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Thu 23 Jan 2020
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Extracting biological information from gene lists
Beginners

Thu 23 Jan 2020

Description

Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting biological themes which turn up in the lists.

This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication.

Course materials are available here.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
Sessions

Number of sessions: 1

# Date Time Venue Trainer
1 Thu 23 Jan 2020   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Simon Andrews
Topics covered

Bioinformatics, Biology, Ontologies, nomenclature and classification, Gene-set enrichment analysis, Pathway or network analysis

Objectives

After this course you should be able to:

  • Understand the principles of gene set enrichment, and the available sources of gene sets
  • Understand the statistics used to assess enrichment, and the different ways these can be applied
  • Run a number of web based gene set enrichment tools
  • Understand the rationale for motif based analysis of gene sets
  • Run motif searches using the MEME suite
Aims

During this course you will learn about:

  • The theory of gene set enrichment, the different types of enrichment test and how they apply to different data
  • The available sources of gene sets to analyse
  • How to run qualitative and quantitative gene set analyses and how to present the results
  • The theory of motif detection and how to prepare your data for such analysis
  • How to run a motif detection and evaluate the results
Format

Presentations, demonstrations and practicals

Registration fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Timetable

Day 1 Topics
Session 1 Gene set analysis Introduction
Session 2 Qualitative Gene set analysis
Session 3 Quantitative Gene set analysis
Session 4 Presenting Results
Session 5 Artefacts and Biases
Session 6 Motif Analysis
Duration

1

Frequency

A number of times per year

Theme
Specialized Training

Booking / availability