Kate Milova MolGen retreat March 24, 2005 1

Microarray experiments. Microarray experiments. Database and Analysis Tools.Database and Analysis Tools.

Kate Milova

cDNA Microarray Facility

March 24, 2005

Kate Milova MolGen retreat March 24, 2005 2

Outline.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.Microarray Platforms at AECOM.

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How to choose a microarray platform.How to choose a microarray platform.

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Before starting your microarray experiment.Before starting your microarray experiment.

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Microarray’s Experts.Microarray’s Experts.

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cDNA Microarray Facility. Home page.cDNA Microarray Facility. Home page.

Introduction aaa

Introduction aaa

Introduction aaa

Introduction aaa

Introduction aaa

Introduction aaa

Introduction aaa

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cDNA Microarray Facility.cDNA Microarray Facility. Services.Services.

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cDNA Microarray Facility. Arrays.cDNA Microarray Facility. Arrays.

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cDNA Microarray Facility. Publications.cDNA Microarray Facility. Publications.

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cDNA Microarray Facility. Database.cDNA Microarray Facility. Database.

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Database Search.Database Search.

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cDNA Microarray Facility. Database.cDNA Microarray Facility. Database.

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Pipeline. LOWESS Normalization.Pipeline. LOWESS Normalization.

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cDNA Microarray Facility. Pipeline. Filtering.cDNA Microarray Facility. Pipeline. Filtering.

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cDNA Microarray Facility. Comparison.cDNA Microarray Facility. Comparison.

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Annotation sources: NCBI.Annotation sources: NCBI.

NCBI Entrez Gene

UniGene

Refseq & NT databases

Blast Search

Blast Software

Unigene ID Gene ID

GO ID

Unigene ID Accession

Unigene ID Blast against Unigene

clusters

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Annotation sources: NCBI.Annotation sources: NCBI.

NCBI

UniGene

Unigene ID Accession

Unigene ID Blast against Unigene

clusters

NCBI UniGene Unigene ID: UniGene Id for cDNA arraysis obtained from the Unigene source file for each particular accession number of the clone.

NCBI UniGene Blast: UniGene Id for Long Oligo arrays

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Annotation sources: NCBI.Annotation sources: NCBI.

NCBI Entrez GeneUnigene ID

Gene ID GO ID

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Annotation sources: NCBI.Annotation sources: NCBI.

NCBI

Refseq & NT databases

Blast Search

Blast Software

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Annotation sources: Gene Ontology.Annotation sources: Gene Ontology.

Gene Ontology

Biological process

Cellular compartment

Molecular function

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cDNA Microarray Facility home pagecDNA Microarray Facility home page

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SummarySummary Global observables “phase transition”:

Quantity Quality Measurement Systematization Understanding.

Intriguing and exciting: <ET>/<Nch> vs. centrality is flat! <ET>/<Nch> vs. √sNN is consistent with freeze-out temperature and has two distinct regions. Both dET /dη and dNch/dη at mid-rapidity scale with ln(sNN) over all measured √sNN (factor of 100 for Nch) landing SIS and RHIC on the same line! What do √s0

NN mean? Centrality shape of dNch/dη looks to be independent of √sNN at RHIC energies and flattens out at lower.

Something is going on at lower SPS energy!

LHC predictions are on the desk! Let’s see what data says!