Table 2 Study characteristics including Journal names, sequencing platforms and authors home countries
From: RNA-seq research landscape in Africa: systematic review reveals disparities and opportunities
References | Journal | Sequencing platform | Statistical method | Downstream analyses method | FDR/Padj cutoff | Africa-specific DEGs | Corresponding author | First author | Last author |
|---|---|---|---|---|---|---|---|---|---|
Abate, Ambrosio [34] | PLoS Pathogen | Illumina HiScan SQ | SAVI algorithm | Characterization tumor microbiome with Pandora | N/A | MYC, ID3, TCF3, DDX3X, CCND3, TP53 | USA, Italy | USA | USA |
Ansari-Pour, Zheng [23] | Nature Communication | Illumina HiSeq2000 | DESeq2 | Somatic variant calling with Platypus | < 0.05 | SYPL1, ZNF217, LAMB3, TP53, P1K3CA, GATA3, KMT2C | UK, USA | UK | USA |
Chama, Amadi [35] | EBioMedicine | Illumina HiSeq2000 | NOIseq | Pathway enrichment analyses with DAVID | N/A | DUOX2, DUOXA2, MUC1, SAA1, SAA2 SAA4, CXCL5 | Zambia, UK | Zambia | Zambia, UK |
Cummings, Bakamutumaho [25] | BMC Critical Care | Illumina HiSeq4000 | DESeq2 | Ingenuity pathway analysis | ≤ 0.01 | STAT3, PPAR, CD28, Nur77, OX40 | USA | USA | USA |
Duffy, Du [36] | BMC Malaria Journal | Illumina HiSeq2000 | Limma | Gene-set enrichment analysis with fgsea R package | < 0.05 | CKAP2L, DTL, EZH2, HJURP, NCAPH, NUSAP1, RRM2, SPAG5 | USA | USA | USA |
Dupnik, Reust [37] | Infection and Immunity | Illumina HiSeq4000 | DESeq2 | Ingenuity pathway analysis | ≤ 0.05 | CDKN2A, NDRG4, MIB2, NEURL, CTR9, HSF2, ELP2, WDR82, HDAC9 | USA | USA | Tanzania, USA |
Estévez, Anibarro [38] | Frontiers Immunology | Ion Torrent Proton Sequencer | DESeq2 | Pathway enrichment analyses with Reactome, Machine Learning-Based Class-Prediction Analysis | < 0.05 | C1QC, ADAMTS2, C1QB, METTL7B, DEFA3, PRR15, PRTNG | Spain | Spain | Spain |
Fedoriw, Selitsky [39] | Nature Modern Pathology | Illumina HiSeq2000 | ConsensusClusterPlus | Gene-set enrichment analysis with MSigDB, | < 0.1 | N/A | USA | USA | USA, Malawi |
Fisher, Smith [40] | Journal of Clinical Virology | Illumina MiSeq | N/A | Drug resistance mutational analyses | N/A | K103N, V106A, Y181C, K65R | South Africa | South Africa | South Africa |
Hatem, Hjort [41] | The Journal of Clinical Endocrinology & Metabolism | Illumina Nextseq 500 | edgeR | Gene-set enrichment analysis with Kolmogorov–Smirnov tests | < 0.05 | LCORL, P2RX7, PIK3C2B, NUMBL, A2ML1, GPNMB, NUMBL, P2RX7, PIK3C2B, ADAMTSL5, ITGAD, NLRP1, PKD1L2 | Sweden | Sweden | Sweden |
Mahady, Kanabar [42] | Functional Foods in Health and Disease | Illumina NovaSeq 6000 | edgeR | Gene ontology analyses with edgeR | ≤ 0.05 | PLGLB2, HCRT, TACR2, AXIN2, DRD1, ID2, RIMS2, CC2D2B, SP5, MISP | USA | USA | USA |
Kaymaz, Oduor [29] | Molecular Cancer Research | Illumina HiSeq2000 | DESeq2 | Gene-set enrichment analysis with MSigDB, single nucleotide variation detection with GATK | < 0.1 | CD19, CD20, CD10, CD79A/B, BCL6 | USA | USA | USA |
