Welcome to AGED
The Alfalfa Gene Index and Expression Atlas Database    
 
Location:  Home  >  Help


A variety of tools have been developed to ensure researchers can effectively and efficiently mine the data included in the AGED website. Below is a brief description of the tools (organized by the tabs located on the top of each page).

 

Search

Search by Keyword

Use any term (including contig IDs, GO ID's, or terms such as 'nitrogen') or combination of terms to generate a list of MSGI 1.2 sequences associated with that term(s). Multiple keywords must be separated line by line. A list of sequences containing the term(s) of interest can be downloaded by clicking on 'download Acc.List' in the top right corner of the results page.

Search by Annotation

Use a list of contigs of interest generated by any of the search tools on AGED (or annotation terms including GO and KEGG IDs) to return annotations for all contigs of interest. Multiple keywords must be separated line by line

Search by Expression Value

Use pull-down menus to identify transcripts from specific tissues with expression levels within defined parameters (ie: the top 10% of genes expressed in that tissue). A second set of parameters can be utilized to define transcripts common to both sets of requirements or unique to each requirement. Search cretirion can be added or removed by clicking or , respectively. The returned sequences can be downloaded by clicking on 'download Acc. List' in the top right corner of the results page.

Identify Differentially Expressed Genes

Users choose two tissues of interest and can identify sequences differentially expressed between them by specifying a user-defined cutoff for fold changes between the two tissues; e.g. comparing B47 Flowers and F56 Flowers with a fold change greater than 5 results in a list of 867 sequences. A list of differentially expressed sequences can be downloaded by clicking on 'download Acc.List' in the top right corner of the results page.

Visualization

Expression profiles of a single or multiple transcripts of interest in all tissues can be visualized.



 

 

BLAST

A user-provided sequence of interest (in FASTA format) can be used to query the MSGI 1.2 assembly by BLASTN (dna vs dna) or TBLASTN (protein vs translated DNA). Customize BLAST parameters (E-value, number of hits reported, and output format) to accommodate down-steam analyses.

 

Download

Download Sequences

A user-defined list of sequences of interest (one sequence ID per line) is pasted into the query box. Hitting 'submit' will automatically download the DNA sequences in FASTA format to your computer.

Download Whole Datasets

This page provides a portal for bulk data downloads including sequences, expression values, and annotations. Currently, two download options are available.

  1. The entire MSGI 1.2 assembly in FASTA format can be downloaded.
  2. The average expression (as RPKM) and associated annotations of the entire MSGI 1.2 assembly can be downloaded.

 

Notes:

The AGED website has been tested on Apple (safari and firefox) and PC (chrome and firefox) computers and browsers to ensure compatibility. Testing using internet explorer identified a few layout problems which can be overcome by refreshing the screen.

 


This suite of expression data provides a platform for Medicago sativa functional genomics, including:

Sample IDSample Description
B47_ES1Elongating Stem Internodes (biological rep 1)
B47_ES2Elongating Stem Internodes (biological rep 2)
B47_ES3Elongating Stem Internodes (biological rep 3)
B47_Flower1Developing Flowers (biological rep 1)
B47_Flower2Developing Flowers (biological rep 2)
B47_Flower3Developing Flowers (biological rep 3)
B47_Leaf1Mature Leaf (biological rep 1)
B47_Leaf2Mature Leaf (biological rep 2)
B47_Leaf3Mature Leaf (biological rep 3)
B47_Nodule1Nitrogen Fixing Nodules (biological rep 1)
B47_Nodule2Nitrogen Fixing Nodules (biological rep 2)
B47_Nodule3Nitrogen Fixing Nodules (biological rep 3)
B47_PES1Post-Elongating Stem Internodes (biological rep 1)
B47_PES2Post-Elongating Stem Internodes (biological rep 2)
B47_PES3Post-Elongating Stem Internodes (biological rep 3)
B47_Root1Whole Root (biological rep 1)
B47_Root2Whole Root (biological rep 2)
B47_Root3Whole Root (biological rep 3)
F56_ES1 Elongating Stem Internodes (biological rep 1)
F56_ES2 Elongating Stem Internodes (biological rep 2)
F56_ES3 Elongating Stem Internodes (biological rep 3)
F56_Flower1Developing Flowers (biological rep 1)
F56_Flower2Developing Flowers (biological rep 2)
F56_Flower3Developing Flowers (biological rep 3)
F56_Leaf1Mature Leaf (biological rep 1)
F56_Leaf2Mature Leaf (biological rep 2)
F56_Leaf3Mature Leaf (biological rep 3)
F56_Nodule1Nitrogen Fixing Nodules (biological rep 1)
F56_Nodule2Nitrogen Fixing Nodules (biological rep 2)
F56_Nodule3Nitrogen Fixing Nodules (biological rep 3)
F56_PES1Post-Elongating Stem Internodes (biological rep 1)
F56_PES2Post-Elongating Stem Internodes (biological rep 2)
F56_PES3Post-Elongating Stem Internodes (biological rep 3)
F56_Root1Whole Root (biological rep 1)
F56_Root2Whole Root (biological rep 2)
F56_Root3Whole Root (biological rep 3)

Funding

  • This work was supported by Funding by the University of Minnesota and the United States Department of Agriculture

Contact

  • For overall questions and collaboration opportunities regarding the AGED: Alfalfa Gene Index and Expression Atlas project, please contact the principle investigator of the project, Dr. Carroll P. Vance: vance004@umn.edu

  • For bioinformatics-related questions and improvement suggestions regarding the AGED: Alfalfa Gene Index and Expression Atlas web server, please contact Dr. Patrick X. Zhao: pzhao@noble.org

References:

  • Broughton WJ, Hernandez G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.) - model food legumes. Plant Soil 252: 55-128
  • Herridge DF, M.B. Peoples, Boddey RM (2008) Global inputs of biological nitrogen fixation in agricultural systems. Plant Soil 311: 1-18



Data & bioinformatic resources were generated by the laboratory of Dr. Carroll P. Vance, USDA-ARS, St. Paul, MN, Dr. Patrick X. Zhao at the Samuel Roberts Noble Foundation, and many international collaborators.