Cohorts are a way of creating custom groupings of the samples and/or cases that you are interested in analyzing further. You may frequently reuse a cohort in multiple analyses. Creating a “saved cohort” allows you to do this. If you have any existing saved cohorts, they will display here for you to view, edit and share.
Create a New Cohort
To create a cohort from Your Dashboard, click on the Create a Cohort link in the Saved Cohorts panel at the bottom of the screen and select either “Filter” or “Barcodes” from the dropdown. The Filter link will display the cohort creation page; filters are explained below. The Barcodes link will display a page where you can upload samples/cases barcodes and create a cohort from them.
If you already have saved cohorts, they will be listed in the Saved Cohorts panel. Click on the Saved Cohorts link in that panel and a page with the details of your saved cohorts will display. Alternatively, to go directly to a given cohort, click on its name and the cohort details page of that cohort will display.
You can also navigate to these functions by using the drop down options in the COHORTS item on the menu bar.
Cohort Creation - Filters
Using the list of data sets and filters on the left, you can select the attributes and features that interest you from ISB-CGC data or user data. You can create a cohort containing multiple programs.
Select Data Set
This panel in the top left of the screen allows you to pick the programs and user data sets that you want included in the cohort.
The drop down list will display the ISB-CGC data sets that the Web App is currently supporting, as well as your user data. By default, the list is sorted by Node (Genomics Data Commons, Proteomics Data Commons, User) with programs listed below each node header. The sort order can be changed by selecting Program next to Sort By.
When an ISB-CGC hosted data set is selected, appropriate filters will display under three tabs. All tabs are not available for all programs, but all programs will have some features available on the CASE tab.
The CASE tab displays clinical and demographic features applicable to the selected program.
The DATA tab displays data types (ex. Aligned Reads, Copy Number Segment Masked) applicable to the selected program.
The MOLECULAR tab displays filters pertaining to mutations.
For USER DATA, there is one tab called “PROJECTS & STUDIES” which allow you to filter by the projects or studies you have uploaded to the system.
Click on a filter name to see the selection values. For example, when you click on “Vital Status”, it expands and provides a list containing “Alive”, “Dead”, and “NA” as values you may choose.
Selected filters will display in the Cohort Filters panel. The Data Set Details panel will update the Total Number of Cases and the Total Number of Samples based on the selected filters.
Individual selections within a filter group are “ORed” together, meaning if any of the conditions are met, they will be in the results. On the other hand, filters are “ANDed” together, meaning that data must meet all filter criteria in order to be selected. There may be times where you have no cases and samples in the results, based on the combination of filters you have chosen.
If you use AND and do not see the data you are expecting in the filter, try OR instead. AND is a more restrictive criteria requiring all filters to be met; OR is less restrictive, requiring only one criteria to be met for the data to display.
You may want to consider adding the term “AND” or “OR” in your saved cohort title since the type of combination used in your cohort does not display in the filters list for a saved cohort.
Note: Hovering over the Disease Code name will display the disease code long name if it’s part of the TCGA, CCLE, or TARGET data set.
The Molecular Tab is only available for TCGA data. It enables the user to filter by Gene Mutation Status, creating a cohort based on the presence of a mutation (of various types) in a gene or genes.
To combine multiple gene filters, select AND (requires all filters to be met for the data to be filtered) or OR (at least one criteria needs to be met for the data to be displayed). You can also filter by Genomic Build.
Programs & Projects Tab
The Programs & Projects Tab is only available for User Data. It displays the programs and projects that are part of the user data set.
Cohort Filters Panel
This panel displays the selected filters for the cohort. Filters are listed under the program name. If you click on the program name, the screeb will change to display the information for that program.
Selecting an X beside a single filter will remove that filter. Selecting Clear All in the top right of the panel will remove all the filters. Note that you cannot removed filters once the cohort has been saved. (See Set Operations below for more ways to add or remove filters from your cohorts.)
Data Set Details Panel
This panel shows the Total Number of Samples and Total Number of Cases for the currently displayed data set based on the selected filters. If there is a small “timer” icon, the calculation is taking place; the results should appear soon.
Data Set Clinical Features Panel
This panel shows a list of images (called “treemaps”) that give a high level breakdown of the selected samples for a handful of features (ex. Disease Code, Vital Status, Gender, Sample Type, Age at Diagnosis, etc.) for the currently displayed data set based on the selected filters.
