[Introduction]
[Table Output]
[Graphical Overview in Genome Browser]
[Graphical Overview in Locus / Alignment view]
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The Alternative Transcripts 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.
The result page contains several sections:
Two links to different graphical representations of the alternative transcripts, which will open in new window:
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.
Moreover, the top tissues for a promoter, based on CAGE-tags (currently only available for Homo sapiens and Mus musculus)
that are 20 bp around the TSS of the corresponding transcripts, are also listed.
For comparability the tpm (tags per million tags) value will be displayed.
The tpm value is calculated by multiplying the number of CAGE-tags per tissue in a promoter by one million and dividing that through the number of all CAGE-tags per tissue in the corresponding organism.
The transcripts assigned to a promoter are listed in the last column ("Transcript"). 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, for details see the element definition).
Additional information like non-coding/coding status or number of CAGE tags around the TSS (for human and mouse transcripts) might be displayed. Click on the link behind the accession number to get detailed information. If redundant transcripts from other sources are available, they are listed in the "Transcript" column..
When one or more transcription factor families (up to 5) are selected in the popup menu and the "Apply" 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. This filter is available for all organisms.
Human promoters can additionally be filtered for overlap with public annotation data, e.g. histone modifications or ChIP-Seq data from ENCODE.
Additionally, promoters with coding transcripts can be selected. All selected filters are combined with AND.
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:
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.
In this example we observe four transcripts on 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).
The graphic consists of four parts:
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 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.
Individual transcripts can be removed from the main sequence panel by clicking on the checkboxes.
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exporting the complete result page to HTML (including all graphics in JPG format) |
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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 |
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selection of a region which can then be exported |
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recalculation of the layout, i.e. the graphics is displayed as it was set up by default |
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