phantasus - Tutorial

#### Tutorial: Project Achilles and the Cancer Cell Line Encyclopedia (CCLE) datasets.

Open Project Achilles Gene Essentiality Scores

Open the Project Achilles gene essentiality scores under the preloaded datasets section. By default, values in the heat map are mapped to colors using the minimum and maximum of each row independently.

Median Absolute Deviation (MAD)

Click the tools icon
and select "Create Calculated Annotation".
Enter "MAD" for the "Annotation name".
Enter "MAD()" for "Formula" and click "OK".
A new row annotation named "MAD" will appear to the right of the heat map.

Filter Rows

Show only the top 500 most variable genes by the median absolute deviation
Click the filter icon
.
Click the "Add" button and set the field name to "MAD".
Click "Switch to top N filter" and enter "500" for "N". Note that 523 rows are now shown because of ties in the median absolute deviation.

Hierarchical Clustering

Click the tools icon
and select "Hierarchical Clustering". Change "Cluster" to "Rows and columns". Click "OK" to run the analysis.
Do haematopoietic cell lines cluster together? Hover over the primary_site annotations to highlight cell lines from the same primary site. You can dynamically cut the dendrogram by dragging the dashed line at the top of the dendrogram.
Hierarchical clustering recursively merges objects based on their pair-wise distance. Objects closest together are merged first, objects furthest apart are merged last. The result is a tree structure, referred to as a dendogram, where the leaf nodes represent the original items and internal (higher) nodes represent the merges that occurred. Click here for a more detailed description of the hierarchical clustering algorithm and here for a comparison of the Pearson and Spearman correlation methods.

Compress Heat Map

Click the fit to window icon
to fit compress the heat map. Click
to return to the normal heat map size.

Remove Row Filter

Click the filter icon
and delete the median absolute deviation filter to show all rows.

Remove Dendrograms

Right-click on the column dendrogram and select "Delete". Do the same for the row dendrogram.

Sort Rows

Click the MAD row annotation header in the heat map once to sort the heat map in ascending order by the median absolute deviation. Click it again to sort the heat map in descending order. Note that you can shift-click to sort multiple columns simultaneously. Alternatively, you can click
to open a sort dialog.

Search Results To Top

Enter "BRAF" in the row search box.
Click
to bring the matches to the top of the heat map.

Visual Enrichment

Double-click on BRAF row to sort by dependency score.
Search columns for "skin".
Do skin cell lines seem to be more dependent on BRAF than cell lines from other lineages?
You can optionally limit your search to within a field by typing the field name followed by a colon ":" and then the term you are looking for.

Nearest Neighbors

Click the tools icon
and select "Nearest Neighbors". Click "OK" to run the analysis.
A new row annotation named "Pearson correlation" will appear.
What genes correlate with BRAF?

Scatter Plot Matrix

Select the first three rows in order to select the top 3 most correlated genes with BRAF and all samples. Click the chart icon
. Change the chart type to "row scatter" to assess the relationships between BRAF, FXR2, and ZNF781 simultaneously.

Append Mutations

Click
to bring up the file open window.
Check "Append rows to current dataset" and select the file CCLE Mutations dataset. Change "Current dataset annotation name" and "New dataset annotation name" to "id" to match the ids in the existing dataset with the id in the mutational dataset. Scroll down to see the mutational data.

Toggle Mutation Visibility

Click
to open the color key.
Click the "Synonymous" check box to visually hide synonymous mutations (note the matrix values are left unchanged).

Annotate Selection

Enter "BRAF" in the row search box.
Click
to bring the matches to the top of the heat map. Double-click to sort the heat map by the BRAF dependency score. Select the seven cell lines that have a dependency score less than or equal to -2. Right-click and select "Annotate Selection". Enter "BRAF_sensitive" for "Annotation name" and "y" for "Annotation value".

New Heat Map

Enter "CCLE" in the row search box to select the CCLE mutation data.
Right-click on the columns and select "Clear Selection" to clear the column selection.
Click the tools icon
and select "New Heat Map". A new tab will open that contains the selected subset of the heat map.

Fisher Exact Test

Click the tools icon
and select "Marker Selection". Change "Metric" to "Fisher Exact Test". Change "Field" to "BRAF_sensitive". Set "Class a" to "BRAF_sensitive" and "Class b" to "". Set "Grouping value" to "4" to group missense, splice site, frame shift, and nonsense mutations together and no mutation, synonymous, in-frame indels, and other non-synonymous mutations together (Click
to see the numerical values used to encode mutation type). Click "OK" to run the analysis.
A new row annotation named "Fisher Exact Test" will appear.
What mutations distinguish BRAF sensitive cell lines from the other cell lines?