How to Use IIDB
Gene Maps
All data search functions are implemented for gene maps derived from the NCBI mouse gene build (version 33) and also the Ensembl mouse gene build (version 29e). You can specify which map to use. The NCBI gene map is the default.
Abbreviations:
TF = Transcription Factor
TFBS = Transcription Factor Binding Site(s)

[abcdef] denotes a link, a button or checkbox on the website
Search for a Gene
List of Annotated Genes
The gene list also indicates the data features available for a specific gene in the 'Available Data' column.
Computationally Predicted Co-regulated Genes
  • [About Gene Groups] describes the algorithm used for predicting co-regulated Gene Clusters.
  • [NCBI Annotated Genes] links to a list of gene groups based on the NCBI gene map
  • [Ensembl Annotated Genes] links to a list of gene groups based on the Ensembl gene map
    Members of a gene group can also be analyzed individually
    • [Analyze Individual Genes of this Group] links to
      • View the microarray expression profile
      • Choose any features such as matrix scan hits, ChIP-chip data etc. for display (described under Features).
LPS Responsive Gene Clusters
Explore ChIP-chip Data
The gene list also indicates the data features available for a specific gene in the 'Available Data' column.
Search
Add Genes to IIDB database
  • [Add Genes for Cis - Regulatory Prediction Annotation] links to
    IIDB form page where you submit a gene for cis - regulatory prediction annotation
    Please, read the instruction
    All submissions are checked for duplications Additional 20kb upstream and 10kb downstream of the gene location are annotated during the overnight process. An email is sent at the end of the process detailing the status of the gene annotation process.
    • Single Gene
      • [Find gene name and geneID] links to
          A help page explaining how to find a gene name and geneID
      • [Find gene coordinates] links to
          A help page explaining how to find the gene chromosomal location
      • Provide the gene name
      • Provide the entrez geneID
      • Provide the chromosome
      • Provide the gene strand
      • Provide the start and end Coordinates of the gene
      • [To Pipeline] links to
        • Upload Summary Page
        • The gene is processed during a nightly cron process
    • Many Genes
      • Use the [upload File] functionality.
      • [To Pipeline] links to
        • Upload Summary Page
        • The file is processed during a nightly cron process
Features
  • IIDB form page where you can choose annotated features to be displayed for a particular gene. Most IIDB pages link to this page. Specifics, such as exon start and end coordinates as well as the gene strand are provided. Also a list of the available data for a particular gene is listed.
  • Specify the region(s) to be analyzed using the 5' Upstream and 3' Downstream text boxes, and the Include Coding Region check box. The strand of the gene is automatically taken into account when selecting the 5' upstream and 3' downstream regions.
  • Choose any of the listed features using the[Check Boxes] next to the feature name
  • [Feature Name] link to
      Pages with more information about that particular feature.
  • Choose any of the listed sub features using the[Check Boxes] next to the sub feature name
  • [Sub Feature Name] link to
      pages with more information about that particular feature.
  • Chose none or more TFs under the 'ChIP-chip Segments' feature heading.
  • [Generate Results] links to
      Summary page (described under Summary).
Summary Page
  • This page lists a brief summary of your search and whether a selected feature was found for a gene
    • Gene name
    • Annotated Features
    • Computationally derived Feature
    • Your login name
    • [Download] links to
        Download page which lets you to save the search result in .gff3 file format to your computer.
    • [here] in the link at the bottom of the page.
      • Starts the Argo genome browser (no additional downloads are required to start Argo) to display your search result.
          [Double clicking on a feature] displayed in the genome browser launches a new window in your internet browser displaying additional information about that feature.
IIDB Use Examples

You can also access the IIDB Feature using the [Features] link described in the 'Multi-Gene Example' below

