BITs: Genome browsers and interpretation of gene lists.

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Updated 21 July 2011 http://dl.dropbox.com/u/18352887/BITS_training_material/Link%20to%20mod5-intro_H1_2011_genomebrowsers.pdf

Integrating biological information ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Reference genome sequences provide a standard genome sequence per species ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],http://www.ncbi.nlm.nih.gov/Genomes/

Finding your way in genomes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Genome Browsers: main players ,[object Object],[object Object],[object Object],[object Object],BITS UCSC Genome Browser training BITS Ensembl Genome Browser training

Ensembl Genome browser ,[object Object],[object Object],[object Object]

28 November 2009 [email_address] /10 http://www.ensembl.org Information about the genomes

[email_address] /10 ! … or click on the figure feature!

28 November 2009 [email_address] /10

28 November 2009 [email_address] /10 [email_address]

TAB SUMMARY DETAILED INFORMATION INFOR-MATION SELEC-TOR DATA MANAGER tab DAS

Ensembl Genome browser ,[object Object],[object Object],[object Object],[object Object],[object Object],http://www.ensembl.org/info/index.html http://www.ensembl.org/Help/Movie?id=188

Tracks are a way to display information on a genome sequence ,[object Object],[object Object],Genome reference tracks Screenshot of Ensembl genome browser

Tracks are a way to display information on a genome sequence ,[object Object],[object Object],[object Object],[object Object],[object Object],http://www.ensembl.org/info/website/upload/bed.html http://www.bits.vib.be/wiki/index.php/.vcf #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ

Biomart, your one stop portal to fetch information ,[object Object],[object Object],Hey, can you tell me how many genes in mouse exist which regulate transcription and are located on Chromosome 19 ?

Biomart, your one stop portal to fetch information ,[object Object],[object Object],Hey, can you tell me how many genes in mouse exist which regulate transcription and are located on Chromosome 19 ? Ensembl Genes Genome sequence (Ensembl) Gene Ontology GO:0009299

Biomart, your one stop portal to fetch information ,[object Object],Translated questions reflect in database choice and Filters Resulting genes are counted and the output set via Attributes

Biomart is available for an increasing number of databases ,[object Object],[object Object]

Gene lists resulting from different analyses can reveal their biology ,[object Object]

Gene lists resulting from different analyses can reveal their biology ,[object Object],DEMO Alternatives g:Profiler http://biit.cs.ut.ee/gprofiler/ Babelomics http://www.babelomics.org/

Galaxy allows you to store your data and to (re)analyse it conveniently ,[object Object]

Galaxy allows you to store your data and to (re)analyse it conveniently ,[object Object],DEMO TOOLS RESULTS DATA SETS

BITs: Genome browsers and interpretation of gene lists.

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BITs: Genome browsers and interpretation of gene lists.