Table 2 Resources and related task completion summary as well as features, sorted alphabetically by resource name
From: Use case driven evaluation of open databases for pediatric cancer research
| Â | ICGC Data Portal | PeCan | PedcBioPortal | Pedican | Xena Browser |
|---|---|---|---|---|---|
Version info | Data Release 27, 04.30.2018 | 2015-2018 | Version 1.14.1, 2018 | 2015 | 03.13.2018 |
UC 1 | Partly (2) | Yes (13) | Partly (3) | Yes (49) | Yes (3) |
UC 2 | Partly | Partly | Partly | Partly | Partly |
UC 3 | Yes | Yes | Yes | Yes | Yes |
UC 4 | Yes | Yes | Yes | No | No |
UC 5 | Yes | No | Yes | No | Yes |
Subtype details | Yes | No | Yes | No | No |
Age filter | Yes | No | Yes | No | Possible by phenotype filter |
Survival data | Yes | No | Yes | No | Possible by phenotype filter |
Enrichment analysis | Gene ontology, pathway targeting compounds | Non-extractable pie charts only for cell cycle, epigenetics, development & signaling | No | Pathway, interactions | Paradigm pathway activity |
Alteration type filter | Type, impact, significance | Single-nucleotide variant, insertion/deletions, somatic variant, copy number variation | Type of copy number alteration, listed gene mutation types | Somatic, germline | Somatic mutation assays |
Other molecular information | Gene expression, miRNA expression, protein expression, DNA methylation a.o. | Missense, silent, frameshift, exon, nonsense, splice, proteindeletion, intron, untrans-lated region, fusion transcript | Various molecular and phenotypic information | Transcription factor, modifications | Copy number, segments, DNA methylation, RNA sequencing on exon or gene expression |
Cancer-related gene filter | Yes (CGC) | No (CGC only) | Mutations noted as to cbioportal cancer genes with 1 or more mutations and all other genes with 2 or more mutations | No | No |