Multi-Gene Example: How to explore the website using Il12b, Il12a, Il15 genes.
  • Click on [NCBI] under View Annotated Genes in the menu bar
  • Use your browser search function by typing Ctrl-F
  • Type il12b into the search box
  • Cick on the [Gene Name] in the Gene ID column
    • This launches the NCBI website in a separate window
    • Close this window
  • Click on [Features]
    Now you are at the same page as described in the 'Single Gene Example' above.
  • In your web browser click the [Back] button in the tool bar
  • Click on [Search for TF factors]
    • This page lets you search for predicted TFBS which may regulate il12b
        (You can navigate to this page directly by using the link [Search Genes for TF binding sites] in the menu bar)
    • Choose Atf3 and Creb1 from the TF selection box
    • Check [0.001] in the Threshold column (this is most stringent threshold)
    • Enter 2000 in the Upstream Region text box . This will limit the search to 2000 nucleotides upstream of the transcription start site of il12b
    • The Search by Gene Identifier text box is already populated with the entrez geneID of il12b
    • Check [Show Conserved Sequences] and [ ATF3] under Show ChIP-chip Segments
    • Click [Submit]
      • This launches the search queries and creates a jnlp file for webstart and .gff3 files specific for your search.
      • A short result summary is displayed
      • click on [Download]
      • Save any file from the download directory to your desktop for later use
      • For more info. about gff3 file format follow the [Gff File Format] link under External Links
    • Click on [here] in the link at the bottom of the page.
      • This launches the webstart enabled Argo genome browser
      • For more info. and how to use Argo follow the [Argo Home Page] link under External Links
          [Double click] on a feature displayed in the genome browser. This launches a new window in your internet browser displaying additional information about that feature.
  • In your web browser click the [Back] button in the tool bar twice
  • Select the [Checkbox] for il12b, il12a and il15 in front of the gene name in the 'Check for TFB site pipeline' column
  • Go to the top of the page
  • Click on [Analyze Genes for TFB sites]
    • This brings you to same screen as before. Here you can search for predicted TFBS and compare their location among the 3 genes
    • Choose Atf3 and Creb1 from the TF selection box
    • Check [0.001] in the Threshold column (this is most stringent threshold)
    • Enter 2000 in the Upstream Region text box . This will limit the search to 2000 nucleotides upstream of the transcription start site of the genes
    • The Search by Gene Identifier text box is already populated with the genes to be analyzed
    • Check [Show Conserved Sequences] and [ ATF3] under Show ChIP-chip Segments
    • Click [Submit]
      • This launches the search queries and creates a jnlp file for webstart and .gff3 files specific for your search.
      • A short result summary is displayed
      • Click on [Download]
      • Save any file from the download directory to your desktop for later use
      • For more info. about gff3 file format follow the [Gff File Format] link under External Links
    • Click on [here] in the link at the bottom of the page.
      • This launches the webstart enabled Argo genome browser
      • For more info. and how to use Argo follow the [Argo Home Page] link under External Links
          [Double click] on a feature displayed in the genome browser. This launches a new window in your internet browser displaying additional information about that feature.
  • In your web browser click the [Back] button in the tool bar twice
  • Select the [Checkbox] for il12b, il12a and il15 in front of the gene name in the 'Check for TFB site pipeline' column
  • Go to the top of the page
  • Click on [Analyze Genes for shared TFB sites]
    • This page lets you search for predicted TFBS upstream of the transcription start site which are shared among the genes.
    • Furthermore, you can also specify a nucleotide length window the predicted TF sites must reside in. For example: a window of 100 means that: TF site at -220 in gene A, TF site at -290 in gene B are within the window and will be reported. But TF site at -440 in gene C will not be reported since it lies beyond the 100 nucleotide window of any of TF sites reported in gene A or B.
    • Choose Atf3 and Creb1 from the Transcription Factor selection box
    • Check [0.01] in the Threshold column (this is least stringent threshold)
    • Enter 2000 in the Upstream Region text box . This will limit the search to 2000 nucleotides upstream of the transcription start site of the genes
    • Enter 400 in the specify TF window text box
    • The Search by Gene Identifier text box is already populated with the genes to be analyzed
    • Check [Show Conserved Sequences] and [ ATF3] under Show ChIP-chip Segments
    • Click [Submit]
      • This launches the search queries and creates a jnlp file for webstart and .gff3 files specific for your search.
      • A short result summary is displayed
      • Click on [Download]
      • Save any file from the download directory to your desktop for later use
      • For more info. about gff3 file format follow the [Gff File Format] link under External Links
    • Click on [here] in the link at the bottom of the page.
      • This launches the webstart enabled Argo genome browser
      • For more info. and how to use Argo follow the [Argo Home Page] link under External Links
          [Double click] on a feature displayed in the genome browser. This launches a new window in your internet browser displaying additional information about that feature.