Introduction to genome browsers
Data used in this workshop
Figure 1
Graphical representation of the BDNF and TrkB
signalling pathway
Figure 2
UCSC Genome Browser: Setup
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UCSC Genome Browser: Understanding gene models
Figure 1
The typical structure of a gene as represented
in the UCSC genome browser
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You should now see something like this
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It is now a lot easier to view a number of
interesting features in the BDNF transcript models
UCSC Genome Browser: BLAT tool
Figure 1
Z score of expression level in Human brain (blue
= low expression, red = high expression)
Figure 2
Z score of expression level in Human brain (blue
= low expression, red = high expression)
Figure 3
Probe A_23_P216779 returns 2 hits for different
chromosomes. One of these has 100% homology over the whole 60 base
sequence, the other has 87% homology over a 24 base region.
Figure 4
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This view makes it easier to check what region
of each transcript is likely to be detected by the probes
UCSC Genome Browser: Gene expression data
Figure 1
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Linnarsson lab mouse cortex single cell data as
autoscaled datatracks
IGV
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You may need to change this back to a smaller
range in the future if you are working with large datasets and/or small
amounts of memory on your computer
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