treatment, “what data set in the public databases most closely
resembles mine?” It is kind of like Blast for a transcriptomics
experiment you’ve done, except instead of asking what sequences
are similar, you are asking what experiments are similar, based on
their transcriptomic profiles!
1. Go to http://atpbsmd.yokohama-cu.ac.jp/cgi/atcast/home.
cgi. Click on AtCAST 3.1. Click on the “> Analyze Public
Data” button about halfway down the page. Under “Find
experimental condition by keyword,” enter “seed” and click
“Search.”
2. Click on the result labeled “Seeds stage8 w/o siliques.” Using
the eFP Browser in Subheading 3.4.1, we saw that one of the
highest level of expressions for ABI3 was seen here. Scroll
down and take a look at the data visualization, seen in Fig. 9.
3. Continue scrolling until you get to the table labeled “List of
experiments. . .” This table compares the overall expression
pattern of the selected experiment with the other experiments
Fig. 9 AtCAST visualization of samples correlated with Stage 8 seeds at the transcriptomic level. Pink edges
denote positive correlation
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G. Alex Mason et al.
resembles mine?” It is kind of like Blast for a transcriptomics
experiment you’ve done, except instead of asking what sequences
are similar, you are asking what experiments are similar, based on
their transcriptomic profiles!
1. Go to http://atpbsmd.yokohama-cu.ac.jp/cgi/atcast/home.
cgi. Click on AtCAST 3.1. Click on the “> Analyze Public
Data” button about halfway down the page. Under “Find
experimental condition by keyword,” enter “seed” and click
“Search.”
2. Click on the result labeled “Seeds stage8 w/o siliques.” Using
the eFP Browser in Subheading 3.4.1, we saw that one of the
highest level of expressions for ABI3 was seen here. Scroll
down and take a look at the data visualization, seen in Fig. 9.
3. Continue scrolling until you get to the table labeled “List of
experiments. . .” This table compares the overall expression
pattern of the selected experiment with the other experiments
Fig. 9 AtCAST visualization of samples correlated with Stage 8 seeds at the transcriptomic level. Pink edges
denote positive correlation
46
G. Alex Mason et al.