MM2Ssetup: MM2S ssGSEA Training Matrix, MB Sample Group information for...

In bhklab/MM2S: Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines

Description

This dataset contains the GMT files required to generate ssGSEA as part of MM2S along with a list of 674 geneset names that constitute the files, as well as the precomputed ssGSEA matrix on Human training data (347 human samples) as well as a list of the original MB subtype classifications for those samples.

Usage

data(MM2Ssetup)

Format

MM2Ssetup is a data file containing four objects:

HumanGMT

GMT file 694 Human Genesets, based on Gene Ontology Biological Processes (GO-BP) for MM2S subtype prediction

MouseGMT

GMT file 694 Mouse Genesets, based on Gene Ontology Biological Processes (GO-BP) for MM2S subtype prediction

MB_SampleInfo

Sample Names and Subtype for 347 Human Samples of the MM2S training set

genesetHuman

List of 694 genesets that are common to mouse and human, and which are part of the GMT files

GenesetStatNormal

List of 674 genesets and p-values (from the Wilcoxon test) for the Normal Subtype. Of these, the top 24 genesets specific to this group, and which overlap with the testing datasets, are selected for generating the ssGSEA rank matrix

GenesetStatWNT

List of 674 genesets and p-values (from the Wilcoxon test) for the Wingless (WNT) Subtype. Of these, the top 24 genesets specific to this group, and which overlap with the testing datasets, are selected for generating the ssGSEA rank matrix

GenesetStatSHH

List of 674 genesets and p-values (from the Wilcoxon test) for the Sonic hedgehog (SHH) Subtype. Of these, the top 24 genesets specific to this group, and which overlap with the testing datasets, are selected for generating the ssGSEA rank matrix

GenesetStatGroup3

List of 674 genesets and p-values (from the Wilcoxon test) for the Group3 Subtype. Of these, the top 24 genesets specific to this group, and which overlap with the testing datasets, are selected for generating the ssGSEA rank matrix

GenesetStatGroup4

List of 674 genesets and p-values (from the Wilcoxon test) for the Group4 Subtype. Of these, the top 24 genesets specific to this group, and which overlap with the testing datasets, are selected for generating the ssGSEA rank matrix

Frozen_ES_Rank_Matrix

Ranked list of 674 genesets per sample of the human training set, sorted in descending order of enrichment scores.

Author(s)

Deena M.A. Gendoo

References

Gendoo, D. M., Smirnov, P., Lupien, M. & Haibe-Kains, B. Personalized diagnosis of medulloblastoma subtypes across patients and model systems. Genomics, doi:10.1016/j.ygeno.2015.05.002 (2015)

Manuscript URL: http://www.sciencedirect.com/science/article/pii/S0888754315000774

Examples

data(MM2Ssetup)

bhklab/MM2S documentation built on Dec. 25, 2021, 10:48 a.m.