MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms

Table 1 Stem cells experimental design

Experiment	Platform	Fib	hESC	hiPSC
Bock	Affymetrix HT-HG-U133A	6	20	12
Briggs	Illumina HumanHT-12 V4	18	3	30
Chung	Affymetrix HuGene-1.0-ST V1	3	8	10
Ebert	Affymetrix HG-U133 Plus2	2	5	3
Guenther	Affymetrix HG-U133 Plus2	2	17	20
Maherali	Affymetrix HG-U133 Plus2	3	3	15
Marchetto	Affymetrix HuGene-1.0-ST V1	6	3	12
Takahashi	Agilent SurePrint G3 GE 8x60K	3	3	3
Total training set	5 platforms	43	62	105
Andrade	Affymetrix HuGene-1.0-ST V1	3	6	15
Hu	Affymetrix HG-U133 Plus2	1	5	12
Kim	Affymetrix HG-U133 Plus2	1	1	3
Loewer	Affymetrix HG-U133 Plus2	4	2	7
Si-Tayeb	Affymetrix HG-U133 Plus2	3	6	6
Vitale	Illumina HumanHT-12 V4	8	3	18
Yu	Affymetrix HG-U133 Plus2	2	10	16
Total test set	3 platforms	22	33	77

A total of 15 studies were analysed, including three human cell types, human Fibroblasts (Fib), human Embryonic Stem Cells (hESC) and human induced Pluripotent Stem Cells (hiPSC) across five different types of microarray platforms. Eight studies from five microarray platforms were considered as a training set [57–64] and seven independent studies from three of the five platforms were considered as a test set [65–71]