Overview of Help-Pages

Transcripts & Probe Sets

Introduction

The Transcripts & Probe Sets section in ElDorado gives an overview of the alternative transcripts known for a single gene. The superpositioning of the transcripts helps to understand how transcripts differ in their exon/intron structure and which transcripts are regulated by distinct promoters. For those species where chips are available, probes from the selected microarrays are displayed in the graphical view to show which of the alternative transcripts are covered by the probes on the chip.

Output

The result page contains three sections:

• A table view of the transcripts

  

  The first column lists the information about organism, chromosomal location, gene name, Genomatix locus ID, and GeneID. Following the links in this column either starts a complete ElDorado analysis or opens the more gene info for the locus. The contig accession number and strand specificity refer to the genomic sequence for this locus and the orientation of the locus as it is annotated in this genomic context. The "-" icon above the organism allows to hide the information for this locus. It can be re-displayed by clicking on the "+" icon.

  The promoter regions belonging to the locus are shown in the next column. For each of the promoter regions the promoter ID, the start and end position, and the length of the promoter are provided. The check boxes allow to select a set of promoter regions for sequence extraction or for further analysis.

  The transcripts assigned to a promoter are listed in the last column. For each transcript, the number of exons and the position of the TSS relative to the promoter region are given. The colored field in front of the transcripts indicates the quality of the transcript (gold, silver, bronze).

• An analysis button to check for the presence of certain transcription factor binding sites in the promoters

  When one or more transcription factor families (up to 5) are selected in the popup menu and the "Show" button is pressed, the page is reloaded and additional information is shown for each promoter: if ALL of the selected binding sites are present this is shown in red.

• A task menu for further analyses

  After selection of the desired length the selected promoters in the above result table can either be extracted or used to start an analysis with GEMS Launcher:

  • Save selected promoters allows to extract the selected promoters in either GenBank or FASTA format. The length of the promoter sequences can be defined by the user; up to 3,000 bps upstream and downstream of the annotated TSS are supported. The extracted promoter sequences are displayed in your browser window with the option to download them to your local hard disk or to copy them to your personal sequence directory.
    If the Excel-format is selected, a tab-delimited file with all results from the table above and the promoter sequences is downloaded. It can be opened directly with Microsoft Excel.
  • "Search for common TF sites in multiple sequences" lets you step into the analysis of common transcription factor binding sites of the selected promoter sequences. The task will produce an output page with a graphical representation of the binding sites found.
  • To define a common framework of transcription factor binding sites based on the set of selected promoter sequences use the task "FrameWorker: Definition of common framework".
  • Potentially functional promoter modules can be found via the task "ModelInspector: Search for promoter modules" (using a highly specific library of predefined promoter modules).
  • To determine conserved sequence regions use "DiAlign: Local multiple alignment".
  • Transcription factor binding sites that are conserved within the alignment can be identified using "DiAlign TF: Multiple alignment plus TF sites".

  Available tasks for selected promoters above
  Select promoter length:   Genomatix optimized length   User defined length: bp upstream of first TSS and bp downstream of last TSS (max. 3000)	Save selected promoters   in GenBank format   in FASTA format   export to EXCEL format Submission of selected promoters to GEMS Analysis Search for common TF sites in multiple sequences FrameWorker: Definition of common framework ModelInspector: Search for promoter modules DiAlign: Local multiple alignment DiAlign TF: Multiple alignment plus TF sites

• A graphical overview of the aligned transcripts and probe sets

  The figure is a graphical representation of the transcripts listed in the table above and their genomic context. The transcripts are arranged by their genomic location. For those species where chips are available, probes from the selected microarrays (default is the newest chip for each organism) are displayed to show which of the alternative transcripts are covered by the probes on the chip.

  In this example there are four transcripts available for the human CAPN12 gene (antisense strand!). They are transcribed from three independent tissue specific promoters (yellow boxes). Two of the transcripts (AK127390 and NM_144691) start from the same promoter but exhibit different 3'UTRs (dark green boxes to the left). A number of probes from the Affymetrix probe set 228705_at (HG-U133_Plus_2) are located in the 3' UTR of the three lower transcripts.

  

  The Java graphic consists of four parts:

  • the main panel with the sequences and annotated elements (middle right)
  • a navigation panel with zoom- and scroll options (lower right)
  • a selection tree with elements to display or hide (left)
  • a toolbar with action buttons (top right)

  For a detailed description of the general features of Genomatix graphics please check the graphics overview.

  The main sequence panel

  The main sequence panel contains all transcripts as listed in the table view of the output. For each transcript, a separate sequence is depicted as a line with all annotated elements. Thus, the transcripts appear below each other with differently annotated exons, introns or UTRs.

  The colored field to the right of the transcript labels indicates the quality of the transcript (gold, silver, bronze).

  The navigation panel

  The view on the sequence can be changed by using the zoom- and scroll element in the lower right part of the graphics. The navigation panel contains a scaled down version of the sequence and a red box which marks the currently selected part of the sequence that is visible in the main sequence panel above. By default, the whole sequence is displayed.

  To zoom in or out, click on the red box in the navigation panel and adjust the box by reducing the size via its handles (the small white boxes top left and bottom right of the red box). The sequence in the main panel will adjust to the selected window.

  If you want to scroll along the sequence, move the red box within the navigation panel by sliding it with the mouse to the desired position. Alternatively you can click anywhere inside the scrollbar to jump to the desired destination.

  The selection panel

  The selection panel contains a tree with all elements that can be toggled on or off for display. Tree hierarchies can be shown or hidden by clicking the + or - symbols respectively. Checkboxes provide the possibility to toggle the visibility of
  • all or selected transcripts
  • all or selected probe sets (blue boxes)
  • all types of sequences elements annotated within ElDorado

  Individual transcripts and probe sets can be removed from the main sequence panel by clicking on the checkboxes.

  For a detailed description of the sequence elements within the selection panel see the description of the detailed graphics in ElDorado.

  The toolbar

  	exporting the complete result page to HTML (including all graphics in JPG format)
  	exporting the graphics or a selected region to a certain format (JPG, PNG, TIFF, PNM), based on the current settings of zoom and element selection
  	selection of a region which can then be exported
  	recalculation of the layout, i.e. the graphics is displayed as it was set up by default