Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools....
-
date post
19-Dec-2015 -
Category
Documents
-
view
219 -
download
0
Transcript of Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools....
![Page 1: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/1.jpg)
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
![Page 2: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/2.jpg)
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
![Page 3: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/3.jpg)
Kate Milova MolGen retreat March 24, 2005 3
Microarray Platforms at AECOM.Microarray Platforms at AECOM.
![Page 4: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/4.jpg)
Kate Milova MolGen retreat March 24, 2005 4
How to choose a microarray platform.How to choose a microarray platform.
![Page 5: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/5.jpg)
Kate Milova MolGen retreat March 24, 2005 5
Before starting your microarray experiment.Before starting your microarray experiment.
![Page 6: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/6.jpg)
Kate Milova MolGen retreat March 24, 2005 6
Microarray’s Experts.Microarray’s Experts.
![Page 7: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/7.jpg)
Kate Milova MolGen retreat March 24, 2005 7
cDNA Microarray Facility. Home page.cDNA Microarray Facility. Home page.
Introduction aaa
Introduction aaa
Introduction aaa
Introduction aaa
Introduction aaa
Introduction aaa
Introduction aaa
![Page 8: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/8.jpg)
Kate Milova MolGen retreat March 24, 2005 8
cDNA Microarray Facility.cDNA Microarray Facility. Services.Services.
![Page 9: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/9.jpg)
Kate Milova MolGen retreat March 24, 2005 9
cDNA Microarray Facility. Arrays.cDNA Microarray Facility. Arrays.
![Page 10: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/10.jpg)
Kate Milova MolGen retreat March 24, 2005 10
cDNA Microarray Facility. Publications.cDNA Microarray Facility. Publications.
![Page 11: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/11.jpg)
Kate Milova MolGen retreat March 24, 2005 11
cDNA Microarray Facility. Database.cDNA Microarray Facility. Database.
![Page 12: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/12.jpg)
Kate Milova MolGen retreat March 24, 2005 12
Database Search.Database Search.
![Page 13: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/13.jpg)
Kate Milova MolGen retreat March 24, 2005 13
cDNA Microarray Facility. Database.cDNA Microarray Facility. Database.
![Page 14: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/14.jpg)
Kate Milova MolGen retreat March 24, 2005 14
Pipeline. LOWESS Normalization.Pipeline. LOWESS Normalization.
![Page 15: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/15.jpg)
Kate Milova MolGen retreat March 24, 2005 15
cDNA Microarray Facility. Pipeline. Filtering.cDNA Microarray Facility. Pipeline. Filtering.
![Page 16: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/16.jpg)
Kate Milova MolGen retreat March 24, 2005 16
cDNA Microarray Facility. Comparison.cDNA Microarray Facility. Comparison.
![Page 17: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/17.jpg)
Kate Milova MolGen retreat March 24, 2005 17
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
![Page 18: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/18.jpg)
Kate Milova MolGen retreat March 24, 2005 18
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
![Page 19: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/19.jpg)
Kate Milova MolGen retreat March 24, 2005 19
Annotation sources: NCBI.Annotation sources: NCBI.
NCBI Entrez GeneUnigene ID
Gene ID GO ID
![Page 20: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/20.jpg)
Kate Milova MolGen retreat March 24, 2005 20
Annotation sources: NCBI.Annotation sources: NCBI.
NCBI
Refseq & NT databases
Blast Search
Blast Software
![Page 21: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/21.jpg)
Kate Milova MolGen retreat March 24, 2005 21
Annotation sources: Gene Ontology.Annotation sources: Gene Ontology.
Gene Ontology
Biological process
Cellular compartment
Molecular function
![Page 22: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/22.jpg)
Kate Milova MolGen retreat March 24, 2005 22
cDNA Microarray Facility home pagecDNA Microarray Facility home page
![Page 23: Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.](https://reader036.fdocuments.us/reader036/viewer/2022062516/56649d365503460f94a0defe/html5/thumbnails/23.jpg)
Kate Milova MolGen retreat March 24, 2005 23
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!