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PrognoChip - BASE: An Information System for the Management of Spotted DNA MicroArray Experiments

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

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PrognoChip - BASE: An Information System for the Management of Spotted DNA MicroArray Experiments

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  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. Measure/ Expression level Hybridization: mix RNAs and apply to array Hybridizationdata read out Spotted DNA Microarray Experiments RNA extraction cy3 labeling Normal Tissue Amplification Amplification RNA extraction cy5 labeling Tumor Tissue

  3. Samples Plate Plate Preparation RNA extraction (protocol) extract Array Fabrication Labeling (protocol) Array Hybridization (protocol) Labeled extract Hybridized Array Scanning (protocol) Images Microarray Experiment Process

  4. Images Channel 1 (cy3) Channel 2 (cy5) Image Analysis Spot Spot Measures Measures Raw Data Channel 1 (cy3) Channel 2 (cy5) Normalization Reporter Normalized value Normalized data (relative expression levels) Microarray Experiment Process (cont.)

  5. Need for an Information System Submit/search/ update PrognoChip- BASE (web-based) Normalization Plug-ins • 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) MIAME describes the minimum information that must be reportedabout microarray experiments, in order to be reproducible, and verifiable.

  6. BASE v1.2 at Lund University BASE v1.2(BioArray Software Environment)is an open source software package that manages all data related to microarrays (supports MIAME) • 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/

  7. PrognoChip-BASE (FORTH-ICS) • 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

  8. PrognoChip-BASE: Login

  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. What is a Reporter Gene structure I1 E1 I2 E2 I3 E3 I4 E4 I5 5’ 3’ E1 E2 E3 E4 Transcriptome E1 E2 E3 E2 E3 E4 Spliceome Transcript 1 Transcript 2 Proteome Reporter (oligonucleotide) Protein 1 Protein 2

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

  12. List of Array Designs

  13. Creation of a New Array Design

  14. Reporter Map Upload

  15. Reporter MapUpload (cont.)

  16. Definition of aReporter Map Format

  17. Creation of anArray Batch

  18. To eacharray batch corresponds a set ofarray slides Creation ofArray BatchandArray Slides

  19. Creation ofArray Slides

  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. List of Reporters

  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. Apoptosis regulator Enzyme activator Apoptosis activator Protease activator Apoptotic protease activator The Gene Ontology Gene Ontology Cellular Component Molecular function Biological Process

  24. TheBiological Process, Molecular Function, and Cellular Component GOAnnotations 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. Gene Ontology Annotations Evidence code GOannotations

  25. As in“Reporter Μap Upload” Reporter Annotation Update Reporter Annotation Update

  26. Define aReporter File Format

  27. Define a Reporter File Format (cont.)

  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. List of Samples

  30. Creation of a New Sample

  31. Extract quality indicators Creation of a New Extract

  32. List of Labels

  33. Labeled extract quality indicators Creation of a New Labeled Extract

  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. Hybridization quality indicator • A hybridization is relatedwith: • two or more labeled extracts • onearray slide Creation of a Hybridization

  36. Creation of a Hybridization: Pick an Array Slide Proceed with scanning

  37. Creation of a Scan • Every hybridization is associated with one or more scans • from differentscanners • Optional: Upload of scanning images • Different image for each channel

  38. View of a Scan • Every scan is associated with one or moreraw data sets • from different image analysis software

  39. Raw Data Set Upload Continue as in “Reporter Μap Upload”

  40. Raw Data Set Fields PrognoChip-BASE additional raw data set fields

  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. List of Experiments

  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. List of Raw Data Sets

  45. Assignment of Raw Data Sets to an Experiment

  46. General Information about an Experiment

  47. Creation of an Initial BioAssaySet Creation of an initialBioAssaySet with the namePrognoChip

  48. Normalization Process Plug-in selection Exporting of results

  49. Plug-in Selection

  50. PrognoChip-BASE Web Site • http://www.ics.forth.gr/isl/projects/PrognoChip/

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