1. Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005

2. Kate Milova MolGen retreat March 24, 2005 2 Outline.  Microarray platforms and services available at AECOM:  cDNA  Long Oligo  Afymetrix  Database ( cDNA & Long Oligo ) structure and content:  Printing information  Chip layout  Annotation  On-line Analysis Tools:  Normalization  Signal filtering  Comparison  Statistical packages and Analysis software  Summary

3. Kate Milova MolGen retreat March 24, 2005 3 Microarray Platforms at AECOM.

4. Kate Milova MolGen retreat March 24, 2005 4 How to choose a microarray platform.

5. Kate Milova MolGen retreat March 24, 2005 5 Before starting your microarray experiment.

6. Kate Milova MolGen retreat March 24, 2005 6 Microarray’s Experts.

7. Kate Milova MolGen retreat March 24, 2005 7 cDNA Microarray Facility. Home page.  Introduction  aaa  Introduction  aaa  Introduction  aaa  Introduction  aaa  Introduction  aaa  Introduction  aaa  Introduction  aaa

8. Kate Milova MolGen retreat March 24, 2005 8 cDNA Microarray Facility.Services. cDNA Microarray Facility. Services.

9. Kate Milova MolGen retreat March 24, 2005 9 cDNA Microarray Facility. Arrays.

10. Kate Milova MolGen retreat March 24, 2005 10 cDNA Microarray Facility. Publications.

11. Kate Milova MolGen retreat March 24, 2005 11 cDNA Microarray Facility. Database.

12. Kate Milova MolGen retreat March 24, 2005 12 Database Search.

13. Kate Milova MolGen retreat March 24, 2005 13 cDNA Microarray Facility. Database.

14. Kate Milova MolGen retreat March 24, 2005 14 Pipeline. LOWESS Normalization.

15. Kate Milova MolGen retreat March 24, 2005 15 cDNA Microarray Facility. Pipeline. Filtering.

16. Kate Milova MolGen retreat March 24, 2005 16 cDNA Microarray Facility. Comparison.

17. Kate Milova MolGen retreat March 24, 2005 17 Annotation sources: NCBI. NCBI Entrez Gene UniGene Refseq & NT databases Blast Search Blast Software Unigene ID  Gene ID  GO ID Unigene ID  Accession Unigene ID  Blast against Unigene clusters

18. Kate Milova MolGen retreat March 24, 2005 18 Annotation sources: NCBI. NCBI UniGene Unigene ID  Accession Unigene ID  Blast against Unigene clusters  NCBI  UniGene  Unigene ID:  UniGene Id for cDNA arrays is obtained from the Unigene source file for each particular accession number of the clone.  NCBI  UniGene  Blast:  UniGene Id for Long Oligo arrays

19. Kate Milova MolGen retreat March 24, 2005 19 Annotation sources: NCBI. NCBI Entrez Gene Unigene ID  Gene ID  GO ID

20. Kate Milova MolGen retreat March 24, 2005 20 Annotation sources: NCBI. NCBI Refseq & NT databases Blast Search Blast Software

21. Kate Milova MolGen retreat March 24, 2005 21 Annotation sources: Gene Ontology. Gene Ontology Biological process Cellular compartment Molecular function

22. Kate Milova MolGen retreat March 24, 2005 22 cDNA Microarray Facility home page

23. Kate Milova MolGen retreat March 24, 2005 23Summary  Global observables “phase transition”:  Quantity  Quality  Measurement  Systematization  Understanding.  Intriguing and exciting:  / vs. centrality is flat!  / vs. √s NN is consistent with freeze-out temperature and has two distinct regions.  Both dE T /dη and dN ch /dη at mid-rapidity scale with ln(s NN ) over all measured √s NN (factor of 100 for N ch ) landing SIS and RHIC on the same line!  What do √s 0 NN mean?  Centrality shape of dN ch /dη looks to be independent of √s NN at RHIC energies and flattens out at lower.  Something is going on at lower SPS energy!  LHC predictions are on the desk! Let’s see what data says!