PAG 2014 Workshop
- Gramene Project Workshop
- Event Info
- PAG 2014
- Tuesday, 14 January 2014, 1:30 PM - 3:40 PM
- Town & Country Hotel, California Room
- Marcela Karey Monaco & Doreen Ware
Visit our booth #305!
See who is at the Plant Genomics Outreach Consortium booth
1:30 PM - Introduction to the Gramene Website
Ken Youens-Clark, Cold Spring Harbor Laboratory
2:00 PM - Plant Reactome
Vindhya Amarashinghe, Oregon State University
2:30 PM - Plant Pathways & Gene Expression Analysis in Gramene
Sushma Naithani, Oregon State University
3:00 PM - Browsing and Comparing Genomes Using the Gramene Ensembl Browser
Joshua Stein, Cold Spring Harbor Laboratory
About the workshop
The Gramene database (http://www.gramene.org) is a curated, open-source, web-accessible data resource for comparative genome 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. Gramene's web interface provides information on genetic and physical maps, sequences, genes, RNA-seq/microarray expression data, proteins, genetic markers, mutants, QTLs, controlled vocabularies and scientific citations, genetic variation data, biological pathways, 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 the new Plant Reactome, a platform for the comparative analysis of plant metabolic and regulatory networks. 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.
Past reference: PAG 2013
- Webinar 1: Introduction to Gramene by Ken Youens-Clark
- Webinar 2: Plant Pathways and Gene Expression analysis at Gramene by Dr. Sushma Naithani.
- Webinar 3: Plant Reactome by Justin Preece
For the cmplete of original videorecordings, please see Gramene's FTP
High speed internet access will be available in the PAG Computer Room, and in the conference/registration area. There will be a hands-on portion of the workshop as the network connection allows. We will provide hand outs and post lectures and exercises in this page.
Gene Expression Exercises
File:Gramene gene exercise 1.doc
File:Gramene gene exercise 2.doc
File:Gramene adding data track exercise 3.doc
Annotation Exercise Data
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).
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.