CSB Assignment Week 3

Assignments for Week 3

Note! This assignment is currently active. All significant changes will be announced on the mailing list.

 
 

Exercises for this week relate to this week's lecture.
Pre-reading for this week will prepare next week's lecture.
Exercises and pre-reading will be topics on next week's quiz.

Exercises

Task:

• Work through the DAVID tutorial published in nature protocols:

Huang et al. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44-57. (pmid: 19131956)

[ PubMed ] [ DOI ] Abstract DAVID bioinformatics resources consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists. This protocol explains how to use DAVID, a high-throughput and integrated data-mining environment, to analyze gene lists derived from high-throughput genomic experiments. The procedure first requires uploading a gene list containing any number of common gene identifiers followed by analysis using one or more text and pathway-mining tools such as gene functional classification, functional annotation chart or clustering and functional annotation table. By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.

• Access the Web version of the article, it conveniently contains the required links.

• Use Demo List 2, provided on the DAVID site for your analysis. Remember to read the description of the gene list.

• Do not use any of the Java tools. As of this writing Java applets in Web browsers are considered fundamentally insecure; Java should be disabled in your browser.

• For each of the analysis steps, think clearly about whether the results support od contradict your expectations about the data. Feel free to discuss your expectations and findings on the mailing list.

• If there are any problems with the assignment, contact me!

Pre-reading

The Encode project is a current paradigm for the integration of multiple -omics datasets for comprehensive annotation of the human genome.

ENCODE Project Consortium (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9:e1001046. (pmid: 21526222)

[ PubMed ] [ DOI ] Abstract The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.