By using the Show More button, you can see additional tree maps. Mousing over an image shows the details of each specific section of the image and the number of samples associated with it.
Programs & Projects Panel
This panel displays a list of images (called “treemaps”) similar to the Data Set Clinical Features panel, but is only available when the User Data tab is selected. This panel displays a high level breakdown of the projects and studies you have uploaded to the system. Hovering over the image will show details of that specific section of the image and the number of samples associated with it.
Saving the Cohort
Click the Save as New Cohort button when you are ready to save the cohort based on the filters you have set. You will be asked for a cohort name and the selected filters will be displayed. Enter the name and click the Create Cohort button.
NOTE: When working with multiple programs you will see a yellow notification box stating, “Your cohort contains samples from multiple programs. Please note that filters will only apply to samples from the program indicated by the tab they were chosen on - they will not apply to samples from other programs in this cohort.”
Cohort Creation - Barcodes
This feature allows you upload or enter your own list of sample or cases barcodes from multiple programs. There is a blue Show Instructions button on both the UPLOAD and ENTER tabs.
This feature allows uploading files with barcodes to create a cohort. Files must be in GDC Data Portal case manifest format, or in comma/tab-delimited case/sample/program format. The file can be a maximum of 32MB. Also, files must be in tab- or comma-delimited format (TSV or CSV) and have an extension of .txt, .csv, or .tsv. After selecting the file and uploading it, the entries will be validated. Any entries which are found to be invalid will be listed, and you can choose to omit them and continue with cohort creation, or select a new file for verification and upload.
GDC Data Portal Case Manifest Files
GDC Data Portal case manifests can be obtained on the ‘Cases’ tab of the Exploration section of the data portal here. JSON case manifests must have a .json extension, and will be validated against the GDC’s JSON schema. The minimum required properties for each entry in the JSON file are the project object and the submitter_id field. The project object must include the project_id property. All other properties will be ignored.
TSV case manifests must have a .tsv extension, and must contain the first three columns of the GDC TSV case manifest in the following order: Case UUID, Case ID, Project. Any other columns will be ignored. Do not remove the header row of the TSV case manifest.
Because the GDC Data Portal case manifest entries are cases, all samples from a case will be included in the cohort.
Below are the instructions which display when the Show Instructions button is clicked.
This feature will allow you to manually input barcodes for cohort creation. There is a maximum length of 10000 characters for the text box. Please use the file upload option if you need to upload more barcodes than will fit in that space.
Below are the instructions which display when the Show Instructions button is clicked.
Manage Saved Cohorts
Selecting Manage Saved Cohorts from the COHORT menu dropdown displays the Cohorts screen, SAVED COHORTS tab. This screen displays your saved cohorts and allows you to view, edit, delete, set operations, and share them. In addition, you can start a new workbook using selected cohorts.
To view a cohort, click on the name of the cohort to display the cohort details. Alternately, you can view the cohort details by clicking on its name in the “Saved Cohorts” panel on the “Your Dashboard” page.
From Cohorts screen, SAVED COHORTS tab, you can perform the following functions. Except for Set Operations, these functions are described in detail in the Cohort Details Screen section, as they are also available there.
Clicking the Set Operations button displays a New Cohort screen where you can create new cohorts from two or more existing cohorts using the union, intersection or complement operations. The Set Operations button will only be available if at least two cohorts are selected on the Cohorts screen.
On the New Cohort screen, enter a name for the new cohort and select a set operation. The intersect and union operations can take any number of cohorts and in any order. The complement operation requires that there is a base cohort, from which the other cohorts will be subtracted. Click Okay to complete the set operation and create the new cohort.
Note: To combine the user uploaded data and the ISB-CGC data, use the Set Operations function. This is possible because the list of barcodes is what is used to create the set operation. For example, to make a cohort of user data samples and ISB-CGC curated samples, Set Union must be used, and to filter user data which is an extension of TCGA or TARGET samples, Set Intersection must be used.
The figure below shows what the results of the set operations will be (represented by I for Intersect, U for Union, and C for Complement). There are two types of sets shown, those that overlap (on the left) and those that are nested (on the right). For the last row (complement operations), the “Subtracted” area is removed from the “Base” area to result in the Complement (C).
