Frequently Asked Questions
What does ProFITS means?
ProFITS is a maize functional database containing protein families involved in the transduction of signalling. It supports three categories, transcription factor (TF), Protein kinases (kinase), and ubiquitin 26S proteasome system related (UPS) proteins. You can browse statistics page for detailed information of each category.
Does ProFITS contain any information except for three categories?
Yes, ProFITS actually contains information of all predicted genes and full length cDNAs. Both functional annotation and related sequences are all available, however, we currently only classify these sequences into three categories. Further identification of these sequences is on our to-do list.
What is the difference between ProFITS with already existed TF databases?
ProFITS is specially concerning maize organism, and it supports three categories including TFs. These three categories may work together to aim users studying signal transduction. Also we provides TF binding sites prediction which can be interrelated TFs. Another disadvantage of existed TF databases is that they do not use newly released maize genome data to do the prediction, which may lead to misleading results.
Can I ask for adding more categories which I am insterested in?
Yes, please contact us using Contact Us page, or mail us at firstname.lastname@example.org directly.
How often does ProFITS update?
It depends. ProFITS is under well maintain and we will update ProFITS once we have something new. Users can also contact us to add their interested categories.
What is your lab focusing?
We mainly focus on plant molecular system biology and provide bioinformatics service. Links to published databases or web severs developed by our lab are accessible at left navigation frame.
What is GO and GO enrichment?
"The Gene Ontology (GO) project provides a controlled vocabulary to describe gene and gene product attributes in any organism. The GO project is a collaborative effort to address the need for consistent descriptions of gene products in different databases. The GO collaborators are developing three structured, controlled vocabularies (ontologies) that describe gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner. There are three separate aspects to this effort: first, we write and maintain the ontologies themselves; second, we make cross-links between the ontologies and the genes and gene products in the collaborating databases, and third, we develop tools that facilitate the creation, maintainence and use of ontologies." Definition from http://www.geneontology.org/ GO enrichment analysis can faciliate users to uncover hidden biological meanings from large volumn of data. And GO enrichment tool in ProFITS is adopted from agriGO and its parameters are specially set for maize organism.
How to use GO enrichment analysis provided by ProFITS?
GO enrichment analysis in ProFITS is based on agriGO, one GO analysis toolkit developed by our lab. Specified parameters are set for maize organism. To use this functionality, user should provide a list of IDs, eg. maize genome locus, maize Affymetrix Genome Array Probesets, and submit the list ( click here to check the sample). Several paramters can be set depending on users' requirement, or users can just use the default setting. The results of GO enrichment analysis can be explored using agriGO platform, and one can inspect the meaning of the results by viewing the help page.
I tried on the GO page and returned a message "Sorry! Less than 10 entries can be mapped with GO. Analysis failed. This may happen if you select wrong species.", what does it mean?
The GO enrichment in ProFITS requires a list of more than 10 GO-mapped genes. Thus you should submit more number of genes to perform the GO analysis correctly.
I am using IE7/8, and Jbrowse does not display correctly. Why?
Bugs were reported while using IE7 or IE8 in Jbrowse, as domenmstrated in the fowllowing image. It seems these browser can not transfer the location correctly.
To resolve this problem, we suggest you choose Firefox or Chrome to explore ProFITS. Or you can manually copy the location to the search box, and click 'Go' to obtain right image as fowllowing.
How to use the search functionalities in the Advance Search page?
ProFITS currently supports two search modes: ID search and ortholog search. The ID search is used for searching maize genome IDs. To use it, users should set up what kind of IDs they are using, i.e. Maize Gene ID or Protein ID. Two kinds of output are available: text table and fasta format. Another search tool, Ortholog Search, is used for searching orthologs of Arabidopsis or rice genes. Users can submit IDs which demonstrated in the following sample list to explore related information.
I am using search functionality, can you show me some samples?
Here is a table of samples.
|Target source||Sample||Search Method|
|Maize Gene ID||GRMZM2G018487||ID search|
|Maize Transcript ID||GRMZM2G018487_T01||ID search|
|Maize Protein ID||GRMZM2G018487_P01||ID search|
|Full length cDNA||BT034120||ID search|
|Arabidopsis Gene Model||AT2G38470.1||Name search|
|Arabidopsis Locus ID||AT2G38470||Name search|
|Arabidopsis Alias||WRKY33||Name search|
|Rice Gene Model||LOC_Os05g27730.1||Name search|
|Rice Locus ID||LOC_Os05g27730||Name search|
There is apparently a format problem in the page of "Protein Kinase & Phosphatase". What happened in Class 1, group 1.3?
This is not a format problem. In PlantsP kinase Classification/PlantsP Phosphatase Classification (PPC), there are some groups/families without description yet. To avoid abundant annotation like 'No Description in PlantsP PPC', we simply used '-' instead. We are looking forward to find out appropriated definition for these groups/families.