science

Metabolomic Pathway Analysis

Metabolomic Pathway Analysis is a science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Metabolomic Pathway Analysis rather than just read about it. In short: Metabolomic Pathway Analysis, shortened to MetPA, is a freely available, user-friendly web server to assist with the identification analysis and visualization of metabolic pathways using metabolomic data. MetPA makes use of advances originally developed for pathway analysis in microarray experiments and applies those principles and concepts to the analysis of metabolic pathways.

Key takeaways

Metabolomic Pathway Analysis belongs to science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Metabolomic Pathway Analysis to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Metabolomic Pathway Analysis from memory before moving on to harder problems.

Reference excerpt

Metabolomic Pathway Analysis, shortened to MetPA, is a freely available, user-friendly web server to assist with the identification analysis and visualization of metabolic pathways using metabolomic data. MetPA makes use of advances originally developed for pathway analysis in microarray experiments and applies those principles and concepts to the analysis of metabolic pathways. For input, MetPA expects either a list of compound names (identified as statistically significant or significant perturbed) or a metabolite concentration table with phenotypic labels (i.e. sick vs. healthy). The list of compounds can include common names, HMDB IDs or KEGG IDs with one compound per row. Compound concentration tables must have samples in rows and compounds in columns. MetPA's output is a series of tables indicating which pathways are significantly enriched (along with accompanying statistics) as well as a variety of graphs or pathway maps illustrating where and how certain pathways were enriched. MetPA's graphical output uses a colorful Google-Maps visualization system that allows simple, intuitive data exploration that lets users employ a computer mouse or track pad to select, drag and place images and to seamlessly zoom in and out. Users can explore MetPA's output using three different views or levels: 1) a metabolome view; 2) a pathway view; 3) a compound view.

MetPA Details As noted above MetPA performs two types of pathway analysis: 1) Pathway (or Metabolite Set) Enrichment Analysis; and 2) Pathway Topological Analysis. Pathway Enrichment Analysis (which is similar to MSEA) identifies which metabolic pathways have compounds (from the input lists) that are over-represented and have significant perturbations to their concentrations. MetPA uses a number of robust statistical measures to identify which metabolites (and therefore which pathways) are over-represented. Pathway Topological Analysis measures the centrality of a metabolite in a metabolic network or a metabolic pathway. Central or highly important metabolites are “hubs”, located in the center of a metabolic pathway or process. MetPA employs a number of topological assessment tools to measure centrality or “hubness” in an objective manner (called Pathway Impact). Pathway impact is a combination of the centrality and pathway enrichment results. It is calculated adding up the importance measures of each of the matched metabolites and then dividing by the sum of the importance measures of all metabolites in each pathway. To begin a session on MetPA users must first have a list of significant compounds derived from a metabolomic tests or compounds and concentration data with information about the phenotype of the organisms under study. The list of compounds can include common names, HMDB IDs or KEGG IDs with one compound per row. Compound concentration tables must have samples in rows and compounds in columns. Once the data is uploaded to MetPA users must choose the organism with which the pathway analysis will be done. Ideally the metabolomic data should be from one of the 15 model organisms listed in the MetPA organism menu. If the organism of interest is not listed, then users may choose a closely related organism. If none of the organisms are thought to be sufficiently close, then users may inquire with the web site developers to see if the organism may be added. Central to the operation of MetPA is its library of metabolic pathways for different model organisms. These were assembled from the KEGG database which were separated into graphical models using the KEGGgraph package. The current MetPA collection contains more than 1170 different metabolic pathways derived from 15 model organisms covering mammals (Humans, Mouse, Rat, Cow, Chicken), fish (Zebrafish), plants (Arabidopsis, Rice) insects (Drosophila) and microbes (Yeast, Escherichia coli, Bacillus subtilis, Staphylococcus aureus, Pseudomonas putida, and Thermotoga maritima.). To simplify viewing and navigation on the server, and to assist with the topological analyses, all the KEGG pathways in MetPA are presented as a network with metabolites serving as nodes and reactions as edges. MetPA provides an extensive tutorial explaining how to upload data and how interpret its output. In 2011 MetPA functions were expanded and integrated into MetaboAnalyst. This integration allows users to perform a more complete analysis and to link to other data processing and data interpretation functions available through MetaboAnalyst.

References

Worked examples

Example 1 — a first encounter with Metabolomic Pathway Analysis

Start with the simplest possible case. Write down what Metabolomic Pathway Analysis claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Metabolomic Pathway Analysis before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Metabolomic Pathway Analysis ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Metabolomic Pathway Analysis

In research: Metabolomic Pathway Analysis appears in science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Metabolomic Pathway Analysis in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Metabolomic Pathway Analysis is common in secondary-school and first-year university syllabi. It links to neighbouring topics Metabolomic databases, so understanding it makes those chapters shorter.
In everyday life: Look for Metabolomic Pathway Analysis outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study Metabolomic Pathway Analysis in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Metabolomic Pathway Analysis means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Metabolomic Pathway Analysis out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Metabolomic Pathway Analysis in simple terms?

Why does Metabolomic Pathway Analysis matter?

Because it connects several science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Metabolomic Pathway Analysis?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Metabolomic Pathway Analysis.