What is MaizeGDB?
Who is involved with MaizeGDB?
Who is funding MaizeGDB?
How can I link to MaizeGDB?
How can I contribute data to MaizeGDB?
How would I assemble a maize proteome for functional analysis.
How can I export list of all genes from a specific span of multiple genomes?
Which databases for gene annotation are used in the metabolic pathway, and how reliable would it be, compared with other function annotation tools, like MAPMAN?
I would like help comparing expression patterns for multiple genes in a locus and from multiple genomes.
Does MaizeGDB offer software for designing of primers?
Can I download all known functional annotation for a set of gene models?
Find all the Mu and Ac insertions in this genomic region:
I want to find a list of ALL UniformMu insertions in genes, and in exons.
I have a new gene, and I want to name it. How do I know my name is OK to use?
What are the new naming conventions for gene models?
I would like to learn about tools that would allow me to find promoter regions and regulatory sequences among genes.
I am interested to find orthologous genes involved in sterol metabolism in maize.
How can I access the expression atlas data from the paper by Sekhon et al 2011?
What is the status of maize proteomics- especially meiotic tissue?
Q: What is MaizeGDB?
A: MaizeGDB is short for Maize Genetics/Genomics Database. It is a
USDA/ARS funded project to integrate the data found in MaizeDB and ZmDB
into a single schema, develop an effective interface to access this data,
and develop additional tools to make data analysis easier.
Our goal in the long term is a true next-generation online maize
Q: Who is involved with MaizeGDB?
A: MaizeGDB's primary team consists of Ethy Cannon (Software
engineer & bioinformatician), Lisa Harper (Curator & outreach coordinator), Mary Schaeffer
(curator emeritus), Carson Andorf (Computational Biologist), Jack Gardiner (Curator), John Portwood (IT-Specialist), Margaret Woodhouse (Curator), Jesse Walsh (Postdoc) and Kyoung Tak Cho (Graduate Student).
Q: Who is funding MaizeGDB?
A: MaizeGDB is currently funded by USDA/ARS.
Q: How can I link to MaizeGDB?
A: Please visit our Linking to MaizeGDB page, which should
provide all the info you need.
Q: How can I contribute data to MaizeGDB?
A: Contact us using the feedback link at the top-right of the page to
arrange to add data to the database. For a detailed explanation of where
MaizeGDB's data come from and how to contribute data, see
Q: How would I assemble a maize proteome for functional analysis?
A: If you would like to download a list of translations of all gene models, you can go to the gene center page,
go to the downloads section and select "B73 RefGen_v3 gene model translations fasta ".
If you would like to use a set of proteins expressed in certain conditions, a literature search is in order.
Q: How can I export list of all genes from a specific span of multiple genomes?
A: We cannot do that yet at MaizeGDB. When we have more reference assemblies, this may be possible.
Q: Which databases for gene annotation are used in the metabolic pathway, and how reliable would it be, compared with other function annotation tools, like MAPMAN?
A: CornCyc handles metabolic pathways while MapMap is more general. Plant metabolic network has a pipeline, called E2P2, where they generate computational predictions of enzymatic functions using the current gene model set. MaizeGDB provided manual curation on several pathways including GO annotation, and we transferred these annotations to MetaCyc. CornCyc is based on v3, and in collaboration with plant metabolic Network (PMN), CornCyc will be maintained and updated with B73 RefGen_v4. MaizeCyc is based on v2 and will not be maintained in the future. MapMan and CornCyc can be accessed through the MaizeGDB Expression Data Center.
Q: I would like help comparing expression patterns for multiple genes in a locus and from multiple genomes.
A: To compare expression levels of genes in a region of the genome, you can use qTeller, a program written by James Schnable, and accessible through MaizeGDB Expression Data Center. Alternatively, you can go to the Genome Browser, make a window that spans your genomic region of interest, select all the expression data tracks, and download the track data from that region. We do not have a tool yet to explore expression of a gene in multiple genomes, as we do not yet have multiple maize genomes, but we soon will.
Q: Does MaizeGDB offer software for designing of primers?
A: Currently MaizeGDB does not offer a primer design software. Many people use Primer3.
Q: Can I download all known functional annotation for a set of gene models?
A: Currently, we do not have a single tool that allows you to access all functional annotation in one place. When we complete our instance of MaizeMine, we will. To access this data currently:
For genes in a contiguous region, open a genome browser window that spans your region of interest, select all tracks with annotations you are interested in, then in the header box, select "Download track data", and press configure. After you chose your options, click GO. You can open the downloaded file in Excel for ease of viewing.
For a custom list of gene models, you can go to Gramene and use BioMart to download annotation.
Gramene offers a great BioMart video tutorial
which will instruct you on how to use it.
Q: I want to find all the Mu and Ac insertions in a specific genomic region
A: Find the region on the genome browser, open the Ac and Mu tracts, and download the track data.
Q: I want to find a list of ALL UniformMu insertions in genes, and in exons.
A: Go to the gene/gene model data center, scroll down, and look under the title Gene Models with UniformMu insertions (version 7).
We do not yet have such a list for all AC insertions. If you would like one, please contact us.
Q: I have a new gene, and I want to name it. How do I know my name is OK to use?
A: Search for your name in the gene/gene model data center to determine if it is already in use. Do the same for the gene name abbreviation.
Then check the nomenclature rules to be sure you are compliant.
If the name has not been used, and it is compliant with the naming rules, then you can name the gene!
If you would like to check with a real person, contact anyone at MaizeGDB,
or Marty Sachs at the Stock Center.
Q: What are the new naming conventions for gene models?
A: These conventions and more can be found on the MaizeGDB Nomenclature page.
You can get here from the "community" drop down menu, under the "data" list.
For Maize, we have a nomenclature committee that determines the nomenclature for many situations.
It is wise to consult theses pages before naming anything.
Q: I would like to learn about tools that would allow me to find promoter regions and regulatory sequences among genes.
A: Currently, we do not have such a tool. There are tools on the web, and a literature search of plant or grass specific tools is recommended.
Q: I am interested to find orthologous genes involved in sterol metabolism in maize.
A: To find the genes in maize predicted to be involved in Sterol metabolism, go to CornCyc in the Expression Data Center.
Enter Sterol into quick search box and enter.
You will get Pathways, Proteins, Compounds, Reactions and EC Numbers associated with "sterol".
There are currently 44 Proteins in the list.
To find orthologs in other species, you can go to each gene model page and in the "Overview" box, you will see a list of orthologes.
Right now you will have to do this one by one.
When we have our MaizeMine tool up and running, batch orthologs can be obtained.
Q: How can I access the expression atlas data from the paper by Sekhon et al 2011?
A: We have the Sekhon expression data available at MaizeGDB in two places.
On the individual gene model pages, you can scroll down to see the EFP browser in the Expression section towards the bottom of the page.
This presents a color coded heat map of expression in cartoon images of various tissues and organs.
The expression atlas can also be seen as a track on the Genome Browser.
Once you select this track, you can see a histogram for every gene model for which there is expression data.
The histogram has a key below, and more information can be found by clicking on the "?" on the title bar of track (the track title is RNA-Seq based Expression Atlas in B73)
Q: What is the status of maize proteomics- especially meiotic tissue?
A: We offer several proteomic tracks on the MaizeGDB Genome Browser, including a proteomic atlas of B73 seed development.
To find more maize proteomics for other developmental conditions, one much search the recent literature.