Genes measured and differentially expressed in each TCGA project.
dataset
posted on 2024-05-16, 17:24 authored by Julián Candia, Luigi FerrucciNumber of measured protein-coding genes after all filters were applied and how many of them were found differentially expressed in either direction, i.e. over-expressed in primary-tumor (FC > 1) or non-tumor (FC < 1) tissue, using Bonferroni or Benjamini-Hochberg (B-H) q—value < 0.05 significance thresholds adjusted for multiple testing.
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widely used methodssmirnov enrichment statisticshare biological functionphenotype permutations combinednew consensus metricmolecular signatures databasefour different choicesenrichment evidence scorecurated pathway collectionsalthough originally developeddownstream exploratory analysisscale omics dataenable detailed benchmarkingcancer genome atlasseq datasets availablepredefined gene setsnowadays extensively utilizedleveraged harmonized rnaseq data analysisgsea performance usingdetailed analysisseq datamicroarray datathyroid cancerobtain cancercancer etiologyseq experimentswork fillsunweighted genetypically derivedremarkable agreementquantitatively assessedprovide guidancehepatocellular carcinomagsea modalitiesfinding suggestsexisting gapdespite differencescurrent guidelinescommon featureschromosomal locationbetter sensitivity
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