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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

DatasetData generationGene ontology analysis
GEO seriesPublicationRNA Quantification PlatformNormalizationAdjustment for covariatesDefinition expressionExpressed genesThreshold FCThreshold PTestMultiple testingGO analysisThreshold GO enrichment pTestMultiple testing
GSE2900Griffiths (2005)Stanford University cDNA lymphochip two color microarrayScaled to geometric mean of sample:reference signal ratio from all array featuresNSSignal threshold98692.5 (from median in > 4 samples)0.1PermutationFDRNANANANA
GSE5418Ockenhouse (2006)Affymetrix U133A GeneChipsRMANSNSNSNo0.01SAM, t-testFDROnto Express and Pathway Architect0.05NSFDR
GSE15221Franklin (2009) and Sharma (2011)Illumina Human WG-6 v2.0Cubic splineNSSignal thresholdNS1.70.01Paired t-testFDROnto ExpressVaryingNSNS
GSE15221Hirako (2018)Illumina Human WG-6 v2.0Cubic splineNSSignal thresholdNS1.50.01Permutation and t-testFDRDAVID, GSEA0.05MultipleFDR
GSE26876de Carvalho (2011)Affymetrix Human Gene 1.0 ST ArrayRMANSNSNS1.50.05Student t-testNoIngenuity pathway analysisNSNSNS
GSE33811Krupka (2012)Affymetrix Human Gene 1.0 ST ArrayRMA and QuantileNSSignal and variation threshold311020.05Paired t-testNoGene set enrichment analysis on selected GO terms0.01Paired t-testFDR
GSE34404Idaghdour (2012)Illumina Human HT-12 BeadChipsQuantileLocation, Sex, Hb, total cell counts (RBCs and WBCs) and ancestrySignal and normality thresholdNS2 (for comparison)0.01ANOVA, ANCOVAFDRGene set enrichment analysis on customized MsigDB database0.05NSBonferroni
GSE55843Jagannathan (2014)Agilent Sure Print G3 Human Gene Expression 8 × 60K v2 gene expression microarraysQuantileNSSignal thresholdNS20.05SAMFDRNANANANA
GSE53292Jaijyan (2015)Illumina Genome Analyzer Iix 72SENSNSNSNSNS0.05t-testNoGeneCodis3, Bingo 2.3 plugin (Cytoscape 2.8.3)0.05NSNS
GSE50957 GSE52166Tran (2016)Illumina HiSeq 2000 2 × 100 PETAMMBatch, Sex, Age, Pre-infection baselineSignal and variation threshold, removal Y chromosomesNS1.50.05LimmaFDRIngenuity pathway analysis0.05Fisher exact testFDR
GSE50957 GSE67184Vallejo (2018)Illumina HiSeq 2000 2 × 100 PECPM, TPMNSSignal thresholdNSNS0.05EdgeRFDRWGSEA, ToppGene, STRING0.05MultipleFDR
GSE64338Subramaniam (2015)Affymetrix Human Gene 1.0 ST ArrayNonlinear normalization based on Li-Wong methodsNSNSNS1.20.001Paired t-testFDRIngenuity Pathway Analysis0.05NSFDR
GSE64493Sullivan (2015)Agilent Sure Print G3 Human Gene Expression 8 × 60K v2 gene expression microarraysQuantileNSSignal thresholdNS1.50.03LimmaFDRDAVID0.05NSFDR
GSE67184Rojas-Penas (2015)Illumina HiSeq 2500 2 × 100 PESNMLocation/time-point, subject (random effect)Signal threshold6154No0.05NSFDRNANANANA
GSE67184Gardinassi (2018)Illumina HiSeq 2500 2 × 100 PENSNSNSNSNo0.05Limma, repeated measures ANOVAFDRGSEA on blood transcriptome modules (BTM, Li et al.)0.05permutationFDR
GSE7586Muehlenbachs (2007)Affymetrix U133 Plus 2.0 GeneChipGC RMANSNSNS2.50.01t-testNoNANANANA
GSE77122Tarawa (2017)Agilent Sure Print G3 Human Gene Expression 8 × 60K gene expression microarraysEach gene expression array dataset was normalized to the in silicon pool for the macrophages cultured with RBCsNSNSNSNo0.05Paired t-testNoDAVID0.05Fisher exact testNo
GSE93664Burl (2017)Affymetrix Human Gene ST 2.0 gene arrayRMANSNSNS20.05NSNoSTRING0.01NSCorrected unspecified
GSE100562Quin (2017)Illumina HiSeq 2500 2 × 50 PENSNSNSNSNo0.05LimmaFDRNANANANA
GSE1124Boldt (2019)Affymetrix U133A + B GeneChipsRMANSSignal thresholdNS1.90.004SAMFDRDAVID and Ingenuity Pathway Analysis0.05NSNS
GSE114076Terkawi (2018)Agilent Sure Print G3 Human Gene Expression 8 × 60K gene expression microarraysEach gene expression array dataset was normalized to the in silicon pool for the neutrophils cultured with RBCsNSNSNS20.01LimmaNoGenomatix GeneRanker, DAVID, NET-GE and Enricher0.05NSCorrected unspecified
GSE97158Rothan (2018)Illumina HiSeq 2500 2 × 51 PETMMBlocking by subject, in two separate models interaction with cell count and time of parasitemia was addedSignal threshold16,4731.50.05LimmaFDRGSEA (camera) on blood transcriptome modules (BTM, Li et al.)0.05Fisher exact testFDR
GSE65928Portugal (2015)Affymetrix Human Gene ST 2.0 gene arrayRMANSNSNSNS0.05ANOVAFDRIngenuity pathway analysisNSNSNS
GSE72058Feintuch (2016)Affymetrix Human Gene 1.0 ST arrayRMA and QuantilePeripheral parasitemiaNSNSNo0.05t-testNoGSEA, CateGOrizer and ingenuity pathway analysis0.2 and 0.06NSFDR
  1. FDR false discovery rate, Hb haemoglobin, NA not available, NS not specified in publication, RBCs red blood cells, RMA Robust Multichip average, SNM supervised normalization of microarray, TMM trimmed mean of M-values, GEO Gene Expression Omnibus, GE gene ontology