1. PROGNOCHIP-BASE, FORTH-ICS 1 PrognoChip-BASE: An Information System for the Management of Spotted DNA MicroArray Experiments Extension of BASE v 1.2.16 (Lund University) Implementation: Haridimos Kondylakis, Dimitris Manakanatas, Manos Kalaitzakis Guidance: Anastasia Analyti, Dimitris Plexousakis Institute of Computer Science, FORTH-ICS, Crete, Greece Department of Computer Science, University of Crete, Greece Molecular Biologists: Dimitris Kafetzopoulos, Thanassis Margaritis Institute of Molecular Biology & Biotechnology, FORTH-IMBB, Crete, Greece

2. PROGNOCHIP-BASE, FORTH-ICS 2 Spotted DNA Microarray Experiments Normal Tissue RNA extraction Amplification cy3 labeling Tumor Tissue RNA extraction Amplification cy5 labeling Hybridization data read out Hybridization: mix RNAs and apply to array Measure/ Expression level

3. PROGNOCHIP-BASE, FORTH-ICS 3 Microarray Experiment Process Plate Array Fabrication Plate Preparation Array Labeled extract extract Samples Labeling (protocol ) RNA extraction (protocol) Images Hybridized Array Hybridization (protocol) Scanning (protocol)

4. PROGNOCHIP-BASE, FORTH-ICS 4 Microarray Experiment Process (cont.) Images Channel 1 (cy3) Channel 2 (cy5) Image Analysis Raw Data SpotMeasuresSpotMeasures Channel 1 (cy3)Channel 2 (cy5) Normalization Normalized data (relative expression levels) ReporterNormalized value

5. PROGNOCHIP-BASE, FORTH-ICS 5 Microarray experimentation involves a massive amount of data for the biologist to organize and analyze:  Data to be stored before the experiment Samples Extracts Labeled extracts Reporters (oligonucleotides) Array Designs Arrays  Data to be stored after the experiment Hybridizations Image files Raw Data (measures from scanned images) Normalized data (relative expression levels) Need for an Information System (web-based) PrognoChip- BASE Normalization Plug-ins Submit/search/ update MIAME describes the minimum information that must be reported about microarray experiments, in order to be reproducible, and verifiable.

6. PROGNOCHIP-BASE, FORTH-ICS 6 BASE v1.2 at Lund University Web-based submission of data and queries Server: Linux, MySQL, php language, Apache web server, C++/Javascript Provides "plug-in"-able normalization, data viewing and analysis tools. Described in: L. H. Saal, C. Troein, J. Vallon-Christersson, S. Gruvberger, A. Borg, and C. Peterson, BioArray Software Environment: A Platform for Comprehensive Management and Analysis of Microarray Data, Genome Biology, 3(8): software0003.1-0003.6, 2002. Available at: http://base.thep.lu.se/ BASE v1.2 (BioArray Software Environment) is an open source software package that manages all data related to microarrays (supports MIAME)

7. PROGNOCHIP-BASE, FORTH-ICS 7 PrognoChip-BASE is based on BASE v1.2.16, which was extended with additional functionality  Forms were modified to help the submitter and end user  Extra fields were added for describing extracts, labeled extracts, hybridizations, and raw data sets  Reporters were annotated with additional descriptors, external databases, and the Gene Ontology (GO)  Extra descriptors were added in the “List View” of main menu items  sorting, based on these descriptors, is provided PrognoChip-BASE (FORTH-ICS)

8. PROGNOCHIP-BASE, FORTH-ICS 8 PrognoChip-BASE: Login

9. PROGNOCHIP-BASE, FORTH-ICS 9 PrognoChip-BASE: Main Steps  Creation and Management of MicroArrays  Reporter Annotation Upload  Management of Reporters  Reporter Annotation Update  Creation and Management of Biomaterials  Creation and Management of Hybridizations  Creation and Management of Experiments

10. PROGNOCHIP-BASE, FORTH-ICS 10 I1I5I4I3I2E4E3E2E1 Gene structure E2E1E3E4 Transcriptome Spliceome E1E2E3E2E4 5’ 3’3’ E3 Proteome Protein 1Protein 2 Transcript 1 Transcript 2 What is a Reporter Reporter (oligonucleotide)

11. PROGNOCHIP-BASE, FORTH-ICS 11 Block Column Row Reporter Id Length Gene name Gene symbol Gene description Block Column Row Reporter: Oligonucleotide Description Based on an array design,we produce a batch of array slides Array design MicroArray Design

12. PROGNOCHIP-BASE, FORTH-ICS 12 List of Array Designs

13. PROGNOCHIP-BASE, FORTH-ICS 13 Creation of a New Array Design

14. PROGNOCHIP-BASE, FORTH-ICS 14 Reporter Map Upload

15. PROGNOCHIP-BASE, FORTH-ICS 15 Reporter Map Upload (cont.)

16. PROGNOCHIP-BASE, FORTH-ICS 16 Definition of a Reporter Map Format

17. PROGNOCHIP-BASE, FORTH-ICS 17 Creation of an Array Batch

18. PROGNOCHIP-BASE, FORTH-ICS 18 Creation of Array Batch and Array Slides To each array batch corresponds a set of array slides

19. PROGNOCHIP-BASE, FORTH-ICS 19 Creation of Array Slides

20. PROGNOCHIP-BASE, FORTH-ICS 20 PrognoChip-BASE: Main Steps  Creation and Management of MicroArrays  Reporter Annotation Upload  Management of Reporters  Reporter Annotation Update  Creation and Management of Biomaterials  Creation and Management of Hybridizations  Creation and Management of Experiments

