science

Immunological Genome Project

Immunological Genome Project 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 Immunological Genome Project rather than just read about it. In short: The Immunological Genome Project (ImmGen) is a collaborative scientific research project that is currently building a gene-expression database for all characterized immune cells in the mouse. The overarching goal of the project is to computationally reconstruct the gene regulatory network in immune cells.

Key takeaways

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

Reference excerpt

The Immunological Genome Project (ImmGen) is a collaborative scientific research project that is currently building a gene-expression database for all characterized immune cells in the mouse. The overarching goal of the project is to computationally reconstruct the gene regulatory network in immune cells. All data generated as part of ImmGen are made freely and publicly available at the ImmGen portal [1]. The ImmGen project began in 2008, as a collaboration between several immunology and computational biology laboratories across the United States, and will be completing its second phase in 2017. Currently, raw data and specialized data browsers from the first and second phases are on www.ImmGen.org.

Project

Background A true understanding of cell differentiation in the immune system will require a general perspective on the transcriptional profile of each cell type of the adaptive and innate immune systems, and how these profiles evolve through cell differentiation or activation by immunogenic or tolerogenic ligands. The ImmGen project aims to establish the roadmap of these transcriptional states.

Gene-expression compendium The first aim of ImmGen is to generate a compendium of whole-genome transcriptional profiles (initially by microarray, now mostly by RNA-sequencing) for nearly all characterized cell populations of the adaptive and innate immune systems in the mouse, at major stages of differentiation and activation. This effort is being carried out by a group of collaborating immunology research laboratories across the U.S. Each of the laboratories brings a unique expertise in a particular cell lineage, and all are employing standardized procedures for cell sorting. The compendium of microarray data currently include over 250 immunologically relevant cell types, from all lymphoid organs and other tissues which are monitored by immune cells.

Publications A series of ImmGen reports was published as the compendium accumulated. Some lineage specific reports described hematopoietic stem cells, natural killer cells, neutrophiles, B and T cells, natural killer cells, macrophage, dendritic cells, alpha beta T cells, gamma delta T cells, activated CD8 T cells, innate lymphoid cells, and lymph node stromal cells. Though most of the transcriptional profiling was done on B6 mice, the effect of genetic variation was also studied. The second phase of ImmGen started profiling activated immune cells. The interferon response was used as a test case.

Bioinformatic gene regulatory network model Several groups of collaborating computational biologists (Regev & Koller) used the data to reverse-engineer the genetic regulatory network in immune cells, and compare it to the human immune system An initial survey of differential splicing across immune lineages was carried out using both microarrays and RNA-sequencing.

Visual representation of data Project participants from Brown University's Computer Sciences Department are also exploring novel representation modes for the ImmGen data, developing and curating the public representation.

Members Participating Immunology laboratories include: The Brenner (NKT, BWH, Boston), Goldrath (Activated CD8 T cells, UCSD, San Diego), Kang (gamma delta T cells, U. Mass, Worcester), Lanier (NK, UCSF, San Francisco), Mathis/Benoist (alpha beta T cells, HMS, Boston), Merad and Randolph (monocytes & macrophages, Mount Sinai, New York and Washington University in St. Louis), Rossi (HSC, Children's, Boston), Turley (DC, DFCI, Boston), and Wagers (HSC, Joslin, Boston) labs. Richard (Randy) Hardy (Fox Chase, Philadelphia), who was an ImmGen member since its initiation, died in June 2016.

Current status As of August 2016, Immgen has profiled more than 250 naive cell populations in the mouse using microarrays, and several dozens of activated cell types using RNA-sequencing.

Data access The project's status and detailed information can be seen at (ImmGen). This site also includes a dedicated data browser, with which users can interactively explore the expression profiles for particular genes, networks of co-regulated genes, and genes that best distinguish different cell types. Raw data are available at the NCBI's Gene Expression Omnibus [2]

Worked examples

Example 1 — a first encounter with Immunological Genome Project

Start with the simplest possible case. Write down what Immunological Genome Project 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 Immunological Genome Project 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 Immunological Genome Project 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 Immunological Genome Project

In research: Immunological Genome Project 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 Immunological Genome Project 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: Immunological Genome Project is common in secondary-school and first-year university syllabi. It links to neighbouring topics Genome projects, Immunology organizations, so understanding it makes those chapters shorter.
In everyday life: Look for Immunological Genome Project 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.

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How to study Immunological Genome Project in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Immunological Genome Project 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 Immunological Genome Project out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Immunological Genome Project in simple terms?

Why does Immunological Genome Project 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 Immunological Genome Project?

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 Immunological Genome Project.