Table 3 Datasets used in the meta-analysis. Description of the 7 datasets used in the meta-analysis with the related reference to the study, specifying the size, the array/sequencing platform, the pre-processing approach used to normalize the data and the type of feature (for example, probeset ID, Refseq ID, Ensembl transcript/gene ID) considered to identified each gene analyzed
Dataset | Samples | Platform | Normalization | Features |
|---|---|---|---|---|
GSE16476Â [48] | 88 | HG-U133_Plus_2 | MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix) | AHCY:200903_s_at; DPYSL3:201431_s_at; NME1:201577_at |
GSE62564Â (SEQC)Â [49] | 498 | Illumina HiSeq 2000 | Reads per million mapped reads (RPM) | AHCY:NM_000687; DPYSL3:NM_001387; NME1:NM_000269 |
E-MTAB-8248Â [50] | 223 | Agilent-020382 Human Custom Microarray 44k | preprocessCore (quantile) | AHCY:A_23_P17575; DPYSL3:A_24_P149036; NME1:A_23_P152804 |
TARGETÂ [51] | 161 | Illumina Hiseq 2000 | Fragments per kilo base of transcript per million mapped fragment (FPKM) | AHCY: ENST00000217426; DPYSL3: ENST00000398514; NME1: ENST00000393196 |
E-MTAB-38Â [52] | 251 | customized 11K olignucleotide-microarray (Agilent) | Variance Stabilization Normalization (VSN) | AHCY: A-MEXP-255.2721, A-MEXP-255.3013, A-MEXP-255.7928; DPYSL3: A-MEXP-255.617, A-MEXP-255.7551; NME1: A-MEXP-255.8195 |
GSE85047Â [53] | 283 | Affymetrix Human Exon 1.0 ST Array | Robust Multichip Average (RMA) | AHCY:3903361; DPYSL3:2880292; NME1: not available |
Westermann [54] | 144 | Illumina Hiseq 2000 and Hiseq 4000 | Transcripts per million (TPM) | AHCY: ENSG00000101444; DPYSL3: ENSG00000113657; NME1: ENSG00000239672 |