21. PROGNOCHIP-BASE, FORTH-ICS 21 List of Reporters

22. PROGNOCHIP-BASE, FORTH-ICS 22 Gene Ontology (GO) GO contains three different sub-ontologies/ taxonomies:  Molecular function  Biological process  Cellular component  Each term is related to its parent term through an is-a or part-of relationship Unique identifier for every term:  GO:0003673(root=Gene Ontology)

23. PROGNOCHIP-BASE, FORTH-ICS 23 The Gene Ontology Gene Ontology Apoptotic protease activator Apoptosis regulator Enzyme activator Apoptosis activator Protease activator Molecular functionBiological Process Cellular Component

24. PROGNOCHIP-BASE, FORTH-ICS 24 Gene Ontology Annotations Evidence codeGO annotations  The Biological Process, Molecular Function, and Cellular Component GO Annotations should be given as semicolon (;) separated strings of the following form: GO_id | GO_name | evidence_code.  However, any part (i.e. "| evidence_code" ) is optional.

25. PROGNOCHIP-BASE, FORTH-ICS 25 Reporter Annotation Update As in “Reporter Μap Upload” Reporter Annotation Update

26. PROGNOCHIP-BASE, FORTH-ICS 26 Define a Reporter File Format

27. PROGNOCHIP-BASE, FORTH-ICS 27 Define a Reporter File Format (cont.)

28. PROGNOCHIP-BASE, FORTH-ICS 28 PrognoChip-BASE: Main Steps  Creation and Management of MicroArrays  Reporter Annotation Upload  Reporter Management  Reporter Annotation Update  Creation and Management of Biomaterials  Creation and Management of Hybridizations  Creation and Management of Experiments

29. PROGNOCHIP-BASE, FORTH-ICS 29 List of Samples

30. PROGNOCHIP-BASE, FORTH-ICS 30 Creation of a New Sample

31. PROGNOCHIP-BASE, FORTH-ICS 31 Creation of a New Extract Extract quality indicators

32. PROGNOCHIP-BASE, FORTH-ICS 32 List of Labels

33. PROGNOCHIP-BASE, FORTH-ICS 33 Creation of a New Labeled Extract Labeled extract quality indicators

34. PROGNOCHIP-BASE, FORTH-ICS 34 PrognoChip-BASE: Main Steps  Creation and Management of MicroArrays  Reporter Annotation Upload  Reporter Management  Reporter Annotation Update  Creation and Management of Biomaterials  Creation and Management of Hybridizations  Creation and Management of Experiments

35. PROGNOCHIP-BASE, FORTH-ICS 35 Creation of a Hybridization Hybridization quality indicator A hybridization is related with: two or more labeled extracts one array slide

36. PROGNOCHIP-BASE, FORTH-ICS 36 Creation of a Hybridization: Pick an Array Slide Proceed with scanning

37. PROGNOCHIP-BASE, FORTH-ICS 37 Creation of a Scan Every hybridization is associated with one or more scans from different scanners Optional: Upload of scanning images Different image for each channel

38. PROGNOCHIP-BASE, FORTH-ICS 38 View of a Scan Every scan is associated with one or more raw data sets from different image analysis software

39. PROGNOCHIP-BASE, FORTH-ICS 39 Raw Data Set Upload Continue as in “Reporter Μap Upload”

40. PROGNOCHIP-BASE, FORTH-ICS 40 Raw Data Set Fields PrognoChip-BASE additional raw data set fields

41. PROGNOCHIP-BASE, FORTH-ICS 41 PrognoChip-BASE: Main Steps  Creation and Management of MicroArrays  Reporter Annotation Upload  Reporter Management  Reporter Annotation Update  Creation and Management of Biomaterials  Creation and Management of Hybridizations  Creation and Management of Experiments

42. PROGNOCHIP-BASE, FORTH-ICS 42 List of Experiments

43. PROGNOCHIP-BASE, FORTH-ICS 43 Creation of a New Experiment If “study experiment” then it is verified that associated raw data sets correspond to the same cancerous and reference sample, but different array designs. Otherwise, a warning is displayed

44. PROGNOCHIP-BASE, FORTH-ICS 44 List of Raw Data Sets

45. PROGNOCHIP-BASE, FORTH-ICS 45 Assignment of Raw Data Sets to an Experiment

46. PROGNOCHIP-BASE, FORTH-ICS 46 General Information about an Experiment

47. PROGNOCHIP-BASE, FORTH-ICS 47 Creation of an Initial BioAssaySet Creation of an initial BioAssaySet with the name PrognoChip

48. PROGNOCHIP-BASE, FORTH-ICS 48 Normalization Process Exporting of results Plug-in selection

49. PROGNOCHIP-BASE, FORTH-ICS 49 Plug-in Selection

50. PROGNOCHIP-BASE, FORTH-ICS 50 PrognoChip-BASE Web Site  http://www.ics.forth.gr/isl/projects/PrognoChip/

51. PROGNOCHIP-BASE, FORTH-ICS 51 Download PrognoChip-BASE  PrognoChip-BASE is released under the GNU General Public License  http://www.gnu.org/licenses/gpl.html  It can be downloaded from:  http://sourceforge.net/projects/prognochip-base/

52. PROGNOCHIP-BASE, FORTH-ICS 52 Acknowledgements The development of PrognoChip-BASE was supported by National and EU funds within the contexts of:  the PrognoChip project (GSRT-EPAN) and  the ACGT project (FP6-IST-026996).PrognoChip 2004-2007 2006-2010

53. PROGNOCHIP-BASE, FORTH-ICS 53 Thank you !!!