Group explorer [Kompatibilitätsmodus]genomecat.leovinus.de/resources/GroupExplorer.pdf · 2018-02-02 · GenomeCAT Manual Example Workflow1 . Filter and group data sets Select some

GenomeCAT Manual

Group Explorer

GenomeCAT Manual Example Workflow1

Group Explorer

The group explorer module is designed to facilitate the comparative analysis of processed data like called CNV, extracted peaks or other types of interesting regions. This module allows the grouping of datasets according to phenotype, experiment type or other attributes. The interactive graphical interface provides various options to identify other attributes. The interactive graphical interface provides various options to identify common features and characteristics that distinguish the groups under investigation. In this module you can:

● merge processed data (tracks) into groups manually or based on user specified attributes

● search the GenomeCAT database for all tracks with aberrations within a certain ● search the GenomeCAT database for all tracks with aberrations within a certain region

● adjust data visualization style using a broad range of layout options● inspect single aberrations in the context of large data sets taking advantage of

an interactive GUIan interactive GUI● plot grouped data as relative frequencies to detect recurrent aberrations● export all data for downstream analysis in other programs

In the following we demonstrate the Group Explorer using published aCGH data of two different stages of Lobular Intraepithelial Neoplasia (Boldt et al., GCC 2010):different stages of Lobular Intraepithelial Neoplasia (Boldt et al., GCC 2010):► Lobular intraepithelial neoplasia grade 3 (LIN3)

► Lobular intraepithelial neoplasia (LIN)


Filter and group data sets

Select some of these To searchSelect some of theseattributes to define filter criteria.

Add “%” to the search term to

To searchfor data assigned to a particular sampleor phenotypespecify name or search term to

extend the searchspecify name or phenotype here and check the box.

determinegenome release(mandatory field)

list of tracksmatching the filtercriteria.

GenomeCAT´s Group Explorer offers comfortable filter and search options to load tracks GenomeCAT´s Group Explorer offers comfortable filter and search options to load tracks specified by distinct attributes.

➔ start the module GroupExplorer with “App->GroupExplorer->open Groupexporer”open the “Load CNV” dialog via the database icon at the top menu➔ open the “Load CNV” dialog via the database icon at the top menu

The example dataset (Lobular Intraepithelial Neoplasia ) has been downloaded from GEO. We smoothed normalized aCGH data with ►CBS and extracted aberrant regions with ►“Extract Regions”. We typed “%GSM%” as search pattern into the name field, set the field <Processing to “FindPeaks” and the


We typed “%GSM%” as search pattern into the name field, set the field <Processing to “FindPeaks” and the sample phenotype to “LIN”. 7 data tracks matched these search criterias.

Filter and group data sets

To load and visualizeTo load and visualizeparticular tracks mark them as “Selected” or use the button belowto select them all.

To change a color for a certain track pick a new color via mouse click into this field.

Some defaultattributes bywhich filtered tracks can be

click into this field.The color editor is opened and any color can be chosen.

tracks can begroupedare listed in this panel. Choosing a grouptype from this For each group a type from thiscombo-box will modify the group list with the proposed colors to the right.

For each group a unique color (taken from a set of 10 distinctcolors) is proposed. To change the preset color click here. To

This dialog assists to merge different datasets which share attributes etc. into one group.

to the right. color click here. To finally set the colors click <Set Color> !

This dialog assists to merge different datasets which share attributes etc. into one group.➔ Assign a group to each selected track by setting a color with <Set Color> . The color of a track

determines the membership of a group. All tracks sharing the same color are considered as one group.

In our example we filtered the tracks representing phenotype two tumor stages with different prognosis, LIN and LIN3, respectively and assigned one color to each tumor stage (in the figure above all tracks for phenotype LIN3 are grouped together by setting the color to blue). As GroupExlorer displays data tracks derived from both phenotypes simultaneously they can be easily distinguished based on their color code.


derived from both phenotypes simultaneously they can be easily distinguished based on their color code.

Explore aberrant regions in Group Explorer

The left hand table The left hand table in the main screen named “ID” shows case identifier, extraction parametersand the assigned and the assigned color for each loaded data set.

.

The main view pan depicts all loaded CNV sets as bars. They can be displayed for each chromosome separately or as genomic view, where all chromosome are shown at once (tab “ALL”). Group Explorer separately or as genomic view, where all chromosome are shown at once (tab “ALL”). Group Explorer features the following layouts styles:Stack:

Displays CNV from top to bottom along their genomic position. Overlapping aberrant regions are moved to the next column, but the first non overlapping region is placed in the first column again. moved to the next column, but the first non overlapping region is placed in the first column again.

Tabular: All CNV identified in a single track are placed and displayed in their own column.

Frequency:This view depicts the relative frequencies of CNV in groups respective the genomic position.


This view depicts the relative frequencies of CNV in groups respective the genomic position.


