1 / 33

Tutorial on Using RAD Study-Annotator

Learn how to use RAD Study-Annotator for analyzing gene expression data from cDNA microarrays. This tutorial covers experimental design, data entry, and visualization.

tammymitchell
Download Presentation

Tutorial on Using RAD Study-Annotator

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Tutorial on Using RAD Study-Annotator

  2. Array Experiments Figure from: David J. Duggan et al. (1999)Expression Profiling using cDNA microarrays. Nature Genetics21: 10-14

  3. HAEC 5038 BioSource split Culture dish 1 Culture dish 2 Culture dish 3 Culture dish 4 TNF treatment (compound_based_treatment) pool Culture dish 1, TNF+ Culture dish 2, TNF+ pool BioSamples TNF+ pooled culture TNF- pooled culture nucleic_acid_extraction TNF+ pooled culture RNA TNF- pooled cultured RNA split split 2, …, 5, 6, ... 2, …, 5, 6, ... TNF+ alqt 1 TNF+ alqt 9 TNF- alqt 1 TNF- alqt 9 Lab. Excts. Amplify and 33P label 33P label Amplify and 33P label 33P label … … … … 18 distinct resulting Labeled Extracts Polacek et al. Physiological Genomics 2003

  4. RAD Querier Screen Shot

  5. Automatic Visualization

  6. RAD Study-Annotator Highlights • Study-centric: allow entering of information relevant to a given microarray study • Data access is restricted by Group and Project • Modular design • Flexible entry points • Batching

  7. Modular Design

  8. Flexible entry points • There are dependencies between forms. • The Study-Annotator tutorial provides guidelines in this regard. • However access to all forms is opened at all times. • Allow choice of depth-first or breadth-first annotation according to which best optimizes batching for the data at hand. • Allow entering of info at different times, without having to fill it all in in the same session.

  9. Batching • If there are similarities between separate instances of a type of entry (eg. BioSource), insert n copies of the entry to be slightly modified later. • Assays #1-20 all scanned with GenePix scanner, using laser power=0.75 • Enabled whenever possible • There are various combinations in which the forms can be used so as to batch the information. The optimal combination for a given dataset will depend on the particular kind of information available for that dataset.

  10. = “is parent of” Module I: Assay to Quantification Array Assay AssayParam RelatedAcquisition Acquisition AcquisitionParam RelatedQuantification Quantification QuantificationParam

  11. Help! • A detailed tutorial on the form usage is available at https://www.cbil.upenn.edu/RAD/tutorial/. • Pop-up window with usage for a specific field (by clicking on “?” next to that field in the form). • Pop-up windows displaying descriptions of protocols already in RAD. • Pop-up windows displaying definitions for certain ontology entries.

  12. Study* StudyDesign StudyFactor Module II: Study Design StudyAssay StudyDesignType StudyDesignAssay Assay OntologyEntry StudyFactorValue * The MGED term for “Study” is “Experiment”

  13. Study Design • One study typically has one study design. • Each study design can fall into one or more “study design type” categories (MGED Ontology: ExperimentalDesignType). • A study design type can be considered as a high-level description of the experimental design. • Examples: replicate_design, dye_swap_design, dose_response_design, time_series_design

  14. Ontology Can add terms

  15. Study Factor • For each study design there might be one or more factors of interest. • The assays in that study design can be grouped together according to the values of such factors. • Study factor is of certain “study factor type” (MGED Ontology: ExperimentalFactorCategory). • Examlpes: developmental_stage, genetic_modification, compund_based_treatment

  16. An Example • Study design: • Name: cell comparison design • Type: • development_or_differentiation_design • species_design • cell_type_comparison_design • Study Factors: • hematopoietic cell population (LT-HSC, ST-HSC, HSC, LCP, MBC) • Type:BioMaterialCharacteristicCategory → developmental_stage • mouse developmental stage (fetal, adult) • Type:BioMaterialCharacteristicCategory → developmental_stage • species (human, mouse) • Type:BioMaterialCharacteristicCategory → organism • stem cell type (hematopoietic, embryonic, neural) • Type: BioMaterialCharacteristicCategory → cell_type

  17. Module III: BioMaterials BioMaterials Descriptive Terms BioMaterialCharacteristic BioSource OntologyEntry (MGED Ontology) Treatment BioSample Treatment Type BioMaterialMeasurement LabeledExtract LabelMethod Legend is parent of: has multiple: produces via a Treament: AssayLEX Channel Assay

  18. HAEC 5038 BioSource split Culture dish 1 Culture dish 2 Culture dish 3 Culture dish 4 TNF treatment (compound_based_treatment) pool Culture dish 1, TNF+ Culture dish 2, TNF+ pool BioSamples TNF+ pooled culture TNF- pooled culture nucleic_acid_extraction TNF+ pooled culture RNA TNF- pooled cultured RNA split split 2, …, 5, 6, ... 2, …, 5, 6, ... TNF+ alqt 1 TNF+ alqt 9 TNF- alqt 1 TNF- alqt 9 Lab. Excts. Amplify and 33P label 33P label Amplify and 33P label 33P label … … … … 18 distinct resulting Labeled Extracts Polacek et al. Physiological Genomics 2003

  19. Ontology

  20. Ontology

  21. Ontology

  22. Miscellaneous Tables • Store information applicable to more than one group of tables. • Entries: • Contact • Protocol and parameter setting • Labeling Method • References

  23. Cautionary Marks • Read the tutorial carefully prior to using any form! • Wait for confirmation after submission before preceding to the next step! • Mandatory and optional fields • Currently update is NOT available (double check all fields before hitting submit button!) • Certain orders are recommended for entering some information (see tutorial) • Require some basic understanding of MGED ontology terms

  24. Why Bother?

  25. Now you are ready to publish! Study-Annotator RAD MAGE-RAD Translator ArrayExpress Many journals require deposition of microarray experiments in a public repository.

  26. EPCon screen shot • Platform tables • Quantification result tables • Processing tables • Analysis result tables • Integrity statistic tables

More Related