Difference between revisions of "Gene.ini"
From PastDB
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gene-browser=<p>Genomic context of the gene. Click on the image to view the gene, its events and its context in the UCSC website</p><p>Track colors:</p><ul><li><b>Black:</b> Group of neighboring cassette exon events (no link to PastDB)</li><li><b>Blue:</b> Simple cassette exon events</li><li><b>Purple:</b> Cassette exon events of intermediate complexity</li><li><b>Red:</b> Complex cassette exon events</li><li><b>Orange:</b> Intron retention events</li><li><b>Dark green:</b>Alternative 3' splice site choice event.</li><li><b>Light green:</b>Alternative 5' splice site choice event.</li></ul><p>See the FAQ section for further explanation.</p> | gene-browser=<p>Genomic context of the gene. Click on the image to view the gene, its events and its context in the UCSC website</p><p>Track colors:</p><ul><li><b>Black:</b> Group of neighboring cassette exon events (no link to PastDB)</li><li><b>Blue:</b> Simple cassette exon events</li><li><b>Purple:</b> Cassette exon events of intermediate complexity</li><li><b>Red:</b> Complex cassette exon events</li><li><b>Orange:</b> Intron retention events</li><li><b>Dark green:</b>Alternative 3' splice site choice event.</li><li><b>Light green:</b>Alternative 5' splice site choice event.</li></ul><p>See the FAQ section for further explanation.</p> | ||
| − | gene-expression=<p>Each of the dots in this plot represents the average expression of the gene across several related samples, using the cRPKM metric. Put your mouse on each dot to see the individual values for each sample.</p><p>Dot colors represent sample groups from a similar biological origin (see legend below).</p><p> Samples can be included/excluded from the plot using the buttons "Show All","Show None","Select All","Select None", or clicking on the sample groups below.</p><p> cRPKM can be converted to TPMs applying the following formula: TPM | + | gene-expression=<p>Each of the dots in this plot represents the average expression of the gene across several related samples, using the cRPKM metric. Put your mouse on each dot to see the individual values for each sample.</p><p>Dot colors represent sample groups from a similar biological origin (see legend below).</p><p> Samples can be included/excluded from the plot using the buttons "Show All","Show None","Select All","Select None", or clicking on the sample groups below.</p><p> cRPKM can be converted to TPMs applying the following formula: TPM &equals 10^6 * cRPKM/sum_all(cRPKM).</p> |
Revision as of 11:42, 5 November 2020
gene-coords=Genomic coordinates of the gene (1-based).
gene-browser=Genomic context of the gene. Click on the image to view the gene, its events and its context in the UCSC website
Track colors:
- Black: Group of neighboring cassette exon events (no link to PastDB)
- Blue: Simple cassette exon events
- Purple: Cassette exon events of intermediate complexity
- Red: Complex cassette exon events
- Orange: Intron retention events
- Dark green:Alternative 3' splice site choice event.
- Light green:Alternative 5' splice site choice event.
See the FAQ section for further explanation.
gene-expression=Each of the dots in this plot represents the average expression of the gene across several related samples, using the cRPKM metric. Put your mouse on each dot to see the individual values for each sample.
Dot colors represent sample groups from a similar biological origin (see legend below).
Samples can be included/excluded from the plot using the buttons "Show All","Show None","Select All","Select None", or clicking on the sample groups below.
cRPKM can be converted to TPMs applying the following formula: TPM &equals 10^6 * cRPKM/sum_all(cRPKM).
Abiotic stress conditions in A. thaliana. Sample information is available in the Supplemental Table 1 of Martín et al.
gene-specialdataset-biotic=Biotic stress conditions in A. thaliana. Sample information is available in the Supplemental Table 1 of Martín et al.
gene-specialdataset-light=Responses to light changes in A. thaliana. Sample information is available in the Supplemental Table 1 of Martín et al.
gene-specialdataset-spl_factors=Experimental manipulation of various RNA-processing factors in A. thaliana. Sample information is available in the Supplemental Table 1 of Martín et al.
gene-associatedevents=Events belonging to the gene of interest. You can click on each of the table columns to sort the events by this column or on each of the events to access to detailed information.
Each colored line corresponds to one of the AS events in this gene (see "Associated Events", above). Each dot corresponds to the average PSI value of the event across several related samples (as in the Gene Expression section, above). To see the individual values for an event, click on the event ID
Events can be toggled on and off with the buttons "Select All Events" and "Select No Events", or by clicking on the boxes next to the event names.
Samples can be toggled on and off with the buttons "Select All Tissues" and "Select No Tissues", or by clicking on the sample groups below.
gene-homology=Homologous genes listed in Ensembl