To optimize display properties you can properties you can additionally modify the transparency by moving those sliders.Less opacity means more transparency more transparency and vice versa.

Set transparency to highlight relevant aberrations.

➔ The bars displaying aberrant regions in the main view can be displayed with a certain degree of transparency, which can be controlled by quality score or ratio value. If “none” is selected the regions are full displayed without any transparency.

For example this feature can be used to distinguish heterozygous from homozygous deletions or to identify hybridizations with low quality or “questionable” CNV.

Further layout options for Transparency maxRatio at least/Transparency maxQuality at least can be found in the Groupexplorer


Further layout options for Transparency maxRatio at least/Transparency maxQuality at least can be found in the Groupexplorerproperties.


The table named “CNV” provides The table named “CNV” provides detailed information about selectedCNVs. How to select a certainregion/CNV is explained in the text below.To show meta data of the associated To show meta data of the associated track for a certain CNV first select the respective item in the table “CNV” by mouse (background color changes).Then switch to the table “ID” . Then switch to the table “ID” . The associated item for the trackis highlighted.

.

Inspect single aberrations in detail

➔ To show detailled information on a certain genomic region or a CNV of interest click with the mouse on the CNV/region of interest. The region exactly beneath the mouse pointer will be highlighted by a horizontal and a vertical bar. The table „CNV“ will be refreshed to highlight all aberrant regions located in the selected region, the item for the selected region will be marked with a hook. in the selected region, the item for the selected region will be marked with a hook.

➔ Select a CNV directly by checking the tick box within the table „CNV“. The newly selected CNV will be highlighted within the chromosome view.

➔ The color of the highlighting bars can be customized in the Panel Group Explorer Properties -Layout .


The color of the highlighting bars can be customized in the Panel Group Explorer Properties -Layout .


Apply display filters to highlight relevant aberrations

➔ Set filters in the panel Group Explorer Properties to remove CNV/bars from the main view pane.

The following filters can be applied:The following filters can be applied:• hide CNV with ratio less than:

CNV with absolute (negative/non negative) ratios less the given threshold are removed from the main CNV view pane.

• hide CNV with quality less than:


• hide CNV with quality less than:CNV with absolute (negative/non negative) quality scores less the given threshold are removed from the main CNV view pane.

Explore aberrant regions in CNVCAT

Change the To inspect a certain genomic region Change thelayout styleto “Frequency” .The frequenciesare generatedbased on

To inspect a certain genomic region select the area my mouse dragging( in contrast to other GenomeCAT view panes there will be no red rectangle marking the selected area)

based on current displayresolution.

Answer the question whether to zoom in with <yes>. The main view is updated to show only the selectedregion (see next slide) .region (see next slide) .

Or choose an already selectedregion from the list “Selected Region” from the top pane.

The “Frequency” view depicts the relative frequencies of aberrant regions within groups and in this way can help to detect recurrent aberrations.this way can help to detect recurrent aberrations.

The frequencies displayed on the screen are dependent on the zoom-factor. f ij = nij /N jn ij − number of tracks within group j having aberrant values at region i ;

If regions from distinct groups overlap, the minimal shared relative frequency is indicated by a separate color (default: grey).The color indicating overlapping frequencies is customizable in the pane Group Explorer

n ij − number of tracks within group j having aberrant values at region i ;N j − total number of tracks within group j ;


(default: grey).The color indicating overlapping frequencies is customizable in the pane Group Explorer Properties.


Zoom in, add annotation tracks and check the region of interest in the UCSC Genome BrowserZoom in, add annotation tracks and check the region of interest in the UCSC Genome Browser

➔ select a particular region by mouse or from the list “Selected Regions” ➔ add public annotation tracks such as DGV (► Database of Genomic Variants) , GC-content or gene lists.➔ add public annotation tracks such as DGV (► Database of Genomic Variants) , GC-content or gene lists.➔ inspect the selected region within the ► UCSC Genomebrowser by clicking on the “world” icon in the top

menu.



Relative frequencies can be exported as text file for further analysis. ➔ start the export dialog by clicking on the <export frequencies> button from the main panel.➔ choose an appropriate window size based on which the frequencies should be calculated➔ choose an appropriate window size based on which the frequencies should be calculated

The export file contains relative and absolute frequencies per group for gains and losses and overlaps for all groups: genomic positions, number of all aberrant regions per group - nof_all_red1 , nof gains per group - nof_pos_red1 , relative frequency gains per group – freq_pos_red1 (likewise for negative values or losses) , overlapping frequency for all groups of


relative frequency gains per group – freq_pos_red1 (likewise for negative values or losses) , overlapping frequency for all groups of gains and losses.

Documents

Group explorer [Kompatibilitätsmodus]genomecat.leovinus.de/resources/GroupExplorer.pdf · 2018-02-02 · GenomeCAT Manual Example Workflow1 . Filter and group data sets Select some