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<ul><li>Basic bioinformatics concepts, databases and tools </li></ul><ul><li>Module 5 </li></ul><ul><li>Genome browsers an...
Integrating biological information <ul><li>Genome databases and browsers </li></ul><ul><ul><li>Integration on a species ba...
Reference genome sequences provide a standard genome sequence per species  <ul><li>Genomes  </li></ul><ul><ul><li>From var...
 
Finding your way in genomes <ul><li>Annotation and terms </li></ul><ul><ul><ul><li>See also  NCBI handbook </li></ul></ul>...
Genome Browsers: main players <ul><li>Three main players  </li></ul><ul><ul><li>MapViewer (NCBI) </li></ul></ul><ul><ul><l...
Ensembl Genome browser <ul><li>We will use this browser in this session </li></ul><ul><ul><li>Information is combination o...
28 November 2009 [email_address] /10 http://www.ensembl.org Information about the genomes
http://www.ensemblgenomes.org
[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 <ul><li>Usefulness: </li></ul><ul><ul><li>One place for all information on a particular gene / stru...
Ensembl Genome browser <ul><li>Usefulness: </li></ul><ul><ul><li>One place for all information on a particular gene / stru...
Tracks are a way to display information on a genome sequence <ul><li>The annotation on a genome-wide scale is displayed in...
Tracks are a way to display information on a genome sequence <ul><li>The annotation on a genome-wide scale is displayed in...
Biomart, your one stop portal to fetch information <ul><li>Biomart  http://www.biomart.org/   </li></ul><ul><ul><li>These ...
Biomart, your one stop portal to fetch information <ul><li>Biomart  http://www.biomart.org/   </li></ul><ul><ul><li>These ...
Biomart, your one stop portal to fetch information <ul><li>Biomart  http://www.biomart.org/   </li></ul>Translated questio...
Biomart is available for an increasing number of databases <ul><li>Biomart </li></ul><ul><ul><li>http://www.biomart.org/  ...
Gene lists resulting from different analyses can reveal their biology  <ul><li>DAVID -  http://david.abcc.ncifcrf.gov/   <...
Gene lists resulting from different analyses can reveal their biology  <ul><li>DAVID -  http://david.abcc.ncifcrf.gov/   <...
Galaxy allows you to store your data and to (re)analyse it conveniently <ul><li>Galaxy -  http://usegalaxy.org   </li></ul>
Galaxy allows you to store your data and to (re)analyse it conveniently <ul><li>Galaxy -  http://usegalaxy.org   </li></ul...
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BITs: Genome browsers and interpretation of gene lists.

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Module 5 Genome browsers and interpreting gene lists.

Part of training session "Basic Bioinformatics concepts, databases and tools" - http://www.bits.vib.be/training

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Transcript of "BITs: Genome browsers and interpretation of gene lists."

