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Barbera van Schaik Bioinformatics laboratory, KEBB.

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Presentation on theme: "Barbera van Schaik Bioinformatics laboratory, KEBB."— Presentation transcript:

1 Barbera van Schaik Bioinformatics laboratory, KEBB

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 products can not be spliced after mutation? Tabel in log. CodonAnticodonAAGen met intron / totaal genen OpmerkingIn aantal RefSeqs Totaal aantal codons atatatIle5/5Geen alternatieve genen zonder intron 25.795122.908 ttgcaaLeu5/6Heeft hiernaast één pseudogen zonder intron 33.173213.163 cctaggPro1/10Hiernaast 3 pseudogenen 35.179314.834 agatctArg5/6Geen pseudo genen 32.746210.889 tacgtaTyr13/13En nog 3 pseudo genen 32.732235.748 tatataTyr1/1Geen pseudo genen 30.169192.409 * TAC en TAT zouden mogelijk de tRNA genen van elkaar kunnen gebruiken i.v.m. wobble base pairing

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

16 Top genes TTN D100 MUC16 FLG LOC730833 TTN SRRM2 MUC19 SYNE2 SYNE1 ZC3H13 PRKA HMCN1 FLG2 DNAH8 GPR98 KIAA1109 MUC19 BRWD1 DNAH11 DYNC2H1 MYCBP2 DYNC2H1 MLL3 C2orf16 MACF1 ALMS1 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

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26 RankGOstat

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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

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