Cohort Details Screen
The cohort details screen displays the details of a specific cohort. The title of the cohort is displayed at the top of the page.
The screen is divided into the following sections:
Current Filters Panel
This panel displays current filters on this cohort or any of its ancestors. Saved filters cannot be removed, but new ones can be added using Edit.
Cohort Details Panel
This panel displays the Internal ISB-CGC Cohort ID (the identifier you use to access this cohort through the APIs), and the number of samples and cases in this cohort. The number of samples may be larger than the number of cases because some cases may have provided multiple samples. This panel also displays “Your Permissions” which can be either Owner or Reader, as well as Revision History. If you have edited the cohort, the filters that were used to originally create the cohort are displayed under the “Creation Filters” header. The newly applied filters (after original creation) are displayed under the “Applied Filters” header.
Select Data Set
This panel displays all the programs and user data sets that are included in the cohort; click on the drop down to see them.
By default, the list is sorted by Node (Genomics Data Commons, Proteomics Data Commons, User) with programs listed below each node header. The sort order can be changed by selecting Program next to Sort By. To see details about a program or data set, select it from the drop down list.
Data Set Details Panel
This panel shows the Total Number of Samples and Total Number of Cases for the currently displayed data set (selected from the Data Set drop down) based on the selected filters.
Data Set Clinical Features Panel
This panel shows a list of images (called “treemaps”) that give a high level breakdown of the selected samples for a handful of features (ex. Disease Code, Vital Status, Gender, Sample Type, Age at Diagnosis, etc.) for the selected program.
By using the “Show More” button, you can see additional tree maps. Mousing over an image shows the details of each specific section of the image and the number of samples associated with it.
Cohort Details Screen functions:
Create a New Workbook
Clicking the New Workbook button brings you to a screen where you can create a new workbook using this cohort.
Edit a cohort
Clicking the Edit button displays the Filters panel. Any filters selected will be added to existing filters. To return to the previous view, save any newly selected filters using the Save Changes button, or cancel adding any new filters by clicking the Cancel link.
Copy a cohort
To create a copy of the cohort, click on the Duplicate button. This will take you to a new copy of the cohort which has the same list of samples and cases; you will be the owner of the copy.
This is how you create a copy of another researcher’s cohort that they have shared with you. (Note: If they later change their cohort, your cohort will not be updated; it will remain the same as it was at the time you duplicated it).
Delete a cohort
Click the Delete button to delete the cohort. Confirm by clicking the second Delete button presented.
Clicking the File Browser button displays a screen with a list of data files associated with your current cohort. This list includes all files which are stored on the Google Cloud, including both controlled access and open access data.
You can use “Show”, “Page”, “Previous” and “Next” to navigate through the list. The columns are sortable by selecting the column header. You can select a subset of the default columns to show by using the “Choose Columns to Display” tool.
You can filter by full or partial Case Barcode on all tabs. To remove the search key word, click the “X” button adjacent to it. Filtering by Case Barcode updates the number to the right of all the other filters.
You may also filter by data type, data category, data format, platform, program, disease code, disease strategy, node (GDC, PDC), build (Hg38, Hg19) and/or experimental strategy. Selecting a filter will update the associated list. The numbers next to the filter refers to the number of files available for that filter.
The tabs “IGV”, “Pathology Images” and “Radiology Images” allow you to filter for files that show you respectively read-level sequence data (viewed using the IGV viewer), pathology images, and radiology images. Please note: only if you have authenticated as a dbGaP authorized user will you be able to select controlled access files to view in the IGV viewer (CCLE data does not require authorization to view the sequence data in the IGV viewer). Details of how to view Sequences, and Pathology and Radiology Images are provided below.
Viewing a Sequence
When available, sequences in a cohort can be viewed using the IGV viewer. To find those sequences that can be viewed, select the IGV link on the File Browser screen. The File Listing panel will display the files that can be viewed with the IGV viewer. Selecting the checkbox in the “View” column (maximum of file files) and clicking the Launch IGV button in the upper panel will display an IGV view of the selected sequence(s) data.
Controlled access files will be viewable by sequence ONLY if you have authenticated as a dbGaP-authorized user.
