Microarray experiments. Database and Analysis Tools.

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Microarray experiments. Database and Analysis
Tools.
Kate Milova cDNA Microarray Facility March
24, 2005
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Outline.

• Microarray platforms and services available at
  AECOM
• cDNA
• Long Oligo
• Afymetrix
• Database (cDNA Long Oligo) structure and
  content
• Printing information
• Chip layout
• Annotation
• On-line Analysis Tools
• Normalization
• Signal filtering
• Comparison
• Statistical packages and Analysis software
• Summary

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Microarray Platforms at AECOM.
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How to choose a microarray platform.
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Before starting your microarray experiment.
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Microarrays Experts.
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cDNA Microarray Facility. Home page.

• Introduction
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cDNA Microarray Facility. Services.
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cDNA Microarray Facility. Arrays.
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cDNA Microarray Facility. Publications.
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cDNA Microarray Facility. Database.
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Database Search.
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cDNA Microarray Facility. Database.
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Pipeline. LOWESS Normalization.
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cDNA Microarray Facility. Pipeline. Filtering.
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cDNA Microarray Facility. Comparison.
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Annotation sources NCBI.
Unigene ID? Accession
UniGene
Unigene ID ? Blast against Unigene clusters
Entrez Gene
Unigene ID ? Gene ID ? GO ID
NCBI
Blast Software
Blast Search
Refseq NT databases
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Annotation sources NCBI.
Unigene ID? Accession
UniGene
Unigene ID ? Blast against Unigene clusters

• NCBI ? UniGene ? Unigene ID
• UniGene Id for cDNA arrays
• is obtained from the Unigene source file for each
  particular accession number of the clone.
• NCBI ? UniGene ? Blast
• UniGene Id for Long Oligo arrays

NCBI
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Annotation sources NCBI.
Entrez Gene
Unigene ID ? Gene ID ? GO ID
NCBI
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Annotation sources NCBI.
NCBI
Blast Software
Blast Search
Refseq NT databases
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Annotation sources Gene Ontology.
Biological process
Gene Ontology
Molecular function
Cellular compartment
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cDNA Microarray Facility home page
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Summary

• Global observables phase transition
• Quantity ? Quality
• Measurement ? Systematization ? Understanding.
• Intriguing and exciting
• ltETgt/ltNchgt vs. centrality is flat!
• ltETgt/ltNchgt vs. vsNN is consistent with
  freeze-out temperature and has two distinct
  regions.
• Both dET /d? and dNch/d? at mid-rapidity scale
  with ln(sNN) over all measured vsNN (factor of
  100 for Nch) landing SIS and RHIC on the same
  line!
• What do vs0NN mean?
• Centrality shape of dNch/d? looks to be
  independent of vsNN at RHIC energies and flattens
  out at lower.
• Something is going on at lower SPS energy!
• LHC predictions are on the desk! Lets see what
  data says!