DNA Arrays

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DNA Arrays

• DNA systematically arrayed at high density,
• virtual genomes for expression studies,
• RNA hybridization to DNA for expression studies,
• comparative genomics,
• DNA hybridization to DNA,
• inter- and intra-species comparisons, etc.
• potential yet to be developed.

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DNA Arrays or, why did my home-brew beer blow up?
http//www.bio.davidson.edu/courses/genomics/chip/
chip.html
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Mind-Blowin Amount of Data, MicroArrays
deCode
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Probes/Targets

• ...Probes are the tethered nucleic acids with
  known sequence,
• the DNA on the chip,
• ...Target is the free nucleic acid sample whose
  identity/abundance is being detected,
• the labeled nucleic acid that is washed over the
  chip.

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DNA Chip
Photolithography in situ probe synthesis
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DNA Array
Deposition spotted probe
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Target Synthesis(expression studies)
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DNA/RNA-Probes

• cDNA arrays, DNA arrays,
• DNA Microarrays,
• oligonucleotide arrays,
• DNA chips.

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DNA Chips

• oligonucleotides systematically synthesized in
  situ at high density.

Affymetrix DNA Chip
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Old School
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Circadian Rhythms

• Relating to, or exhibiting approximately 24-hour
  periodicity,
• circa (latin), around dies (latin), day.

• Circadian clocks
• Internal Biochemical Oscillators,
• found in all eukaryotes,
• eubacteria as well.

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Humans?

• Details of mammalian clocks were elucidated by
  classical and genomic work, first accomplished in
  Drosophila.

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The Experiment?in Arabidopsis

• DNA representing gt 8000 Arabidopsis genes (out of
  nearly 26,000 total) has been arrayed by
  Affymetrix, the chip is available for purchase,
• mRNA from whole tissue is extracted and labeled,
• hybridized to the chip,
• fluorescence is measured for each gene.

Thenmass data analysis.
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Experimental ConditionsReference (7)
amplitude
Entrainment
lt- Period (24h) -gt
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WEB Figures

• http//www.scienceonline.org/
• - search -

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Supplemental Data
Link
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Gene Expression Technologies

• DNA Chips (Affymetrix) and MicroArrays can
  measure mRNA concentration of thousands of genes
  simultaneously
• General scheme Extract RNA, synthesize labeled
  cDNA or cRNA, Hybridize with DNA on chip.

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The Experiment

• After hybridization,
• Scan the Chip and obtain an image file,
• Image Analysis (find spots, measure signal and
  noise).
• Output File,
• Affymetrix chips Measure each genes signal and
  make a present/absent call.
• cDNA MicroArrays competing hybridization of
  target and control. For each gene the log ratio
  of target and control.

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Preprocessing From one experiment to many

• Chip and Channel Normalization
• Aim bring readings of all experiments to the
  same scale,
• Cause different RNA amounts, labeling efficiency
  and image acquisition parameters,
• Method Multiply readings of each array/channel
  by a scaling factor such that
• The sum of the scaled readings will be the same
  for all arrays
• Find scaling factor by a linear fit of the highly
  expressed genes.

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Preprocessing From one experiment to many

• Filtering of Genes
• Remove genes that are absent in most experiments
• Remove genes that are constant in all experiments
• Remove genes with low readings which are not
  reliable.

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We can ask many questions?

• Supervised Methods (directed analysis),
• which genes are expressed differently in two
  known types of conditions?
• what is the minimal set of genes needed to
  distinguish one type of condition from the
  others?
• Unsupervised Methods (undirected analysis),
• what set of genes behave similarly in the
  experiments?
• how many different types of conditions are there?

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Unsupervised Analysis

• Goal A Find groups of genes that have correlated
  expression profiles,
• these genes are believed to belong to the same
  biological process and/or are co-regulated.
• Goal B Divide conditions to groups with similar
  gene expression profiles,
• example define drugs according to their effect
  on gene expression.

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