Kelly, Amadi [43] | EBioMedicine | Illumina HiSeq2000 | NOIseq | Ingenuity pathway analysis | < 0.02 | PRSS1, PRSS3, CPA2, CPA3, TMPRSS15, DPP4, GGT1 | USA | UK, Zambia | USA |
Lai, Cortes [44] | American Society for Microbiology Journals | Illumina HiSeq 2500 | DESeq2 | Ingenuity pathway analysis | < 0.1 | CD8A, EOMES, LAG3, KLRC4-KLRK1, POU2AF1, FAIM3, KLRK1 | South Africa, UK | UK | South Africa, UK |
Popescu, Tembo [45] | Gates Open Research | Illumina HiSeq 2500 | DESeq2 | Ingenuity pathway analysis | < 0.1 | PML, SOCS1, TICAM1, APOL1, GRINA, RMI2, ZBP1, IL27 | Canada | Canada | Canada |
Lidenge, Kossenkov [46] | PLoS Pathogens | Illumina Nextseq 500 | DESeq2 | Ingenuity pathway analysis | < 0.05 | TLR8, MMP13, TMOD2. KCNQ3, ADAMTS1, CD8A, MCTP1, CEP19 | USA | Tanzania, USA | USA |
Liu, Speranza [47] | Genome Biology | Illumina HiSeq 2500 | edgeR | Ingenuity pathway analysis | < 0.05 | CXCL10, CCL2/MCP-1, CCL8/MCP2, CXCL11 | UK | UK | UK |
Lombardo, Coffey [48] | Blood Advances | Illumina HiSeq | DESeq2 | Variant calling with GATK | N/A | ID3, TP53, SMARCA4, ZNF587, FOXO1 | USA | USA | USA |
Mulindwa, Matovu [49] | BMC Medical Genomics | Illumina NextSeq500 | DESeq2 | Pathway enrichment analyses with DAVID | < 0.1 | C4BPA, FBN2, PROS1, TFPI, LAMC1, MYL9, RBPJ | Uganda | Uganda | Germany |
Panea, Love [50] | Blood Advances | Illumina HiSeq 2500 | Custom scripts | Copy number variation analysis with GATK4 | N/A | IGLL5, BACH2, BTG2, BCL6, BCL7A, TCL1A, IRF8, CXCR4, ZFP36L1, and S1PR2 | USA | USA | USA |
Wichers, Tonkin-Hill [51] | Elife | Illumina HiSeq 2500 | Limma | Functional enrichment analysis with gprofiler | < 0.05 | MSP1, MSP2, MSP4, MSP10, EBA175, REX1, AMA1 | Germany | Germany | Germany |
Vlasova-St Louis, Musubire [52] | BMC Medical Genomics | Illumina HiSeq 2500 | Cufflinks | Ingenuity pathway analysis | < 0.05 | C1QA, C1QB, C1QC, CFD, CXCL1, CXCR1, ICAM1, IL6, IL8, IL11 | USA | USA | USA |
Tso, Kossenkov [53] | PLoS Pathogens | Illumina HiSeq 2500 | DESeq2 | Ingenuity pathway analysis | < 0.05 | SEPT1, GPR182, MYLK2, COL10A1, NOS2, PROX1, CD177, MMP9, ADAM19, PALD1, ITGA9, TIE1 | USA | USA | USA |
Tran, Jones [54] | Scientific Reports | Illumina HiSeq2000 | edgeR | Ingenuity pathway analysis | < 0.05 | IL1RN, MAPK1, TRIM24, NKX2-3, TNF, IL1B, RELA, NFKB1A | USA | USA | USA |
Silterra, Gillette [55] | The Journal of Infectious Diseases | Illumina HiSeq 2500 | Support vector machine (SVM) | SVM modeling | N/A | N/A | USA | USA | USA |
Schmitz, Young [56] | Nature | Illumina HiSeq2000 | N/A | Mutational profiling, Gene copy number analysis | N/A | MYC, ID3, DDX3X, TCF3, SMARCA4, NCOR2, GNA13, MKI67, EXOSC6, WDR90 | USA | USA | USA |
Rothen, Murie [57] | PLoS One | Illumina HiSeq2000 | edgeR | Hypergeometric gene testing with GeneOverlap R package | < 0.05 | CSP, LSA-1, EXP-1, M143, M144, M147, M230, M237 | Switzerland | Switzerland | USA |
Rose, Bruce [58] | PLoS Pathogens | Illumina HiSeq 2500 | N/A | Phylogenetic analysis | N/A | N/A | USA | USA | USA |