Evalue Zvalue Comparison

1
E-value / Z-value Comparison

• 10-02-2004 Nijmegen
• Tim Hulsen

2
Summary

• (1) SCOP comparison
• (2) BBH comparison
• Equal SwissProt name
• Co-expression
• Conserved gene order
• (3) Conclusions

3
SCOP comparison

• E/Z sequence lt SCOP structural
• Astral SCOP database release 1.63 PDB sets with
  10, 30, 50, 70, 90 and 100 maximum identity to
  each other
• Coverage how much of the pairs within a SCOP
  class have E/ZgtTH
• Errors per query how much of the queries give
  a hit which is not within a SCOP class

4
SCOP comparison
-

5
BBH comparison
E 12695 BBH, Z 12817 BBH

• Best Bidirectional Hits calculated for
  Human-Mouse
• Biofacet (Protein World) -gt Smith-Waterman with
  Z-values
• Paracel -gt Smith-Waterman with E-values

6
BBH comparison Equal SwissProt name

• Benchmarking of orthology through conservation of
  function
• Easy-to-read functional annotation SwissProt
  name
• Equal e.g.
• ANDR_HUMAN lt-gt ANDR_MOUSE

7
BBH comparison Equal SwissProt name

• E-value 297/1896 0.157
• Z-value 153/2018 0.076

8
BBH comparison Co-expression

• Comparison of expression profiles of each best
  bidirectional hit
• Using GeneLogic Expressor data set

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BBH comparison Co-expression
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BBH comparison Co-expression

• Calculation of the correlation coefficient
• N?xy (?x)(?y)
• r ---------------------------------------
• sqrt( (N?x2 - (?x)2)(N?y2 (?y)2))
• Measured over the 12 corresponding SNOMED tissue
  categories

11
BBH comparison Co-expression

• E-value 345 pairs compared 0.329
• Z-value 307 pairs compared 0.310

12
BBH comparison Conserved gene order
Human
How much of the neighboring gene pairs A-B in
human, that have at least one orthologous gene
pair A-B in mouse, have a neighboring
orthologous gene pair A-B in mouse?
Gene A Gene B
Mouse
Gene A Gene B
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BBH comparison Conserved gene order

• E-value 21/74 0.284
• Z-value 18/96 0.188

14
Conclusions

• SCOP comparison Z-value only better than E-value
  when high identity to each other (90,100)
• BBH comparison
• Equal SwissProt name EgtgtZ
• Co-expression EgtZ
• Conserved gene order EgtgtZ
• Added value of Z-value is (very) doubtful