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Latest revision as of 03:44, 13 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, PhD
Contents
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.
Dr. Doreen Ware will also be giving a talk on Gramene during the Maize Conference.
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
There will be free wireless internet access in the conference room.
Workshop Exercises
Annotation Exercises
Annotation Exercise Data
- Upload your own data & create custom browser tracks. Test files at
http://brie.cshl.edu/data/Zea_mays/
- Genome assembly conversion. Test file with RefGen_v2 coordinates: File:Test qtls v2.txt
- BLAST exercise: Sorghum variegatum Sh1 CDS in fasta: File:SvSh1 CDS.txt
Gene Expression Exercises
- Upload your own (quantitative) gene expression data & project onto MaizeCyc. Test file: File:Maizecyc up exp CHLOROPHYLL-SYN test.txt 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/
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.
