Ontology Annotation Tree browser tool (OAT) Getting started

OAT - How to start a session Click here to go to query page.

OAT - Query 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 probe sets were annotated to the ontology. Following a hyperlinked number will result in a list of the respective probe sets.

OAT – Browsing (2) By pressing ”[+]” in front of a keyword, the associated c hildren of the term are displayed.

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

OAT – Browsing (4) This example from the MeSH tree illustrates that Enzyme Induction have a low probability (1.3%) and is therefore significant, but Molecular Sequence Data have a very high probability (99,8%) and should therefore be present in almost every query of this magnitude. NOTE: The number of submitted probe sets affects the probability; more probes increase the chance of an annotation. The level of significance of an direct annotation is given by the probability of that this annotation occurs by chance.

OAT – Report (1) Continue to expand and contract the nodes in the tree, until a satisfying level of details is 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 Protein Kinases and Myelin Basic Proteins Choose if you want your report based on genes or annotated terms 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. Below a list of tables is found, one for each keyword that was marked.

OAT – Report (4) The elements of the Report-table A hyperlink to the definition of the term. 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 yourself 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 welcome.