Using the Image Pathology Viewer
All tissue slide images from the TCGA program are currently unavailable for viewing. (Diagnostic images will display.)
When available, pathology images can be viewed using the caMicroscope tool (see more about caMicroscope provide here). These are the pathology images that are associated with TCGA samples. To find images that can be viewed, open a saved cohort and select the File Browser button. You can also select the File Browser link from the Dashboard Saved Cohorts panel. The files associated with your cohort will be shown. Click on Pathology Images to see a list of available pathology images. Hovering over the File Name and clicking on “Open in caMicroscope” will open the image file in a new tab using caMicroscope. (HINT: using a smaller cohort will provide faster response in creating the list of files available).
To zoom into the image, either click the left button or use your wheel to zoom in. Use your mouse to move around the image. To zoom out of the image, shift-slick the left mouse button or use your wheel to zoom out. Selecting caMicroscope at the top of page will send you to the caMicroscope homepage. If you hover over the Slide Barcode section on the top right hand side you will see metadata information listed.
Viewing a Radiology Image
To find images that can be viewed, open a saved cohort and select the File Browser button. You can also click the File Browser link from the Dashboard Saved Cohorts panel. The files associated with your cohort will be shown. Click the Radiology Images tab to view a list of available radiology images. Hovering over the Study Instance UID column and clicking on “Open in CHIF Viewer” will open the series Selection panel in a new tab using Osimis DICOM. (HINT: Using a smaller cohort will provide faster response in creating the list of files available.)
For a more detailed step-by-step process of Viewing Radiology Images using the Osimis DICOM viewer please go here.
Download File List as CSV
To download a list of files that are part of this cohort, select the CSV button in the upper right on the File Listing panel (on all tabs) on the File Browser screen.
The file contains the following information for each file:
Genomic Data Commons(GDC) File UUID
Google Cloud Storage(GCS) location
Genomic Data Commons(GDC) Index
Index File Google Cloud Storage(GCS) location
Access Type (open or controlled access)
Export File List to BigQuery
To export the File List to BigQuery, select the BigQuery button on the File Browser screen. You will need to have registered a Google Cloud Project and a BigQuery dataset to be able to export to BigQuery. More information on how to register a BigQuery Dataset can be found here. You can either make a new table or append to an existing table. You can also give the table a unique name; if left blank, a name will be provided for the table.
The table will contain the following information (for each of the data type tabs):
Export File List to Google Cloud Storage
To export the File List to Google Cloud Storage (GCS), select the GCS button on the File Browser screen. You will need to have registered a Google Cloud Project and a GCS Object to be able to export to GCS. More information on how to register a GCS bucket can be found here. You can also give the object a unique name; if left blank, a name will be provided for the bucket. You will be able to select either CSV or JSON as the file format for exporting into Cloud Storage. All exported files are converted into zip files.
The file will contain the following information (for each of the data type tabs):
Cohort export to CSV
Click the CSV button to download the cohort in CSV format. The file will contain a list of sample and cases IDs in the cohort.
Cohort export to BigQuery
Clicking the BigQuery button allows you to create a new table or append to an existing table. You must have registered a BigQuery data set with a Google Cloud Project on the registered Google Cloud Projects details page. More information on how to register a BigQuery data set can be found here.
If a user wants to export a cohort to their own premade table, it is required to have the following columns:
Note: You shouldn’t ever set UUID to ‘required’ because sometimes a sample doesn’t have a UUID, and the attempt to insert a ‘null’ will cause the cohort export to fail.
Cohort export to Cloud Storage
Clicking the GCS button allows you to save the details of the cohort in a specified Google Cloud Storage location. You must have a registered Google Cloud Storage (GCS) bucket with a Google Cloud Project on the registered Google Cloud Projects details page. More information on how to register a GCS bucket can be found here. You will be able to select either CSV or JSON as the file format for exporting into Cloud Storage. All exported files are converted into zip files.
Selecting Public Cohorts from the COHORT menu dropdown displays the Cohorts screen, PUBLIC COHORTS tab. This screen displays details about any public cohorts currently available in the Web App. It displays the cohort name, number of cases, number of samples and the last date each program was updated. Public cohorts can be used for “New Workbook” and “Set Operations”.
To create new workbooks based on a public cohort, check the checkbox adjacent to the public cohort and click on the New Workbook button.