QTLtoGene Rice Help

Welcome to QTLtoGene rice!

About QTLtoGene Rice:

Welcome to QTLtoGene rice, which is a rice from phenotype to genotype integrated search platform. The aim is providing bioinformatics support for researchers researching or looking for phenotype-related genes. Through the collection information from existing major rice public database with analysis and organizing , enabling users to use simple text query interface and some useful tools to analyze and find rice functional genes of interest and understanding from all aspects of its function .

QTLtoGene including several parts:
Candidate gene search and epistatic gene search section provide users inquiries of a specific section or the genome-wide gene information.
Rice gene network presents a uniform probability rice gene function interaction network which combine from different sources of data, such as the expression of the chip data, protein interaction data and literature data mining based on its credibility. User can use a list of known functional gene as seed to find some new genes with relevant functional or with gene interoperability.
QTLtoGene Rice provides users with electronic PCR within Arabidopsis or rice genome, including the current release of Arabidopsis genome and two subspecies genomes of rice, as well as the existing 12 wild rice BAC clones sequences.
QTLtoGene Rice contains data infromation from a series of international and domestic public database including TIGR,RAP,Gramene,Oryzabase,RiceGE,riceFOX,Tos17,RMD.Through our interface users can query the genes location, annotation, expression, functional classification, as well as the mutation phenotypes and interaction network and other information to conduct a comprehensive search. In the query results can also get the expression state of specific gene, whether there are mutant line information, predictable phenotype and function, in addition to the database by integrating various functional analysis, the user can quickly query the specific gene's sequence, the two sub-species gene sequence variation, the different expression and promoter sequence analysis.

Getting started: use candidate gene search

QTLtoGene to provide users with a powerful search function, candidate gene search can be used to find or filter genes which interested in.
First of all, to enter the candidate gene search interface. When nothing is input and submitted directly can be get the entire genes results. All the submit and clear bottons in this page can be used to submit queries and to remove all content.
1. The first part is to select species and choose to search the marker range or location of the query part of the chromosome.

Users can enter a query marker interval, databases collected about 26,000 Rice molecular markers' physical location (mainly from Gramene and TIGR), can automatically identify the molecular markers and enter into a correct chromosome and physical location . (Note that the database only contain single position unit molecular markers, some of multi-loci markers such as RFLP inquiries may cause confusion and does not contain, the user can, through the database e-PCR part with primer sequence of markers to check the marker position, and select a specific site in the following location on chromosome.)
Chromosome select part can choose a specific chromosome or a search of all chromosomes. (When inputting specific molecular markers it will automatically identify the corresponding chromosome)
Start chromosome location and molecular markers can be mixed query, the database will automatically identify the region of the smallest section and gives the results.

2. Gene annotation and gene ontoloty part

This part provides a description of gene inquiries, including the gene TIGR LOC ID, gene names or synonyms, and query with a key word to gene describe. In addition it can also search by Arabidopsis homolog ID. The inquiry here does not support wildcard query, but ignore the lower or uper case.
The following two sections are the GO key word search and GO types select query. GO types are based on the GO ID and ranked from small to big, multi-options. In the right side, the AND and OR options diecide the left checkbox AND-OR search.

3. Known functional gene ontology part

This part provides the user searching with known functional gene ontology. Inquiries have three parts, which are the functional ontology, the growth and development related ontology and environment-related ontology.

4. Gene expression part

This can partly be two types of expression information analysis, are differential expressed under different conditions and tissue expression.
Differentially expressed under different conditions that we use the microarray data and in accordance with previous reports differential expression analysis results. Users can select the appropriate conditions can be found in the conditions of the differentially expressed genes.
Gene tissue expression used data come from Yale Virtual Center for Cellular Expression Profiling of Rice, to determine the rice gene whether expressed in various tissue.

5. QTL and mutation pehnotype information part

This part mainly involve phenotype information. QTL(Quantitive traits Loci) mapping provided a link between complex phenotype and a specific chromosome segment, the use of different previously traits QTL information, can serve as a follow-up support to find QTG(Quantitive traits genes).
At the same time this part provides phenotypic information from several major mutant database. Users can direct queries or select the appropriate type of mutation phenotype in order to find the gene corresponding with that phenotype.
In this section also provides genes' predicted pehnotype using RiceNet from known gene mutation phenotype, now covers about 6,000 genes.

The structure of search results

Through the search can get a list of results, each page contains the results of 100 genes, users can flip up and down can also specify a particular page, or directly click to download all the results of gene list.
The results of the first column of the table gives the gene TIGR LOC ID, click on the link will go to Rice Genome Browser corresponding gene region, and can click to download the appropriate sequence and analysis of sequence information.
The second column is all of the gene information in the database. The third column gives the RiceGE on the public database of gene expression microarray value chart, the user can quickly the status of gene expression.
Other columns are given some gene basic information, including location, gene name, describe and predicted phenotype, some information will be omitted as a result of the column width display impact.

