Help
HRGD Help
Summary
As an analysis workbench for heterosis research, HRGD provides a series of tools and viewers for analyzing gene function, chromosome distribution, and expression patterns. In this section you will find detailed instructions on how to efficiently utilize these tools and viewers. If you have further questions or suggestions, please do not hesitate to contact us.
Database Search

1.what¡¯s in our database

HRGD contains heterosis related genes generated from different species (rice, maize, wheat) using different technology (SAGE, Microarraym, SSH et.al), and biomaterials in different development stage (seedling, tillering, booting, heading, flowering, filling...), and from different tissues (panicle, leaf, root, flag leaf). The database also contains expression information (expression pattern, change ratio, change trend, genetic class), sequence information (CDS sequences, gene sequences) and function information. Also has categorized literature and web resources. In the Search page, users can access all data hosted in HRGD and retrieve a combination of different data types by setting various search options. In the Search Result page, HRGD provides links to the detailed sequence records and direct access to the HRGD-embedded analysis tools.

2.General search guide

  • There are four modules in the ¡®search¡¯ and ¡®filter¡¯ option part, separately. Select them to active the module.
  • The ¡®Species¡¯ and the ¡®Ratio¡¯ modules do not support multiple selections.
  • Press and hold 'Ctrl' or ¡®Shift¡¯ for multiple selections.
  • You could select one or more modules to further narrow your search scope and optimize your request.
  • You also could found dataset of your interested through choosing 'and' or 'or' for intersection or combination data among any methods, stage and tissue modules.

3.About the Search Result Page

The search is case-sensitive. A gene list report page will be return. To view the details of each entry, click the corresponding accession number. You also could choose the gene sequences option to got sequence information. A download file is generated if selected the ¡®Gene Sequences

4.Search Example

  • 1) You may query rice heterosis related genes from panicles at filling stage generated using microarray technology by setting 'species'=rice, 'method'=microarray, 'method'=microarray, 'tissues'=panicle, and 'development stages'=filling (Figure 1).
  • 2) You could further search the interaction dataset of SAGE and Microarray using 'Ctrl'. (e.g. Figure 2).
  • 3) We also provide four options for further filter and an alternative display option (Figure 3).
  • 4)Click on the 'Search' button, you will receive the search result page as illustrated below in Figure 4. It will display a list of hyperlinked gene records that allow users to view more details.
  • 5) Click on the gene name (accession name) to view the gene detail information (Figure 5).
GO Function Classification System

1.What¡¯s the GO function classification system (GFCS)?

GO (Gene ontology) is one of the daily tools for downstream gene function annotation tool; GFCS is a useful tool for plotting GO annotation results. We integrate the GO database and exploit the analysis tools, and Users could define their interested genes, analyze and browse the GO function category.

2. General Guide

  • This tool can be accessed either by clicking the 'GO Function Classification System ' button at the home page or by browsing its independent page under 'Tools'.
  • Through activation the option, choose the interested dataset. You could draw figures or got the gene list information. It will take several minutes, please wait patiently (Figure 6).
  • The tree view section used for browsing the ontologies. The expanded node now displays all of the children of that node. To collapse the node, click on the minus sign next to the term.
  • To expand a node, click on the plus sign next to the node/term.
  • Click on the AccnTree, a SVG figure and SVG viewer software could be downloaded freely.
KEGG Pathway Annotation System

1.What¡¯s in the KEGG Pathway Annotation System?

KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks and also on the structure relationships. We annotated our heterosis related genes according the KEGG database and integrated them in our database.

2.General Guide

  • Selected pathways of your interested from (Figure 7)
  • Click on the ¡®show gene list¡¯ and ¡®draw figure¡¯, the Figure 8 and Figure 9 will present. The genes which annotated in the figure colored green and the detail information listed in the table.
Expression Pattern Filter System

what¡¯s EPFS

The heterosis related genes were classified into 12 different distribution patterns, and plotted the intensity of gene expression as fold changes (Figure 10). The prepared figures of each tissue are installed in the database, users could chick on the hyperlink and view them, also could save as .jpg file.
Chromosome Distribution
  • 1.A graphic browser is used to view the heterosis related genes distribution at the chromosome levels (Figure 11)
  • 2.Hold the mouse over a region to display the gene list items. Click on the accession name to display the gene record page
  • 3.Users also could simply query the database by gene name or search a region by 9311_Chr01_NNNN.
Sequence Blast
BLAST tools, used to compare user-supplied data to the in-house prepared database encompassing gene, cDNAs, protein sequences.