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The Penn Experience with MAGE-TAB. John Brestelli Elisabetta Manduchi Junmin Liu Jonathan Schug Chris Stoeckert NCI MAGE Workshop Jan 24, 2008. http://www.cbil.upenn.edu/RAD/. Support diabetes research. Support research on protozoan parasites. MAGE-TAB Studies so far ….

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The penn experience with mage tab

The Penn Experience with MAGE-TAB

John Brestelli

Elisabetta Manduchi

Junmin Liu

Jonathan Schug

Chris Stoeckert

NCI MAGE Workshop Jan 24, 2008





Mage tab studies so far
MAGE-TAB Studies so far …

  • Started with MAGE-Tab spec available in 2006 (i.e. before MAGE-Tab v1.0 finalized) and built a framework (MR_Ti) around it by the end of 2006.

  • Have loaded 22 studies into RAD (our local database) using MAGE-TAB over the past year.

  • MAGE-TAB generated from templates (original submissions) and from downloaded studies.

  • Species covered: human, mouse, Plasmodium, Toxoplasma

  • Applications covered: expression profiles, chromatin immunoprecipitation, genomic polymorphisms.



Lessons learned
Lessons Learned

  • Positive response from data submittors for spreadsheets.

    • Provide examples and templates with areas to be filled in colored.

    • Pretty much use all fields except “release date” and “comment”

    • 22 studies, 2 are hand-coded by biologists, 4 are generated by templates which are filled in by biologists. It is very useful from our data loading aspect. But it is hard for biologists to understand the format and manually generate without any help like providing templates.

  • Ontology terms provided by curator

    • Menus were messy and hard to navigate (but probably could be overcome technically)

  • Adaptable to non-array technologies

    • Final touches on a complicated Taqman study on ES cell differentiation protocols


Do mage tab templates have to follow mage tab specifications
Do MAGE-TAB templates have to follow MAGE-TAB specifications?

Of course, but the biologists filling them out don’t need to know that!


Mage tab tools and process
MAGE-TAB Tools and Process specifications?

  • Methods used for MAGE-Tab generation

    • Manually generate a MAGE-Tab

    • MAGE-Tab template then convert to MAGE-Tab

    • MAGE-ML, convert to MAGE-Tab using mage2tab developed by us.

    • GEO-Importer, MAGE-Tab converter (from ArrayExpress)

  • Mage2graph: visualization

  • Mage-checker: validation

  • LoadMageDoc plugin


Handling mage docs in unified way
Handling MAGE docs in unified way specifications?

mage doc

common objects

processors

validators

translator

O/R layer

ontology matrix

Mage doc

in other formats

graph

GUS DB


Mr ti overview

MagemlReader specifications?

use

MageTabReader

SoftReader

BaseProcessor

MergeTreatmentSerials

use

NamingBioSamples

ProcessModule

NamingScans

MR_TiException

BaseValidator

ProtocolHasMageType

use

ValidationRule

StudyDesignHasMageType

AssayHasFactorValues

VoToGusTranslator

use

VoToMageTab

VoToDot

make

ServiceFactroy

read-in

Config.xml

MR_Tilogger

use

SqlReporter

SqlTester

use

GUS

Commit

MR_Ti overview

Reader

VO’

Processor

VO

Validator

VO

Translator

GusObj

Study->submit

Reporter

Tester


Mage tab tools and process1
MAGE-TAB Tools and Process specifications?

Initial contact with investigator/

Review publication

Download SOFT files

from GEO/ Review publication

Provide appropriate

MAGE-TAB template

MAGE-ML files

From ArrayExpress

If Affymetrix, use ArrayExpress converter tool to generate MAGE-Tab; if cDNA array, in-house script to generate template

.

Get filled in template

Convert to MAGE-Tab

using mage2tab

Convert to MAGE-Tab

using template2tab

Review tab files and fill in protocols, experimental factors, ontology terms as needed.

Validate, load, and check graph


Details
Details specifications?

EPConDB

  • 2904 Survivin transgenic mice pancreatic islet profile (MAGE-ML)

  • 2929 Genome-wide location analysis of HNF Transcription Factors in Hepatocytes and Pancreatic Islets (MAGE-ML)

  • 2944 Sox4 null mice e12.5 pancreas (templates)

  • 3021 Neurogenin3 deficiency and Embryonic Pancreatic Gene Expression (SOFT)

  • 3042 Foxa2 controls vesicle docking and insulin secretion in mature beta-cells (generated by PIs)

  • 3061 Gene expression profiling of Nkx2-2 Mutant and Wild-Type - e12.5 and e13.5 Pancreata (templates)

  • 3100 Gene expression profiling in the endocrine pancreas (templates)

  • 3121 Gene expression profiling of MafA, MafB, and MafA/MafB Mutants in E18.5 pancreas (templates)

    T1Dbase

  • 3144 Expression data from NOD-scid vs B6-scid pancreas, submandibular glands, & lacrimal glands (SOFT)

  • 3203 Gene expression in PBMCs from children with diabetes (SOFT)

    PlasmoDB (SOFT)

  • 21 Molecular mechanism for switching of P.falciparum invasion pathways into human erythrocytes

  • 22 P.falciparum strain 3D7, SIR2 knockout

  • 23 Invasion by P. falciparum merozoites suggests a hierarchy of molecular interactions

  • 29 Regulation of sexual development of Plasmodium by translational repression.

  • 51 Expression profile of 3D7 clones 3D7AH1S2 and 3D7S8.4 at ring, trophozite and schizont stages.

  • 52 CD36 panned clones

  • 55 Identification of genome wide gene copy number polymorphisms in Plasmodium falciparum

  • 64 Tetracyclines Specifically Target the Apicoplast of the Malaria Parasite Plasmodium falciparum

  • 85 Whole genome analysis of mRNA decay in P. falciparum

  • 161 Plasmodium falciparum W2/Dd2 Day 8 gametocytes

    ToxoDB (generated by PIs)

  • 42 Expression profiling of the 3 archetypal T. gondii lineages

  • 101 Effects of Glucose Starvation in Toxoplasma gondii


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