FAQ

Last updated: a year ago (view history), Time to read: 3 mins

Q1. Will I be charged for using St. Jude Cloud: PeCan?

A.) You will not incur any costs for using PeCan. This is an open source tool for exploring curated datasets.

Q2. How do I navigate through PeCan?

A.) There are various ways to navigate PeCan: A user can begin searching a gene or variant in the search engine; a user can use the navigational membrane to browse from data facet to data facet; or a user can select begin exploring all the data available for a selected data facet.

Q3. How do I navigate to ProteinPaint?

A.) There are various ways to access ProteinPaint. First, a user may directly search for a gene which will then default to the hg19 reference genome and the Pediatric dataset. Or, a user can navigate directly into the Variant Resources data facet and then select the ProteinPaint tab which will default to the hg19 reference genome and the Pediatric dataset. Or, a user may filter the sunburst and then explore the Variant Resources data facet which will default to the hg19 reference genome and the Pediatric dataset with the filtered subtype also populated.

tip

There are other data sets (e.g. ClinVar, COMSIC, etc), depending on reference genome selected. Additionally, the user can move coordinates by using the internal search within the UI.

Q4. What are data facets?

A.) Data Facets represent a distinct type of post-processed genomic data for collections of pediatric cancer samples. Each data facet can be explored via a designated interface.

Q5. What use cases does this platform serve?

A.) See our use case section for examples.

Q6. What is PIE? Is it free?

A.) Pecan PIE (the Pediatric Cancer Variant Pathogenicity Information Exchange) is a cloud-based variant classification and interpretation service. It annotates and ranks variants by putative pathogenicity, then displays them in an interactive web interface for formal review and classification following ACMG guidelines. The portal also contains a repository of expert-reviewed germline mutations that may predispose individuals to cancer. It is free for non-commercial use. For more information go here.

Q7. How do I request data from PeCan?

A. At this time, a user cannot request samples from PeCan. The data will need to be requested through our Genomics Platform Data Browser. There are ways to access tables of expression data from the ProteinPaint UI. Read more about this here.

warning

Not all of the data found in PeCan is accessible in St. Jude Cloud’s Genomics Platform, thus we do not host any of our collaborator’s data at this time.

Q8. Will St. Jude Cloud host my institution’s data in the data browser or on PeCan?

A.) If you are interested in collaborating with St. Jude Cloud, please contact us at support@stjude.cloud for more information.

Q9. Where is the data from?

A.) See our Data Availability page for more details.

Q10. Can I build cohorts?

A.) This feature will be implemented in the future. However, a user can currently lasso samples in the Expression facet, gather a list of samples from the table view in Mutational Signatures, and/or populate data tables from ProteinPaint and GenomePaint.

Q11. What features are coming next?

A.) St. Jude Cloud is working with the COMET team to enable the remaining histology slides and also develop the Epigenetic Data Facet that will comprise of Methylation data. We are also working with the COMET team to build an image search where it will compare H&E slides with histological images in our database. Additionally, we are working on cohort building and sample pages. We would love to hear your feedback and any ideas you may have for future feature developments. If you have a feature request, please email support@stjude.cloud. Check out our quarterly newsletter for updates by subscribing here.