  1. 1. <ul><li>Basic bioinformatics concepts, databases and tools </li></ul><ul><li>Module 5 </li></ul><ul><li>Genome browsers and </li></ul><ul><li>interpretation of gene lists </li></ul><ul><li>Dr. Joachim Jacob </li></ul><ul><li>http://www.bits.vib.be </li></ul>Updated 21 July 2011 http://dl.dropbox.com/u/18352887/BITS_training_material/Link%20to%20mod5-intro_H1_2011_genomebrowsers.pdf
  2. 2. Integrating biological information <ul><li>Genome databases and browsers </li></ul><ul><ul><li>Integration on a species basis all biological information: Ensembl Genome Browser </li></ul></ul><ul><ul><ul><li>http://www.ensembl.org/ </li></ul></ul></ul><ul><li>Table Browsers </li></ul><ul><ul><li>Retrieving biological (not only sequence) data applying various criteria: Biomart </li></ul></ul><ul><li>http://www.biomart.org/ </li></ul><ul><li>Interpreting gene lists </li></ul><ul><ul><li>'What is the biology behind my gene list': DAVID </li></ul></ul><ul><li>http://david.abcc.ncifcrf.gov/ </li></ul>
  3. 3. Reference genome sequences provide a standard genome sequence per species <ul><li>Genomes </li></ul><ul><ul><li>From various sequence sources, a genome is assembled </li></ul></ul><ul><ul><ul><li>By NCBI: currently assembly 37 in human (or 'build') (2010) </li></ul></ul></ul><ul><ul><ul><li>By Celera: commercial </li></ul></ul></ul><ul><ul><li>Each build differs! </li></ul></ul><ul><ul><ul><li>1. Data freeze: all data for assembling (ignoring new data from that point) </li></ul></ul></ul><ul><ul><ul><li>2. Assembly process and annotation </li></ul></ul></ul><ul><ul><ul><li>3. Release of the Build: Reference Sequence Genom e </li></ul></ul></ul>http://www.ncbi.nlm.nih.gov/Genomes/
  4. 5. Finding your way in genomes <ul><li>Annotation and terms </li></ul><ul><ul><ul><li>See also NCBI handbook </li></ul></ul></ul><ul><ul><li>Locus = place on the genome, ~ a gene (different alleles) </li></ul></ul><ul><ul><li>Location: </li></ul></ul><ul><ul><ul><li>Rough location by staining of chromosomes e.g. 18q12.1 -> chromosome 18, long arm (=q, small arm is p) </li></ul></ul></ul><ul><ul><ul><li>Exact bases on genomes (assembly must be mentioned!) </li></ul></ul></ul>
  5. 6. Genome Browsers: main players <ul><li>Three main players </li></ul><ul><ul><li>MapViewer (NCBI) </li></ul></ul><ul><ul><li>UCSC Genome Browser </li></ul></ul><ul><ul><li>Ensembl Genome browser </li></ul></ul>BITS UCSC Genome Browser training BITS Ensembl Genome Browser training
  6. 7. Ensembl Genome browser <ul><li>We will use this browser in this session </li></ul><ul><ul><li>Information is combination of automatic annotation and manually curated s ources (ENS >< Havana (Vega) genes) </li></ul></ul><ul><ul><li>All entries can be accessed through the browser, each with its own clear identifiers </li></ul></ul>
  7. 8. 28 November 2009 [email_address] /10 http://www.ensembl.org Information about the genomes
  8. 9. http://www.ensemblgenomes.org
  9. 10. [email_address] /10 ! … or click on the figure feature!
  10. 11. 28 November 2009 [email_address] /10
  11. 12. 28 November 2009 [email_address] /10 [email_address]
  12. 13. TAB SUMMARY DETAILED INFORMATION INFOR-MATION SELEC-TOR DATA MANAGER tab DAS
  13. 14. Ensembl Genome browser <ul><li>Usefulness: </li></ul><ul><ul><li>One place for all information on a particular gene / structure / location / variation </li></ul></ul><ul><ul><li>But also: </li></ul></ul><ul><ul><ul><li>Comparison to other species </li></ul></ul></ul><ul><li>The Ensembl Team has a lot of training movies and examples available. Check them out! </li></ul>http://www.ensembl.org/info/index.html http://www.ensembl.org/Help/Movie?id=188
  14. 15. Ensembl Genome browser <ul><li>Usefulness: </li></ul><ul><ul><li>One place for all information on a particular gene / structure / location / variation </li></ul></ul><ul><ul><li>But also: </li></ul></ul><ul><ul><ul><li>Comparison to other species </li></ul></ul></ul><ul><li>The Ensembl Team has a lot of training movies and examples available. Check them out! </li></ul>http://www.ensembl.org/info/index.html http://www.ensembl.org/Help/Movie?id=188
  15. 16. Tracks are a way to display information on a genome sequence <ul><li>The annotation on a genome-wide scale is displayed in tracks. </li></ul><ul><ul><li>Relevant database content can be formatted in tracks and displayed on a reference genome </li></ul></ul>Genome reference tracks Screenshot of Ensembl genome browser
  16. 17. Tracks are a way to display information on a genome sequence <ul><li>The annotation on a genome-wide scale is displayed in tracks, most used formats: </li></ul><ul><ul><li>- each base receives a value: dense continuous data: WIG format (e.g. %GC) </li></ul></ul><ul><ul><li>- annotation has a start and a stop coordinate: bed format (e.g. gene annotations) </li></ul></ul><ul><li>Example </li></ul><ul><ul><li>Variations in genomes are reported in vcf format </li></ul></ul>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
  17. 18. Biomart, your one stop portal to fetch information <ul><li>Biomart http://www.biomart.org/ </li></ul><ul><ul><li>These questions are easy: </li></ul></ul>Hey, can you tell me how many genes in mouse exist which regulate transcription and are located on Chromosome 19 ?
  18. 19. Biomart, your one stop portal to fetch information <ul><li>Biomart http://www.biomart.org/ </li></ul><ul><ul><li>These questions are easy: </li></ul></ul>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
  19. 20. Biomart, your one stop portal to fetch information <ul><li>Biomart http://www.biomart.org/ </li></ul>Translated questions reflect in database choice and Filters Resulting genes are counted and the output set via Attributes
  20. 21. Biomart is available for an increasing number of databases <ul><li>Biomart </li></ul><ul><ul><li>http://www.biomart.org/ </li></ul></ul>
  21. 22. Gene lists resulting from different analyses can reveal their biology <ul><li>DAVID - http://david.abcc.ncifcrf.gov/ </li></ul>
  22. 23. Gene lists resulting from different analyses can reveal their biology <ul><li>DAVID - http://david.abcc.ncifcrf.gov/ </li></ul>DEMO Alternatives g:Profiler http://biit.cs.ut.ee/gprofiler/ Babelomics http://www.babelomics.org/
  23. 24. Galaxy allows you to store your data and to (re)analyse it conveniently <ul><li>Galaxy - http://usegalaxy.org </li></ul>
  24. 25. Galaxy allows you to store your data and to (re)analyse it conveniently <ul><li>Galaxy - http://usegalaxy.org </li></ul>DEMO TOOLS RESULTS DATA SETS
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