Bioinformatics Workshop
Supplemental Session Materials
October 27th, 2006
SACNAS National Conference,
Tampa, FL
Session Chair(s):
Dr. Elba Serrano
(serrano@nmsu.edu)
Dr. Mandana Sassanfar
(mandana@mit.edu)
Session Speaker(s):
Bioinformatics Workshop
Supplemental Session Materials
October 27th, 2006
SACNAS National Conference,
Tampa, FL
Session Chair(s):
Dr. Elba Serrano
(serrano@nmsu.edu)
Dr. Mandana Sassanfar
(mandana@mit.edu)
Session Speaker(s):
|
|
Dr. Elba Serrano |
Building a SACNAS Postdoctoral Bioinfomatics Network
Dr. SerranoÕs Links:
Statistical Data Mining Tutorials
A gene expression/molecular abundance repository supporting MIAME compliant data submissions, and a curated, online resource for gene expression data browsing, query and retrieval.
NCI Gene Expression Data Portal:
As of
October 21, 2006, the Gene Expression Data Portal (GEDP) has been
replaced
by the caArray Data Portal. All GEDP data indicated below has
been
migrated into the caArray Data Portal and can be accessed via the
links below. Please visit the caArray Data Portal for all future Microarray data submissions.
|
|
Dr. TuShun Powers |
|
|
Charlie Whittaker |
Using the UCSC Genome Browser to Analyze Genomic Data in
the Context of Cancer and Development
Summary:
The free
availability of dozens of sequenced metazoan genomes enables examination of
gene content, variation, regulation and expression that were inconceivable as
recently as 5 years ago. Many of these genomes are already under analyzed and novel
sequencing technologies will clearly exacerbate this analysis gap. A basic appreciation
of genomics data and methods, combined with good ideas is all that is required
to begin taking advantage of this wealth of available data.
Most kinds of genomics data consist of chromosomal coordinates with attached annotations. For example, if an exon of geneX is on + strand of chromosome 12, starting at position 100 and ending at position 200, the information could be stored in a tab-separated format that looks like this:
|
Chromosome |
Start |
End |
Strand |
Annotation |
|
chr12 |
100 |
200 |
+ |
Exon_of_geneX |
The scale of the data is enormous with millions of these types of data available for each sequenced genome. In order to use the data, researchers need a way to visualize the information in a meaningful way and a way to ask questions of the data. The tools provided by the UCSC genome informatics group do an exceptional job of meeting both these needs.
Lecture Notes:
OpenHelix UCSC Training Material
Problem Sets:
Session Exercises and Problems
Useful Links:
DOE Joint Genome Institute (JGI)
|
|
Dr. Rudy Alarcon |
Identification of hypoxia regulated microRNAs: Biomarker discovery through microarray profiling
|
|
Dr. Mandana
Sassanfar |
Mandana Info
