QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA) 软件分析
IPA做得不错，但是收费，这里分析一下这个软件是怎么设计的，有哪些核心的数据和分析模块。
软件链接：QIAGEN Ingenuity Pathway Analysis (QIAGEN IPA) 软件价格：4万美金/年，一个普通的研究所/学院，每年发30篇10分以上的paper，那每篇的成本就是1万人民币，太贵了。
国内目前也就30家买了，那每年的营收大概就是120万美金，全球x5，那就是一年600万美金的营收。
宣传资料：You may be missing a research breakthrough — here’s why
分析流程：QIAGEN IPA: Applications and experimental approaches
分析教程：A better approach to pathway analysis
个人点评
IPA的idea人人都可以想到，主要是在于劳力密集的data curation。
都是已知的知识，也没有什么高深的算法，就我看，基本的分析模块就不该收费，你压根没有智力投入啊。
进阶分析模块可以收费，你有独特的算法，但是科技服务是真的不好做，也不赚钱。那不如索性对科研玩家全部免费。
专注做To business的业务，To consumer就不要做了。比如面向药厂、面向基因测序企业的项目可以做。定位一定要明确，不然做不大也做不好。
简介
Understand complex 'omics data to accelerate your research
Discover why QIAGEN Ingenuity Pathway Analysis (IPA) is the leading pathway analysis application among the life science research community and is cited in tens of thousands of articles for the analysis, integration and interpretation of data derived from ‘omics experiments. Such experiments include
- RNA-seq,
- small RNA-seq,
- metabolomics,
- proteomics,
- microarrays including miRNA and SNP, and
- small-scale experiments.
With QIAGEN IPA you can predict downstream effects and identify new targets or candidate biomarkers. QIAGEN Ingenuity Pathway Analysis helps you perform insightful data analysis and interpretation to understand your experimental results within the context of various biological systems.
IPA Features 具体分析内容
Pattern Search
Which analyses activate this Canonical Pathway through the same genes as in my analysis?
Which analyses of diseased tissue are the “opposite” of the gene signature for my drug, and may benefit from treatment with the drug?
Do any analyses have an interaction network or Regulator Effects network similar to the one in my analysis?
Start with any network or pathway from an analysis, or simply place genes of interest into a new My Pathway, then either overlay a dataset or manually color the genes with the MAP paint bucket to “activate” or “inhibit” them.
Graphical Summary
These inferred relationships help you visualize related biological activities.
Activity Plot
Visualize and explore the activity of a single QIAGEN IPA entity, such as an Upstream Regulator, Causal Network, Canonical Pathway, Disease or Function, across >96,000 OmicSoft Land analyses.
Analysis Match
Broaden the scope of your discovery when you evaluate your dataset in the context of over 100,000 IPA analyses.
Path Designer
Transform your networks and pathways in QIAGEN IPA into publication-quality pathway graphics rich with color, customized text and fonts, biological icons, organelles, and custom backgrounds.
Phosphorylation Analysis
Changes in the phosphorylation states of proteins provide an important regulatory mechanism in mammalian cells. Discover upstream regulators and causal network master regulators that may be driving the changes in phosphorylation levels of the proteins in your phosphoproteomics dataset.
IsoProfiler
IsoProfiler helps you to identify and prioritize isoforms having interesting biological properties relevant to your research. Find genes with RNA transcripts having unusual pattern(s) of expression such as isoform switching or with known diseases or functions.
Causal Network Analysis
Generates multi-leveled regulatory networks that may explain the gene expression changes exhibited in a dataset. It enables the discovery of novel regulatory mechanisms by expanding upstream analysis to include regulators that are not directly connected to targets in the dataset.
BioProfiler
BioProfiler searches the QIAGEN IPA Knowledge Base of scientific information to generate molecular profiles of diseases, phenotypes, and biological processes (e.g., apoptosis) listing all the genes and compounds that have been associated with the profiled term.
Regulator Effects
Provides insights into your data by integrating Upstream Regulator results with Downstream Effects results to create causal hypotheses that explain what may be occurring upstream to cause particular phenotypic or functional outcomes downstream.
Biomarker Filter
Rapidly identify the best biomarker candidates based on biological characteristics most relevant to the discovery study.
Gene and ChemView
QIAGEN IPA's Search & Explore capabilities offer researchers access to the most current Findings available on genes, drugs, chemicals, protein families, normal cellular and disease processes, and signaling and metabolic pathways.
Comparison Analysis
Quickly visualize trends and similarities across analyses using heat maps for Canonical Pathway, Downstream Effects, Upstream regulators and Causal Network Analyses. Prioritize by score, hierarchical cluster or trend.
Mechanistic Networks
Automatically generate plausible signaling cascades describing potential mechanism of action leading to observed gene expression changes.
Downstream Effects Analysis
Identify whether significant downstream biological processes are increased or decreased based on gene expression results.
Molecule Activity Predictor (MAP)
Interrogate sub-networks and Canonical Pathways and generate hypotheses 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.
Canonical Pathway
Pathway Analysis, Canonical Pathways, Overlapping Pathways, Pathway Import and scoring. Determine most significantly affected pathways. Analyze your data in the context of established signaling and metabolic pathways.
Tox Lists and Tox Functions
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.
Disease View
Provides details associated with the disease or biological function such as molecules associated with that disease or function, known drug targets, drugs known to target those molecules, and more.
Upstream Regulator Analysis
Predict upstream molecules, including microRNA and transcription factors, which may be causing the observed gene expression changes.
Isoform View
Understand the structure and function of both human and mouse isoforms (splice variants).
Interaction Network Analysis
Build and explore transcriptional networks, microRNA-mRNA target networks, phosphorylation cascades and Protein-Protein or Protein-DNA interaction networks. Identify regulatory events that lead from signaling events to transcriptional effects.
MicroRNA Target Filter
Reduce the number of steps it takes to confidently, quickly, and easily identify mRNA targets by letting you examine microRNA-mRNA pairings, explore the related biological context, and filter based on relevant biological information as well as the expression information.
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