Evalue Zvalue Comparison 10 02 2004 Nijmegen Tim
- Slides: 14
E-value / Z-value Comparison 10 -02 -2004 Nijmegen Tim Hulsen
Summary • (1) SCOP comparison • (2) BBH comparison: – Equal Swiss. Prot name – Co-expression – Conserved gene order • (3) Conclusions
SCOP comparison • E/Z: sequence < 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/Z>TH • ‘Errors per query’: how much of the queries give a hit which is not within a SCOP class
- SCOP comparison +
BBH comparison E: 12695 BBH, Z: 12817 BBH Best Bidirectional Hits calculated for Human-Mouse: • Biofacet (Protein World) -> Smith. Waterman with Zvalues • Paracel -> Smith. Waterman with Evalues
BBH comparison: Equal Swiss. Prot name • Benchmarking of orthology through conservation of function • Easy-to-read functional annotation: Swiss. Prot name • ‘Equal’: e. g. ANDR_HUMAN <-> ANDR_MOUSE
BBH comparison: Equal Swiss. Prot name • E-value: 297/1896 = 0. 157 • Z-value: 153/2018 = 0. 076
BBH comparison: Co-expression • Comparison of expression profiles of each best bidirectional hit • Using Gene. Logic Expressor data set: organism samples fragments tissue SNOMED categories tissue categories human 3269 44792 115 15 mouse 859 36701 25 12
BBH comparison: Co-expression HUMAN MOUSE 1 Blood vessel 2 Cardiovascular system 9 Male genital system 8 Male genital system 3 Digestive organs 10 Musculoskeletal system 9 Musculoskeletal system 11 Nervous system 10 Nervous system 4 Digestive system - 5 Endocrine gland - 12 Product of conception 6 Female genital system 5 Female genital system 13 Respiratory system 11 Respiratory system 7 Hematopoietic system 6 Hematopoietic system 14 Topographic region - 8 Integumentary system 7 Integumentary system 15 Urinary tract 12 Urinary tract
BBH comparison: Co-expression • Calculation of the correlation coefficient: N xy – ( x)( y) r = -------------------sqrt( (N x 2 - ( x)2)(N y 2 – ( y)2)) • Measured over the 12 corresponding SNOMED tissue categories
BBH comparison: Co-expression • E-value: 345 pairs compared: 0. 329 • Z-value: 307 pairs compared: 0. 310
BBH comparison: Conserved gene order Human Gene A Gene B Mouse Gene A’ Gene B’ 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?
BBH comparison: Conserved gene order • E-value: 21/74 = 0. 284 • Z-value: 18/96 = 0. 188
Conclusions • SCOP comparison: Z-value only better than E-value when high identity to each other (90%, 100%) • BBH comparison: – Equal Swiss. Prot name: E>>Z – Co-expression: E>Z – Conserved gene order: E>>Z • Added value of Z-value is (very) doubtful
