The Genome Gamble, Knowledge or Carnage

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The Genome Gamble, Knowledge or Carnage?

• Comparative Genomics Leading the Way _at_ Organon

Tim Hulsen, Oss, November 11, 2003
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Summary

• (1) An introduction to orthology and paralogy
• (2) Orthology determination within eukaryotes
• (3) Testing the advantages of our ortholog set
• (4) Using evolutionary conservation of
  co-expression for function prediction
• (5) Evolutionary conservation of chromosomal
  distance and orientation

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(1) An introduction to orthology and paralogy

• Homologous genes genes that have a common
  ancestor
• Orthologous genes genes that evolved from a
  common ancestor through a speciation event (?
  equivalents in different species)
• Paralogous genes genes that evolved from a
  common ancestor through a duplication event

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Orthology and paralogy explained graphically
(from http//www.ncbi.nlm.nih.gov/Education/BLASTi
nfo/Orthology.html)
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The importance of orthology and paralogy

• Orthology relationships especially important for
  function prediction orthologous genes generally
  have the same function but in different species
• Paralogy relationships can be used for function
  prediction too paralogous genes are often
  involved in the same process, but have different
  molecular functions (e.g. globins)

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(2) Orthology determination within eukaryotes

• Not much eukaryotic orthology available at this
  moment
• euKaryotic Orthologous Groups (KOG,NCBI)
• Inparanoid
• OrthoMCL
• Existing databases are either too inclusive or
  too restrict
• Most methods rely on best bidirectional hit
  (E-value), while orthology is an evolutionary
  principle.. should be determined using
  phylogenetic trees!

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Our orthology determination
within eukaryotes

• Hs
• 
  At, Ce, Dm, Ec, Gt, Hs, Mm, Sc, Sp
• Zgt20, RHgt0.5QL
• 24,263 groups

GENOME
Hs-Mm 85,848 pairs Hs-Dm 55,934 pairs etc.
TREE SCANNING
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Our orthology determination using phylogenetic
trees

• Example BMP6 (Bone Morphogenetic Protein 6) ? 5
  orthologous relations are defined, all Hs-Mm

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The ortholog database Eukaryortho
http//t2.teras.sara.nl4086
(only accessible from Organon, CMBI and SARA)
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(3) Testing the advantages of our ortholog set

• Quality of orthology difficult to test
• Orthologs should have more or less the same
  function --gt use conservation of function as an
  orthology benchmark
• Gene Ontology (GO) database hierarchical system
  of function and location descriptions
• Orthologs are in same functional category when
  they are in the same 4th level GO Molecular
  Function class

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GO molecular function benchmark

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• 1
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• Molecular function one of the three subroots
  (together with biological process and cellular
  location)
• True orthologs should share a 4th level
  molecular function (here GO0019912)
• Our Hs-Mm ortholog set 67
• KOG Hs-Mm ortholog set 51

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Co-expression benchmark

• Second method comparing expression profiles of
  each orthologous gene pair
• Using GeneLogic Expressor data set
• Human chips 3269 samples, 44792 fragments, 115
  tissue categories, 15 SNOMED tissue categories
• Mouse chips 859 samples, 36701 fragments, 25
  tissue categories, 12 SNOMED tissue categories

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SNOMED tissue categories used for co-expression
calculation
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Calculating the correlation

• N?xy (?x)(?y)
• r ----------------------------------------------
  ---
• sqrt( (N?x2 - (?x)2)(N?y2 (?y)2) )

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Co-expression comparison of our ortholog set to
the KOG set
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(4) Using evolutionary conservation of
co-expression for function prediction
Human
Gene A Gene B
Co-expression Cab (-1ltcorr.lt1)
(Co-expression calculated over 115 tissues in
human, 25 in mouse)
Human/Mouse
Gene A Gene B
Cab gt Cab
? Increases probability that A and B are involved
in the same process
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GO biological process benchmark

• 0
• 1
• 2
• 3
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• Biological process one of the three subroots
  (together with cellular location and molecular
  function)
• Both orthologs and paralogs are often involved in
  the same process/pathway (sharing a 4th level
  biological process, here GO0007584)

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Conservation of co-expression used in function
prediction
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The importance of (conserved) co-expression for
function prediction

• Co-expression without conservation can already be
  used for function prediction
• Paralogous conservation gives a 2x higher
  accuracy
• Orthologous conservation gives a 3x or 4x higher
  accuracy
• Alternative for GO Biological Process KEGG
  Pathway database ? similar results

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(5) Evolutionary conservation of chromosomal
distance and orientation
Human
Gene A Gene B
Distance Dab ( bp) Orientation Oab
(??,??,??) Co-expression Cab (-1ltcorr.lt1)
Dab lt Dab Oab Oab Cab gt Cab
(Co-expression calculated over 115 tissues in
human, 25 in mouse)
Human/Mouse
Gene A Gene B
? Increases probability that A and B are involved
in the same process
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Function prediction using co-expression and
chromosomal distance (without conservation)
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Conservation of chromosomal distance used in
function prediction
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The importance of chromosomal distance and
orientation for function prediction

• Chromosomal distance in eukaryotes less important
  than in prokaryotes (due to the absence of
  operons)
• Only genes with distance lt 1 Mbp seem to be
  coregulated
• Conservation of relative orientation seems to be
  important only for very close gene pairs
• Limited number of genes can be functional
  annotated using the conservation of chromosomal
  distance and orientation

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Conclusions

• Orthologous and paralogous relations can be used
  to improve function prediction
• Our orthologous pairs of Protein World proteins
  perform better than KOG, in terms of
  co-expression and involvement in the same process
• Chromosomal distance and relative orientation
  between genes can be used for function prediction
  too, in a limited number of cases
• Future plans find examples where the function of
  a protein can be predicted using these methods

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Credits

• Martijn Huynen
• Peter Groenen
• Others at Comics
• Others at Organon Bioinf.