How to use the section of epistatic gene search?

QTL mapping some time will give epistatic effect, the performance of the two QTL interaction section. Initially, we tried a total of gene expression, protein interactions and similar functions that may be linked to the QTL positioning has been the model of interaction.
The use of gene function has been RiceNet interaction network, we will section candidate gene search and the two candidate genes within the section of the interaction between the combination of the two search for the existence of epistatic section may exist in the candidate gene interaction between functional.
First select the two regions of information, can enter search molecular markers or specific location similar with the single region.
Subsequent search is same with single region part, all search terms will be used in both two regions.

How to use RiceNet?

RiceNet rice is a probability network which describes the functions interaction between rice genes, the current integration data including five sources of information, including the co-expression network build with 226 affimatrix rice chips from the NCBI GEO public database , UCDavids Rice kinase protein protein interaction database, the rice protein interaction network predicted from Arabidopsis protein interaction database using homology,
As well as more than 40,000 articles the rice-related literature abstract in PubMed obtained to build a co-cited network and related Arabidopsis homologs were mentioned.

Submitting a interesting gene or the list of a group known function genes to RiceNet, it will be give out the gene pair within these genes are linked and the others linked to these genes, and rank with the level of ranking scores.
RiceNet use of the known functional genes to find genes associated with, or learn more about the interaction between these genes. RiceNet covers about 60% of the rice genome, to expand the function annotation in those genes lack of information.

How to use e-PCR?

Rice e-PCR is to use the NCBI e-PCR software, by submitting the primer sequence information to scan the database and gives the location of primers and mismatch.
Currently the database contains the version 8 of Arabidopsis genome sequence and cDNA as well as the CDS, as well as rice Nipponbare No. 5 version of the genome and cDNA and CDS and the 9311 genome sequence. At the same time contains 12 wild rice BAC clone sequence from the Arizona Center.
Primer entered the following format:
Markername ForwardPrimer ReversePrimer ProductsizeRange

Four column data separated by Tab format.
Because of the need to scan the entire genome sequence, the service may need to run a few minutes, please be patient.

Example

QTL mapping get a Rice heading date QTL, in the molecular marker interval RM204 and RZ398.
In this example we will show how to use QTLtoGene with two different strategies and eventually combined to find related functional candidate genes.
First of all, by entering the molecular markers to view the a total number of genes in the region.

Than screening of candidate genes with further conditions. The most direct way is through the mutation phenotype search, here we have chosen the Tos17 database Heading dataand Growth-related mutant phenotype options. Can also directly choose the gene phenotype network prediction part of the related type phenotypes to include the more likely candidate genes.

Here are six possible candidate genes contain the related traits. Of these candidate genes described combined with the preliminary analysis of the phenotype's molecular biology, we believe that LOC_Os06g06900 could be the most likely phenotype-related candidate genes in these genes.
Click on expression will link to RiceGE, rice public database microarray data can browse. We found that the gene most highly expressed in the early inflorescence that may be related to flowering.

Click on the results of gene names will be redirect to Rice Genome Browser corresponding gene region, we can get the gene sequence and other information. Click on the below options Nipponbare vs BGI 93-11 SNPs / Indels we can see that the gene sequence differences in the sequence between two sub-species. Analysis showed that the gene has nocoding differences in coding sequence, further expand the display area and found a insertion xxbp in the core promoter region, which suggest that the gene may be differences in the promoter between two sub-species, resulting in the variability of expression and to bring to phenotypic differences.

Click for details information, we find that this gene is a photosensitive associated genes, and further information of their homologs in Arabidopsis present that the Arabidopsis mutant gene study shows that the gene in response to the red light and may have some connect with flowering.
Use of the detailed information parts of the two rice subspecies MPSS expression can find out the gene expression differences between the two subspecies. One can also analyze the promoter sequence.

According to the literature heading date traits may be associated with genes regulate flowering, gibberellin-related genes as well as the clock-related genes, we get the related known functions Arabidopsis genes to find Rice homologous gene, combined with heading date genes have been cloned in rice, a total of 52 genes have been found out. If these genes are not located in the above-mentioned region of the QTL, we can use these genes as seed, through RiceNet to find other genes related. Select the highest score genes to determine whether the candidate is located in the QTL region.

Through two strategies we find the same candidate gene, from bioinformatics data has evidence in support of the gene for the most likely candidate genes. The next step we can back to the original mapping population and get the gene sequence to confirm genetic variation and can also further validate the gene's molecular biology function.

We pay due attention to the content in this website. However, we do not provide warranty or assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, product or process disclosed in relation to all the data and documents available from this website.
Something should be note is the database provided only to its original information, and its predicted results for the follow-up only to provide a functional verification of possible choices and some help information on the exact gene function and phenotype of the study is still to go through the molecular biological verification.