Fig. 1: Harmonization and integration of proteome Medulloblastoma (MB) datasets. | Nature Communications

Fig. 1: Harmonization and integration of proteome Medulloblastoma (MB) datasets.

From: Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level

Fig. 1

NIPALS principal component analyses (PCA) of measured FFPE samples (n = 62) with assignment to (A) the four main molecular MB subgroups2, (B) age of measured samples, (C) measured TMT batch. D Overview of analyzed datasets. PCA of data before (E) and after (F, G) data harmonization using ComBat in the HarmonizR framework annotated for the source of the samples (F) and for main molecular MB subgroups (n = 167, source data file has been provided). H Protein abundance of the the WNT and SHH MB marker FILAMIN A (nSHH_Archer = 15, nWNT_Archer = 3, nOthers_Archer = 27, nSHH_Forget = 10, nWNT_Forget = 5, nOthers_Forget = 23, nSHH_Petralia = 7, nWNT_Petralia = 1, nOthers_Petralia = 14, nSHH_FFPE = 25, nWNT_FFPE = 10, nOthers_FFPE = 27, nSHH_combined = 57, nWNT_combined = 19, nOthers_combined = 91, two-tailed, unpaired t test, pshhArchervsOtherArcher = n.s., pWNTArchervsOtherArcher = n.s., pshhForgetvsOtherForget < 0.0001, pWNTForgetvsOtherForget < 0.0001, pshhPetraliavsOtherPetralia = 0.02, pwntPetraliavsOtherPetralia = n.s., pshhFFPEvsOtherFFPE < 0.0001, pwntFFPEvsOtherFFPE < 0.0001, pshhcombinedvsOthercombined < 0.0001, pshhcombinedvsOthercombined < 0.0001) SHH MB marker GAB1 (nSHH_Archer = 15, nOthers_Archer = 30, nSHH_Forget = 10, nOthers_Forget = 28, nSHH_Petralia = 7, nOthers_Petralia = 15, nSHH_FFPE = 25, nOthers_FFPE = 37, nSHH_combined = 57, nOthers_combined = 110, two-tailed,unpaired t test, pshhArchervsOtherArcher = n.s., pshhPetraliavsOtherPetralia = 0.008, pshhFFPEOtherFFPE < 0.0001, pshhcombinedOthercombined < 0.0001)., and the WNT MB marker CTNNB1 (nWNT_Archer = 3, nOthers_Archer = 42, nWNT_Forget = 5, nOthers_Forget = 33, nWNT_Petralia = 1, nOthers_Petralia = 21, nWNT_FFPE = 10, nOthers_FFPE = 52, nWNT_combined = 19, nOthers_combined = 148, two-tailed, unpaired t test, pwntArchervsOtherArcher = n.s., pwntForgetvsOtherForget < 0.0001, pwntPetraliavsOtherPetralia = n.s., pwntFFPEOtherFFPE < 0.0001, pwntcombinedOthercombined < 0.0001). Data are presented as mean values ± SD in each dataset individually and in the joint dataset after harmonization PCAs are based on ≥70% valid values, *: p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, n.d. = not detected, NS = not significant, n represents biologically independent human samples.

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