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I want to run experiments on the data used in PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF link

So far, the paper has reduced the dimension to

  • ammon's horn
  • amygdala
  • anterior cingulate cortex
  • caudate nucleus
  • dorsolateral prefrontal cortex
  • first cervical spinal cord segment
  • frontal cortex
  • hypothalamus
  • putamen
  • substantia nigra

on the samples/patients GTEX-[11GSP, 11O72, 11OF3, 11TUW, Q2AG, QDT8, XAB4]

I assume they are using it.

Gene read count.    GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_reads.gct.gz

A small amount of the data is

Name               Description  GTEX-111CU-1826-SM-5GZYN  GTEX-111FC-0226-SM-5N9B8  GTEX-111VG-2326-SM-5N9BK  ...
ENSG00000223972.4  DDX11L1      0                         0                         0                         ...

From what I can gather, ENSG00000223972.4 DDX11L1 is the DEAD/H-box helicase 11 like 1

Therefore, I assumed that looking for the term first cervical spinal cord segment would give me the name and description.

Therefore, I am wondering if I have the correct data set.

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  • $\begingroup$ It’s not clear what you’re asking. ENSG00000223972 Is indeed a gene ID. But the terms you list are brain regions, not genes, presumably indicating the sample source $\endgroup$
    – cmungall
    Sep 16, 2022 at 5:10

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