Ontology Annotation Treebrowser tool (OAT) Getting started

OAT - How to start a session Click hear to go to input page.

OAT - Input form 1. Paste your probe sets here2. Choose ontology3. 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 c hildren of the keyword are displayed.

OAT – Browsing (3) The definition of the keyword is linked into E- lab/SRS. This indicates that three keyword-annotations can be found at this level and bellow. This indicates that two genes are annotated at this level and bellow. This indicates that two genes are annotated directly at this level. Let us look closer on a node in the ontology tree

OAT – Browsing (4) The level of significance of an direct annotation is given by the probability of that this annotation occurs by chance. 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. The number of submitted probe sets affects the probability: more probes increase the chance of an annotation.

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 annotated- keywords 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 definition of the keyword. The source of the annotation A hyperlink to HG_U95 database. A hyperlink to the reference of the 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.