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

Dr. TuShun Powers

Dr. Charlie Whittaker

Dr. Rodolfo Alarcon

Dr. Mandana Sassanfar

 


 

Dr. Elba Serrano

serrano@nmsu.edu

 

Building a SACNAS Postdoctoral Bioinfomatics Network

 

Dr. Serrano’s Links:

Statistical Data Mining Tutorials

Gene Expression Omnibus:

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

serrano@nmsu.edu

 


Microarrays for a Sensorineural Project from the Ground Up

 

 

 

Charlie Whittaker

charliew@mit.edu

 

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:

Session Presentation

OpenHelix UCSC Training Material

 

Problem Sets:

Session Exercises and Problems

 

Useful Links:

OpenHelix

UCSC Genome Informatics

Ensembl

The Broad Institute

DOE Joint Genome Institute (JGI)

NCBI Entrez

 

 

Dr. Rudy Alarcon

Rodolfo.Alarcon@brooks.af.mil

 


Identification of hypoxia regulated microRNAs: Biomarker discovery through microarray profiling

 

 

Dr. Mandana Sassanfar

mandana@mit.edu

 


Mandana Info