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Barbera van Schaik Bioinformatics laboratory, KEBB

Barbera van Schaik Bioinformatics laboratory, KEBB. tRNA project. Introduction. Department of neurogenetics. Mutation found in tRNA splicing complex: Lethality halfway pregnancy Brains stop growing Questions: Which genes are affected? Which gene categories are affected?. Background.

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Barbera van Schaik Bioinformatics laboratory, KEBB

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  1. Barbera van Schaik Bioinformatics laboratory, KEBB tRNA project

  2. Introduction

  3. Department of neurogenetics Mutation found in tRNA splicing complex: Lethality halfway pregnancy Brains stop growing Questions: Which genes are affected? Which gene categories are affected?

  4. Background

  5. Reminder: translation http://www.scq.ubc.ca/changing-the-language-of-dna/

  6. Codon table http://nl.wikipedia.org/wiki/Basepaar

  7. tRNA genes

  8. Wobble base pairing Crick (1966), JMB http://nl.wikipedia.org/wiki/Basepaar

  9. HS genome about codons International Human Genome Sequencing Consortium (2001), Nature

  10. tRNA splicing Abelson et al (1998), JBC

  11. Review: Mutations in translation machinery and disease Scheper et al (2007), Nature reviews genetics

  12. tRNA mutations and disease Scheper et al (2007), Nature reviews genetics

  13. Methods / Preliminary results

  14. Which tRNA productscan not be spliced after mutation? Tabel in log. * TAC en TAT zouden mogelijk de tRNA genen van elkaar kunnen gebruiken i.v.m. wobble base pairing

  15. Determine affected genesand gene categories Determine frequency and percentage of codons in all RefSeq sequences Rank GO statistics (BeiBbarth) Rank statistics Perry&Emiel

  16. Top genes PRKA PRKA PRKA HMCN1 FLG2 DNAH8 GPR98 KIAA1109 MUC19 BRWD1 BRWD1 DNAH11 DYNC2H1 MYCBP2 DYNC2H1 DYNC2H1 TTN TTN TTN TTN D100 MUC16 FLG LOC730833 TTN SRRM2 MUC19 SYNE2 SYNE1 SYNE1 ZC3H13 MLL3 C2orf16 MACF1 ALMS1 STARD9 STARD9 MKI67 NEB From: top50_refseq_count_aga.txt

  17. Common gene categories Count list Metabolic process (nucleotide, RNA, biopolymer, protein modification) Cell adhesion Tim BeiBbarth, http://gostat.wehi.edu.au/

  18. Common gene categories Percentage list aga Metabolic process (nucleotide, RNA, biopolymer) ata, tat, ttg Sensory perception (smell, chemical stimulus) G-protein coupled receptor protein signaling pathway cct RNA metabolic process Regulation of transcription tac G-protein coupled receptor protein signaling pathway Multicellular organismal process Cell surface receptor linked signal transduction Tim BeiBbarth, http://gostat.wehi.edu.au/

  19. GO analysis Perry/Emiel On first sight same categories Furthermore remarkable: Countlist has many significant GO categories

  20. Preliminary conclusions Long transcripts can not (or less efficient) be translated Effect on categories: Metabolism (Biopolymer metabolic process) Neurological processes (among others: sensory perception)

  21. To do New list with all RefSeq entries per codon Run GO analysis again Visualize GO categories (they could be in the same branche) Which GO categories are untouched? Is there a difference between GO list tRNAs with/without intron

  22. Perry en Emiel

  23. Perry en Emiel

  24. Perry en Emiel

  25. Perry en Emiel

  26. RankGOstat

  27. RankGOstat

  28. To do New list with all RefSeq entries per codon Run GO analysis again Visualize GO categories (they could be in the same branche) Which GO categories are untouched? Is there a difference between GO list tRNAs with/without intron

  29. ---

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