With the avalanche of genomic information in neuroblastoma, software solutions that can integrate and make this information comprehensive are in great demand.
Methods:
We designed a web-based program to facilitate integrative analysis of genomic data for neuroblastoma. Next to a series of richly annotated neuroblastoma samples generated in our lab and profiled in various ways, the database also contains a large volume of other public neuroblastoma datasets and thousands of profiles from other tumor types and normal tissues.
Results:
The R2 program, which has its roots in neuroblastoma research, has a user friendly interface enabling a wide range of interconnected analyses, which can be harnessed by users with limited or no bioinformatics training.
Aside from mRNA expression data, R2 is also being employed for various other technologies such as aCGH, SNP, methylation, ChIPseq, Exome and even whole genome sequencing data. Various different technologies can be combined in integrative analyses and visualizations.
Examples of R2 usage include: KaplanScan for prognostic analyses; GeneSignature metagene creation and successive use to classify patient cohorts from within the platform. MegaSampler allows for the comparison of neuroblastoma profiles against up to 70.000+ publicly available samples of various tissues/cancers that also reside in our ever expanding data repository. Integrative correlation analyses can be performed to find associations between gene expression, methylation and/or variation status. R2 also harbours an embedded genome browser with many features including ChIPseq (chromatin / TF), (somatic) mutation and variation viewing combined with gene expression or other high throughput data.
Conclusions:
R2 provides a valuable resource for high throughput data of Neuroblastoma. The R2 program and database has been used in more than 320 publications and is publicly accessible via http://r2.amc.nl. R2 will help researchers in identifying important genes and biological processes in neuroblastoma.