PMC RMS biobank

PMC RMS biobank app

This app was developed at the Drost group at the Prinses Máxima Center for Pediatric Oncology.

This app contains molecular data from 19 rhabdomyosarcoma (RMS) samples, including gene expression and predicted gene fusion from bulk mRNA sequencing data, copy number alterations against a panel of normals (PoN) and somatic mutations against paired germline samples.

For more information about data collection and analysis, please refer to the original publication.

Data available

This app is independent from the official Princess Máxima Center website.

Click on the icon below to find us on the official platforms.

Gene Expression

Check the expression (log2 transcripts per million, TPM) of genes in RMS samples.

Gene symbol

Guide

eRMS : Embryonal RMS

P3F aRMS : PAX3-FOXO1 alveolar RMS

P7F aRMS : PAX7-FOXO1 alveolar RMS

FN aRMS : Fusion negative alveolar RMS

Standard : for tumoroids, the standrad model generated from the primary tumor

Second : for tumoroids, a secondary model generated from the primary tumor

Late : for tumoroids, the standard model at a later passage

Expression per subtype
Expression per sample

Gene fusion

Check fusions detected in the RNA sequencing data in RMS samples.

Somatic mutations

Check non-synonymous somatic mutations in cancer genes (1,914) detected by whole-genome sequencing in RMS samples.

Search by

Gene

Sample

Gene symbol

Select a sample

Allele frequency (AF)

Use the slider to specify the ranges for variant allele frequency (AF)

Query result
Cancer driver genes

Copy number alterations (CNAs)

Check copy number alterations in cancer genes (1,1914) detected by whole-genome sequencing in RMS samples.
When selecting genes only significant alterations (called as gains or losses compared to a Panel of Normals [PoN]) will be displayed.
By selecting samples, circos plots containing genome-wide alterations from tumors (outer circle) and tumoroids (inner circle) will be displayed.
No cutoffs for gains or losses are applied in the circos plots; the y-axis is represented in log2 scale.

Query CNAs

Search gene

Generate CN plots

Gene symbol

Select a sample

Query result

Gene expression and drug response

Find correlations between drug area under the curve (AUC) and baseline gene expression (log2TPM) in RMS tumoroid samples. Only protein coding genes were used to perform correlations.

Gene symbol

Correlate expression to

Drug

Drug class

Select a drug

Select a drug class

Download TPM matrix

Our team

Michael Meister (Coordinator of the Soft Tissue Sarcoma division) : M.T.Meister@prinsesmaximacentrum.nl

Marian Groot Koerkamp (Head technician and Data steward) : M.GrootKoerkamp@prinsesmaximacentrum.nl

Terezinha Souza (Data analyst and App developer) : T.M.deSouza@prinsesmaximacentrum.nl

Frank Holstege (Principal Investigator) : F.C.P.Holstege@prinsesmaximacentrum.nl

Jarno Drost (Principal Investigator) : J.Drost@prinsesmaximacentrum.nl