Revision as of 17:45, 12 March 2014

Title

Gramene - Comparative Plant Genomics Database Workshop

Event Info

Maize Genetics Conference 2014

Date/Time

Thursday, 13 March 2014, 4:00 - 6:00 PM local Beijing time

Venue

Beijing International Convention Center, Room 308

Organizer

Marcela Karey Monaco

Workshop Agenda

4:00 PM - Introduction to the Gramene Website

4:30 PM - Browsing and Comparing Genomes Using the Gramene Ensembl Browser

5:00 PM - Plant Pathways & Gene Expression Analysis in Gramene

5:30 PM - Plant Reactome

About the workshop

The Gramene database (http://www.gramene.org) is a curated resource for comparative functional genomic analysis in plants. The database provides agricultural researchers and plant breeders with very valuable biological and genomic information on several crops and model plant species, including maize. Gramene's web interface provides information on genetic and physical maps, sequences, genes, genetic variation data, RNA-seq and microarray expression data, proteins, genetic markers, mutants, QTLs, controlled ontology vocabularies biological pathways, scientific citations, and provides displays and tools that integrate these various types of information, so that the user may visually make comparisons between the diverse genomes.

This workshop will review the available data sets at Gramene and provide demonstration of how to use our tools to answer various biological and research questions. Attendees will learn about the types of data available at Gramene, get tips on navigating the website, and use the database and tools to find data for their own projects. The workshop will feature a maize demo session on how to search the Gramene databases using various tools (simple search, Gramene Mart, BLAST), download the data to a personal computer, upload custom data for analysis, visualization and making publication-quality figures.

The workshop is geared for the community of plant researchers and breeders; beginners, as well as frequent users of the Gramene database alike. Attendees may also wish to bring their own data to work with during the workshop.

Workshop material

• TBD

You may also want to visit our Gramene poster throughout the Maize meeting.

Past reference

YouTube webinars

• Webinar 1: Introduction to Gramene by Ken Youens-Clark

http://www.youtube.com/watch?v=wEaoJTTqWvI

• Webinar 2: Plant Pathways and Gene Expression analysis at Gramene by Dr. Sushma Naithani.

http://www.youtube.com/watch?feature=player_embedded&v=umlpHVon1OM

• Webinar 3: Plant Reactome by Justin Preece

http://www.youtube.com/watch?v=wbkuTeIcKjI

For the complete of original videorecordings, please see Gramene's FTP

Internet Access

Workshop Exercises

Gene Expression Exercises

Gramene FTP site

Annotation Exercises

File:MGC Exercises.docx

Annotation Exercise Data

• Upload your own data & create custom browser tracks. Test files at

http://brie.cshl.edu/data/Zea_mays/

• Upload your own (quantitative) gene expression data & project onto MaizeCyc. Test file includes only upregulated genes mapping to the chlorophyllide a biosynthesis pathway with expression data for five tissues.

Data source: ftp://ftp.gramene.org/pub/gramene/pathways/maizecyc/manuscript/

• Genome assembly conversion. Test file with RefGen_v2 coordinates

• BLAST exercise: Sorghum variegatum Sh1 CDS in fasta

Questions

For more information for the workshop, please e-mail Marcela Karey Monaco: mmonaco@cshl.edu

Acknowledgments

The Gramene Project is a collaboration between Cold Spring Harbor Laboratory (CSHL), Oregon State University (OSU), the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL - EBI), the Ontario Cancer Research Institute (OCIR), and the American Society of Plant Biologists (ASPB).

Sponsored by

The Gramene Project is funded by the NSF award IOS:1127112 (IPGA: Gramene - Exploring Function through Comparative Genomics and Network Analysis).

Partial support comes from the USDA and USDA-ARS.