Session ii g1 overview genomics and gene expression mmc-good
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Transcript of Session ii g1 overview genomics and gene expression mmc-good
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Microarray Dataset: quick mining and gene profile analysis using online tools
Dr. Etienne Z. GNIMPIEBA
Sioux Falls, March 2013
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Plan Gene expression measurement Microarray processGene expression data storesData mining / queringData analysisExample: ATP13A2 profile in stress
conditions
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Gene expression measurement
Higher-plex techniques: SAGEDNA microarrayTiling arrayRNA-SeqNGS
Low-to-mid-plex techniques: Reporter geneNorthern blotWestern blotFluorescent in situ hybridizationReverse transcription PCR
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What is a Microarray?
“A DNA microarray is a multiplex technology consisting of thousands of oligonucleotide spots, each containing picomoles of a specific DNA sequence.”
Used to quantitate mRNA or DNAMany applications:
◦mRNA or DNA levels◦SNP identification◦ChIP-on-Chip
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Hypotheses
Microarrays are usually hypothesis-generating:◦ They highlight specific genes or features that are
particularly interesting for follow-up experiments◦ There are many interesting exceptions
Biomarkers Pathway analyses
This does not reduce the importance of experimental design◦ the low statistical power of array studies make good
design even more important and very challenging
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Microarray process (1/3)• Image analysis
(genepix)• Normalization (R)• Pre-treatment• Differential
expression• Clustering• Data mining• Annotation
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Microarray process (2/3)
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Microarray process (3/3)High density
filters(macroarrays)
Glass slides (microarrays)
Oligonucleotides chips
Detail: Detail: Detail:
Size: 12cm x 8cm Size: 5,4cm x 0,9cm Size: 1,28cm x 1,28cm
•2400 clones by membrane•radioactive labelling•1 experimental condition by membrane
•10000 clones by slide•fluorescent labelling•2 experimental conditions by slide
•300000 oligonucleotides by slide•fluorescent labelling•1 experimental condition by slide
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Gene expression data management
DatabaseMicroarray Experiment
Sets
Sample Profiles Date Reported
ArrayExpress at EBI 24,838 708,914 October 28, 2011
ArrayTrack™ 1,622 50,953 February 11, 2012
caArray at NCI 41 1,741 November 15, 2006
Gene Expression Omnibus - NCBI 25,859 641,770 October 28, 2011
Genevestigator database 2,500 65,000 January 2012
MUSC database ~45 555 April 1, 2007
Stanford Microarray database 82,542 Not reported October 23, 2011
UNC Microarray database ~31 2,093 April 1, 2007
UNC modENCODE Microarray database ~6 180 July 17, 2009
UPenn RAD database ~100 ~2,500 September 1, 2007
UPSC-BASE ~100 Not reported November 15, 2007
SAGEGEOGUDMAP (421)MGIBIOGPS
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Data mining / querying
Problem specificationQueryExtractionStorage LoadPretreat / prepare for analysis
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Data analysis (1/3)Question-Answer
◦ Experimental condition profile: group comparison
◦ Annotation profile: systems biological involved◦ Clustering profile: co-regulation◦ Time course profile: time variation◦ …
Descriptive ◦ Boxplot (SD, MEAN, MEDIAN, )◦ Scatter plot
Predictive / inference (clustering)Modeling (machine learning, simulation)
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Data analysis (2/3)
3 Questions ◦What is the right dataset (experimental condition)?
◦ Is dataset is ready for analysis (quality)?
◦What is the expression profile for a given gene?
◦Significant differential expression in groups comparison
Tools◦ArrayExpress (EBI)
◦Boxplot
◦GEO2R (LIMMA, profile graph,)
◦….
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Data analysis (3/3)
Boxplot
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Example: ATP13A2 profile in stress conditions
Specification: ATP13A2 profile in stress conditions
Data querying: ◦GEO◦Array Express ◦Gene Atlas
Data analysis: ◦Online: GEO2R, Genospace, …◦Desktop: R, ArrayTrack, …
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Significant differential expression !!!
Kerry Bemis slides