pathology endpoints, understand pharmacological response, and support mechanism of action and mechanism of toxicity hypothesis generation. IPA-Biomarker Analysis - IPA-Biomarker identifies the most biologically relevant and promising molecular biomarker candidates from datasets generated at every step of the drug discovery process. Data Upload Wizard - Can be used to quickly upload data from multiple formats without time-consuming data formatting steps. And, analyze datasets with mixed gene and protein identifiers. Analysis Summaries - Creates an automated, focused, and summarized output of analysis results. Communicate and Collaborate - IPA’s tools and pathways can be used to share hypotheses and insights with other research teams and collaborators. Integrate knowledge from multiple sites and data repositories and share findings of interest in order to streamline the workflow and communicate more easily with colleagues. Share - Can be used to invite collaborators to review and integrate analysis results and pathways. Report - Can be used to export results, tables of annotations, bibliographies, and high-resolution images to include in reports and presentations. Interactive Pathways - Can be used to insert fully referenced pathways that provide access to the underlying biological information into e-mails or presentations. Application Programming Interfaces (APIs) - Can be used to integrate IPA with in-house software applications. Integration - IPA can be integrated with 3rd party software tools to streamline workflows. IPA’s Knowledge Base - Biological and Chemical Information - IPA’s expert-extracted content includes modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. Additional Sources Beyond Literature Findings - In addition to expert extraction of findings from the literature, IPA includes content from high quality databases such as - EntrezGene, RefSeq, OMIM, Gene Ontology, Gene Expression Body Atlas from GNF, KEGG (metabolic pathways) and LIGAND (enzyme/substrate reactions). IPA also contains key findings and relationships curated by Ingenuity scientists that describe - FDA approved drugs and clinical candidates, Cell Signaling Pathways, and Toxicity Lists and Pathways. And more. Note: See Ingenuity Pathways Knowledge Base (G6G Product Number 20018) for additional info. System Requirements Operating System Vista, Windows XP and Macintosh 10.3.9, 10.4.10. Web Browser Internet Explorer 6.0 or higher. Firefox 1.5 or higher is recommended. For Mac OS, Safari. Memory Minimum of 512MB RAM (1GB RAM recommended). Java Runtime Environment Version 1.4.2 or higher. Ingenuity Pathways Analysis can be accessed as a web-hosted or a deployed solution. Manufacturer Home office; see web site for international locations.
1700 Seaport Blvd. Third Floor Redwood City, CA 94063 Tel: 650.381.5100 Fax: 650.381.5190 Email: info@ingenuity.com support@ingenuity.com Manufacturer's Web Site www.ingenuity. com/products/pathways_analysis.html Price Contact manufacturer G6G Product Number 20017 G6G Manufacturer Number 101440 |
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