Table 2 Comparison of methodological approaches for analysis of gene expression data
From: Use of gene expression studies to investigate the human immunological response to malaria infection
Dataset | Data generation | Gene ontology analysis | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
GEO series | Publication | RNA Quantification Platform | Normalization | Adjustment for covariates | Definition expression | Expressed genes | Threshold FC | Threshold P | Test | Multiple testing | GO analysis | Threshold GO enrichment p | Test | Multiple testing |
GSE2900 | Griffiths (2005) | Stanford University cDNA lymphochip two color microarray | Scaled to geometric mean of sample:reference signal ratio from all array features | NS | Signal threshold | 9869 | 2.5 (from median in > 4 samples) | 0.1 | Permutation | FDR | NA | NA | NA | NA |
GSE5418 | Ockenhouse (2006) | Affymetrix U133A GeneChips | RMA | NS | NS | NS | No | 0.01 | SAM, t-test | FDR | Onto Express and Pathway Architect | 0.05 | NS | FDR |
GSE15221 | Franklin (2009) and Sharma (2011) | Illumina Human WG-6 v2.0 | Cubic spline | NS | Signal threshold | NS | 1.7 | 0.01 | Paired t-test | FDR | Onto Express | Varying | NS | NS |
GSE15221 | Hirako (2018) | Illumina Human WG-6 v2.0 | Cubic spline | NS | Signal threshold | NS | 1.5 | 0.01 | Permutation and t-test | FDR | DAVID, GSEA | 0.05 | Multiple | FDR |
GSE26876 | de Carvalho (2011) | Affymetrix Human Gene 1.0 ST Array | RMA | NS | NS | NS | 1.5 | 0.05 | Student t-test | No | Ingenuity pathway analysis | NS | NS | NS |
GSE33811 | Krupka (2012) | Affymetrix Human Gene 1.0 ST Array | RMA and Quantile | NS | Signal and variation threshold | 3110 | 2 | 0.05 | Paired t-test | No | Gene set enrichment analysis on selected GO terms | 0.01 | Paired t-test | FDR |
GSE34404 | Idaghdour (2012) | Illumina Human HT-12 BeadChips | Quantile | Location, Sex, Hb, total cell counts (RBCs and WBCs) and ancestry | Signal and normality threshold | NS | 2 (for comparison) | 0.01 | ANOVA, ANCOVA | FDR | Gene set enrichment analysis on customized MsigDB database | 0.05 | NS | Bonferroni |
GSE55843 | Jagannathan (2014) | Agilent Sure Print G3 Human Gene Expression 8 × 60K v2 gene expression microarrays | Quantile | NS | Signal threshold | NS | 2 | 0.05 | SAM | FDR | NA | NA | NA | NA |
GSE53292 | Jaijyan (2015) | Illumina Genome Analyzer Iix 72SE | NS | NS | NS | NS | NS | 0.05 | t-test | No | GeneCodis3, Bingo 2.3 plugin (Cytoscape 2.8.3) | 0.05 | NS | NS |
GSE50957 GSE52166 | Tran (2016) | Illumina HiSeq 2000 2 × 100 PE | TAMM | Batch, Sex, Age, Pre-infection baseline | Signal and variation threshold, removal Y chromosomes | NS | 1.5 | 0.05 | Limma | FDR | Ingenuity pathway analysis | 0.05 | Fisher exact test | FDR |
GSE50957 GSE67184 | Vallejo (2018) | Illumina HiSeq 2000 2 × 100 PE | CPM, TPM | NS | Signal threshold | NS | NS | 0.05 | EdgeR | FDR | WGSEA, ToppGene, STRING | 0.05 | Multiple | FDR |
GSE64338 | Subramaniam (2015) | Affymetrix Human Gene 1.0 ST Array | Nonlinear normalization based on Li-Wong methods | NS | NS | NS | 1.2 | 0.001 | Paired t-test | FDR | Ingenuity Pathway Analysis | 0.05 | NS | FDR |
GSE64493 | Sullivan (2015) | Agilent Sure Print G3 Human Gene Expression 8 × 60K v2 gene expression microarrays | Quantile | NS | Signal threshold | NS | 1.5 | 0.03 | Limma | FDR | DAVID | 0.05 | NS | FDR |
GSE67184 | Rojas-Penas (2015) | Illumina HiSeq 2500 2 × 100 PE | SNM | Location/time-point, subject (random effect) | Signal threshold | 6154 | No | 0.05 | NS | FDR | NA | NA | NA | NA |
GSE67184 | Gardinassi (2018) | Illumina HiSeq 2500 2 × 100 PE | NS | NS | NS | NS | No | 0.05 | Limma, repeated measures ANOVA | FDR | GSEA on blood transcriptome modules (BTM, Li et al.) | 0.05 | permutation | FDR |
GSE7586 | Muehlenbachs (2007) | Affymetrix U133 Plus 2.0 GeneChip | GC RMA | NS | NS | NS | 2.5 | 0.01 | t-test | No | NA | NA | NA | NA |
GSE77122 | Tarawa (2017) | Agilent Sure Print G3 Human Gene Expression 8 × 60K gene expression microarrays | Each gene expression array dataset was normalized to the in silicon pool for the macrophages cultured with RBCs | NS | NS | NS | No | 0.05 | Paired t-test | No | DAVID | 0.05 | Fisher exact test | No |
GSE93664 | Burl (2017) | Affymetrix Human Gene ST 2.0 gene array | RMA | NS | NS | NS | 2 | 0.05 | NS | No | STRING | 0.01 | NS | Corrected unspecified |
GSE100562 | Quin (2017) | Illumina HiSeq 2500 2 × 50 PE | NS | NS | NS | NS | No | 0.05 | Limma | FDR | NA | NA | NA | NA |
GSE1124 | Boldt (2019) | Affymetrix U133A + B GeneChips | RMA | NS | Signal threshold | NS | 1.9 | 0.004 | SAM | FDR | DAVID and Ingenuity Pathway Analysis | 0.05 | NS | NS |
GSE114076 | Terkawi (2018) | Agilent Sure Print G3 Human Gene Expression 8 × 60K gene expression microarrays | Each gene expression array dataset was normalized to the in silicon pool for the neutrophils cultured with RBCs | NS | NS | NS | 2 | 0.01 | Limma | No | Genomatix GeneRanker, DAVID, NET-GE and Enricher | 0.05 | NS | Corrected unspecified |
GSE97158 | Rothan (2018) | Illumina HiSeq 2500 2 × 51 PE | TMM | Blocking by subject, in two separate models interaction with cell count and time of parasitemia was added | Signal threshold | 16,473 | 1.5 | 0.05 | Limma | FDR | GSEA (camera) on blood transcriptome modules (BTM, Li et al.) | 0.05 | Fisher exact test | FDR |
GSE65928 | Portugal (2015) | Affymetrix Human Gene ST 2.0 gene array | RMA | NS | NS | NS | NS | 0.05 | ANOVA | FDR | Ingenuity pathway analysis | NS | NS | NS |
GSE72058 | Feintuch (2016) | Affymetrix Human Gene 1.0 ST array | RMA and Quantile | Peripheral parasitemia | NS | NS | No | 0.05 | t-test | No | GSEA, CateGOrizer and ingenuity pathway analysis | 0.2 and 0.06 | NS | FDR |