Transcript Ontology Annoyation Treebrowser (OAT)

Ontology Annotation Treebrowser tool
(OAT)
Getting started
OAT - How to start a session
Click hear to go to
input page.
OAT - Input form
2. Choose ontology
1. Paste your probe sets here
3. Press Submit button
OAT – Browsing (1)
First number tells you
how many probe sets
you submitted.
Second number tells you
how many of the probes
sets was annotated to the
ontology.
Following the
hyperlinked number
generates a list of the
probe sets.
OAT – Browsing (2)
By pressing ”[+]” in front of a keyword, the associated
children of the keyword are displayed.
OAT – Browsing (3)
Let us look closer on a node in the ontology tree
ThisThis
indicates
indicates
thatthat
twotwo
genes
genes
are are
annotated
annotated
at
thisdirectly
level and
at bellow.
this level.
The definition ofThis
the indicates that three
keyword-annotations
can
keyword is linked
into Ebe found at this level and
lab/SRS.
bellow.
OAT – Browsing (4)
The level of significance
of an direct annotation is
given by the probability
of that this annotation
occurs by chance.
The number of submitted
probe sets affects the
probability: more probes
increase the chance of an
annotation.
This example from the MeSH tree illustrates that
Enzyme Activation have a low probability (2.8%) and
is therefore significant, but Molecular Sequence Data
have a very high probability (98,6%) and should
therefore be present in almost every analysis.
OAT – Report (1)
Continue to expand and contract the nodes
in the tree, until a satisfying level of details
are reached.
The next step is to summarize the
interesting parts in a report.
OAT – Report (2)
To make a report of the most
interesting keyword-annotations,
just mark the checkboxes.
In our example we are
interested of
Fibroblasts,
Enivronment and
Public Health
and Physics.
Choose if you want your report
based on genes or annotatedkeywords in the dropdown
meny. Then press the grey
button.
OAT – Report (3)
At the top of the report
general information of
your submission can be
found.
Bellow a list of tables
is found, one for each
keyword that was
checked.
OAT – Report (4)
The elements of the Report-table
A hyperlink to the A hyperlink toThe
HG_U95
source of
A hyperlink
the
to the
definition of the
database.
annotation reference of the
keyword.
annotation.
OAT – Further information
You can now consider your self trained on the OAT-tool.
Enjoy it.
Anders Bresell will gladly answer any remaining
question. (e.g. ”What data is used?”, ”I still doesn’t get
the part of significance?” or ”What programming
language was used?” )
Any suggestions of improvements are also
welcomed.
E-mail: [email protected]