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MirOB Onthology


Based on the excellent Hanahan and Weinberg Cancer Hallmarks conception, which seems to be the most appropriate for integrative view on cancer, we have created novel cancer-related process ontology - Cancer pathogenic processes (CPP). It comprises various molecular and cellular phenomena that occur in cancer. The major accent of CPP is a specific drug and radiation responses.

How to use MirOB



Now public version of MirOB have several main functions:

(For use some function (GO networks, Dataset analysis) you must register and receive confirmation.)

For start the work, just click to the "Do research" button:

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By default, you will see "Build a gene networks" mode:

Enter the genes official names (NCBI notation) in the "Inter gene set" field and then press "Go" button.
By default gene network build only from interactions with 2 mechanizm: "transcription regulations" and "binding of microRNA".

If you want use more interactions -- click on the "advanced options" button. On "Filters" box, you can choose which interactions mechanisms will be used for build gene networks:


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If you want use "cancer networks", "shortest path" or "dataset analysis"* mode, just click on the combobox:

(*"dataset analysis" mode will active in future versions of MirOB)

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"Cancer networks" mode:

Just choose cancer type and then press "Go" button.

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"Shortest path" mode

"Start genes" field: start gene or set of genes
"Intermediate genes": genes through which the path must necessarily pass
"Finish genes" field: start gene or set of genes

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The first thing you will see is the key switch to the shortest path:



By default, you are in the construction of a typical network, if you want to find the shortest path between single or multiple vertices, just click on the "Shortest path."



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The first field is called "agents" - is the main field. This is where you should make a list of participants in the network

Participants must match the names of gene symbols from NCBI gene. (for ex.: ASAP, UROD, SRY, DERMO or DIABLO):


As you can see, the agents can be separated by different symbols: ",", " ", ";", or tab.
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The next field allows you to choose a layout for network visualization:


You can change the template after the post-build network. To do this, simply click on the desired layout.

If you click on the name of the template ForceDirected below will open three sliders for additional network management:


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The final step - selection of filters that serve as criteria for which data visualization. Strictly speaking, the filters can significantly reduce amount of unnecessary information in the network.



Also you can reduce not significance nodes, by clicking on the "only mutual links".

Checkbox "show edge labels" works including after the formation of the network.

Then press the submit button and wait for the formation of a network in the right panel.


Pathway dataviz example:


Pathogenetic processes network example:




Info

Union Genes (
)
:
Order:

Set 1 unique genes (
)
:
Order:

Set 2 unique genes (
)
:
Order:
Drugs and Targets there..
Oncosupressions microRNA chart there..
Oncogenic microRNA chart there..
graphviz test: