Gene Page Information Sitemap

 
Gene Page Information
Contents
Data Description
Basic Gene Search
How to use Advanced Search
  Annotation/Attribute Filters
  Select Results Columns
About Search Results

Data Description [ Top | Back]
The gene models all start with the prefix MC (Magnaporthe Community). These initially are exactly the same as the Broad version 6 gene models (prefixed MGG). The MGOS genes are MC_00001 to MC_11043 and the Broad genes are MGG_00001 to MGG_11043. The MC genes will diverge from the MGG genes as the community provides annotations.

Currently, new genes cannot be added, but this feature will be added soon. New genes will start at MC_80000 to distinguish them from the original MGG genes.

See Broad Gene Finding Methods to learn about how the initial genes were predicted.


Basic Gene Search [ Top | Back ]
You can search AGCoL gene models with the following options:
  • AGCoL Gene Names
  • Evidence Names like EST Contigs, FL-cDNA, TIGR, SAGE Tags, BROAD names, FGL Names
  • M.oryzae Genbank Names and any synonyms found in the Genbank record.
    The non-aligning genes are arbitrarily assigned to Chr0.
  • UniProt Description


  • A wildcard search using * can also be performed. Type the part of the name you know and use an asterisk (*) for parts you don't know. For e.g. transcript* will give the search results for transcription factor, reverse transcriptase, transcriptional ... and so on.

    How to use Advanced Search [ Top | Back ]
    This section describes how to search for genes using the Advanced Search page.
      1. Click the linkg for the organism to search the genes.


      2.

    Optional: Specify search filters to restrict the search results. See details on Annotation/Attribute Filters.

      3. Optional: Select the search results output columns. View details about the select results columns.
      4. Click the Show Count button to preview the number of records that will be selected by the search. Click the Show Results button to start the search.
    Note: The description of your search is displayed in the left hand portion of the screen, e.g.

    Annotation/Attribute Filters [ Top | Back ]

      This section describes how to use search filters to restrict the search results.
     
      Has a Broad Gene Match
      Limit the results to genes that have a corresponding Broad ID.
      Has a Genbank Gene Match
      Limit the results to genes that match a non-hypothetical/predicted genbank record.
      Secreted Protein Match
      Limit the results to genes that are predicted to encode secreted proteins.
      Best UniProt Match
      You can restrict the search results based on the UniProt ID or description or keyword match for the gene by selecting the UniProt type (ID/Descirption/Keyword) and specifying the search term.
    Note: You can search the genes that do not have any match to UniProt by selecting the 'No UniProt Match' option.
      GO
      You can restrict the search based on the UniProt GO classification for the genes. You can search for the genes based on the GO category of Molecular function, Biological process or cellular components. You can also restrict the search based on specific GO terms. This will restrict the search to include only those genes that have GO (category/Term) matching to the the value specified.
      Number of EST contig hits
      You can filter the search results based on the number of EST contig hits for the genes. For example you can restrict the search results to show only those genes that have greater than 1 EST contig hit.
      Number of SAGE Tag hits
      You can filter the search results based on the number of SAGE Tag hits for the genes. For example you can restrict the search results to show only those genes that have less than 2 SAGE Tag hit.
      Microarray Matches
      You can display all the genes with a match to Microarray (Version 1 or Version 2) gene by selecting the 'Yes' radio button for the corresponding version of the microarray. Select 'No' to display all genes that are not on the corresponding version of the Microarray.
      Chromosome Location
      You can filter the search results based on the location of the gene on chromosome or between a region on a chromosome. For example you can restrict the search results to show only those genes that are on chromosome I of M. oryzae and are between 1bp to 100000bp.
      You can filter the search results based on the number of FL-cDNA hits for the genes. For example you can restrict the search results to show only those genes that have exactly 1 FL-cDNA hit.
      You can filter the search results for genes that have TIGR gene prediction as evidence.
      Secreted protein (only for M. grisea genes)
      You can filter the search results for genes that have secreted protein as evidence.
      Has Genbank M. grisea gene match (only for M. grisea genes)
      You can filter the search results for genes that have match to Genbank M. grisea genes.

    Select Results Columns [ Top | Back ]

      You can specify following columns to display on the results page (See details about various table columns):
     

    About Search Results [ Top | Back ]
      This section describes the search results.
     

    Description of Table Columns:


    • Gene: Shows the lists of genes that matched the search criteria. Links to more detailed information of the gene.

    • UniProt (ID/Description/Keyword): Shows the UniProt (ID/Description/Keywords) match for the gene along with the BLAST e-value. Links to ExPASy Proteomics Server (UniProtKB/TrEMBL database).

    • GO: Shows the list of GO Term along with GO ID and GO Category for the gene.

    • Genome Location: Shows the location of the gene on the genome. Links to the genome browser. You can view other features aligned to the gene in the genome browser.

    • EST Contig: Shows the PAVE EST Contigs that were mapped to the gene. Links to MGOS PAVE which has more detail information about the EST contigs.

    • SAGE Tag: Shows the SAGE Tags that were mapped to the gene. Links to the SAGE Tag page which has more detail information about the SAGE Tags.

    • Genbank Genes: Shows the Genbank M. grisea genes.
      The name format for the Genbank genes is <common name>:: <genbank id>
      All Genbank M. grisea genes were extracted, along with the alternative names so that the user can search MGOS using the name they are familiar with.

    • Microarray Match: Shows the Microarray gene that was mapped to the gene.
      The format is <array version>: <array gene name>