Please correct me wherever I am wrong as my knowledge of genomics is nill.
Thanks. Let's start with the clinical matrix dataset. Here's what I understand from variables whose names start with GENOMIC_ID_TCGA_PANCAN.. for eg. _GENOMIC_ID_TCGA_PANCAN_HumanMethylation27
They seem to be some sort of flag variable denoting the gene (eg. HumanMethylation27) present in the sample. If the value is not NaN (it looks like it is the patient ID when it isn't), then the gene is present in the sample.
Also, I did not understand what _RFS, _RFS_UNIT & _RFS_IND mean. It seems like _TIME_TO_EVENT means the time it took for the cell to mutate.
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Identifiers _EVENT: event in this case it is overall survival event _INTEGRATION: id used for integrating data on the xena browser and across cohort _OS : overall survival time _OS_IND : overall survival event _OS_UNIT: overall survival time unit _PANCAN_CNA_PANCAN_K8: 2012 pancan paper publication data _PANCAN_Cluster_Cluster_PANCAN: 2012 pancan paper publication data _PANCAN_DNAMethyl_PANCAN: 2012 pancan paper publication data _PANCAN_RPPA_PANCAN_K8: 2012 pancan paper publication data _PANCAN_UNC_RNAseq_PANCAN_K16: 2012 pancan paper publication data _PANCAN_miRNA_PANCAN: 2012 pancan paper publication data _PANCAN_mutation_PANCAN: 2012 pancan paper publication data _PATIENT: TCGA patient id _RFS: recurrent free survival (xena curated, note: i trust the overall survival data much better) _RFS_IND: recurrece free survival event _RFS_UNIT: RFS time unit _TIME_TO_EVENT: time to event (in this case, it is exactly like overall survival event) _TIME_TO_EVENT_UNIT: time unit _cohort: cohort name (also used as cohort id) _primary_disease: primary_disease _primary_site: primary organ of origin age_at_initial_pathologic_diagnosis gender sampleID: sample id (same as _INTEGRATION) sample_type: sample type sample_type_id
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@jingchunzhu / Mary -- are the "Sample IDs" in Xena Browser:
- TCGA Barcodes?
- TCGA UUIDs?
- Xena-specific identifiers?
_GENOMIC_ID_TCGA_PANCAN_HumanMethylation27
is denoting the genomic sample ID in the Methylations 27K dataset. TCGA gives different IDs for each sample in each dataset.
It now makes sense now why fields like
_PANCAN_mutation_PANCAN
are encoded as missing /sample_id
rather than binary (0
/1
).