1. Bioinformatics and Chips Bioinformatics is a very integral part of each step in a chip project. Bioinformatics is a very integral part of each step in a chip project.

2. Steps in a Chip Project 1 Biological question 2 Design experiment 3 Design chip 4 Run experiment 5 Read out chip 6 Treat data 7 Biological answer First overview, then details

3. Biological Question A chip experiment is only worth doing, if it answers a question that is worth asking.

4. Design Experiment Not every question can be answered with a chip experiment. Some questions that can be answered with a chip experiment can also be answered with another (cheaper) experiment.

5. Design experiment Probes on the chip: Unique Reproducible

6. Run Experiment Like every binding study, chip experiments have a thermodynamic and a kinetic component.

7. Run Experiment Binding thermodynamics:  G =  H - T  S  G = - R T ln(K)  G = 1.4 kCal/M ~ Factor 10 in K 1 H-bond ~ 1 – 4 kCal/M

8. Chip Read Out is ‘Solved’ And, what is more, it has nothing to do with bioinformatics.

9. Treat Data I assume this has been discussed in other sessions in this course.

10. Biological Answer This is not just bioinformatics. Everything you know can, and should, be used at this stage.

11. Knowledge needed No matter what chip-array software you use, you will want to know all there is to know about the genes/proteins that are on the chip. So, up-to-date databases are always needed.

12. Some tools BLAST SRS KEGG www.cmbi.kun.nl

13. BLAST

14. BLAST

15. BLAST

16. BLAST

17. SRS

18. SRS

19. SRS

20. SRS

21. SRS

22. KEGG

23. KEGG

24. KEGG

25. KEGG

26. KEGG

27. KEGG

28. SwissProt ID CRAM_CRAAB STANDARD; PRT; 46 AA. AC P01542; DT 21-JUL-1986 (Rel. 01, Created) DT 21-JUL-1986 (Rel. 01, Last sequence update) DT 01-NOV-1997 (Rel. 35, Last annotation update) DE CRAMBIN. GN THI2. OS Crambe abyssinica (Abyssinian crambe). OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; OC core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; OC Crambe.

29. SwissProt RN [1] RP SEQUENCE. RX MEDLINE; 82046542. RA TEETER M.M., MAZER J.A., L'ITALIEN J.J.; RT "Primary structure of the hydrophobic plant protein crambin."; RL Biochemistry 20:5437-5443(1981). CC -!- FUNCTION: THE FUNCTION OF THIS HYDROPHOBIC PLANT CC SEED PROTEIN IS NOT KNOWN. CC -!- SIMILARITY: BELONGS TO THE PLANT THIONIN FAMILY. DR PIR; A01805; KECX. DR PDB; 1CRN; 16-APR-87. DR PDB; 1CBN; 31-JAN-94.

30. SwissProt FT DISULFID 3 40 FT DISULFID 4 32 FT DISULFID 16 26 FT VARIANT 22 22 P -> S. FT VARIANT 25 25 I -> L. FT STRAND 2 3 FT HELIX 7 16 FT TURN 17 19 FT HELIX 23 30 FT TURN 31 31 FT STRAND 33 34 FT TURN 42 43 SQ SEQUENCE 46 AA; 4736 MW; F6ADE458 CRC32; >P1;CRAM_CRAAB TTCCPSIVAR SNFNVCRLPG TPEAICATYT GCIIIPGATC PGDYAN*

31. Significance

32. Pointers www. cmbi.kun.nl/ www. cmbi.kun.nl/srs/ www. cmbi.kun.nl/bioinf/tools/blast.shtml www. genome.ad.jp/kegg/ www. affymetrix.com/ www. dmd.nl/arrayNL/arrayNL.html www. gene-chips.com/ (the blank in there is not real, but needed if you use this Windows thing)

33. Pointers www. BioASP.nl Bioinformatica.pagina.nl jura.ebi.ac.uk:8765/gqsrv/submit Soon an CMBI/BioASP: Pedant (the blank in there is not real, but needed if you use this Windows thing)