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Table 6 Differentially expressed pathways in POLR3B mutant patients using ToppGene

From: Intellectual disability associated with craniofacial dysmorphism due to POLR3B mutation and defect in spliceosomal machinery

Category ID p-value q-value Bonferroni Hit count in query list Hit count in genome Hit in query list
KEGG pathway
  Ribosome 2.12E−10 4.83E−07 16 88 RPL26,RPL27,RPL31,RPL34,RPL39,RPL41,RPS16,RPS17,RPS21,RPS24,RPS27,RPS27A,RPL35,RPL7,RSL24D1,RPL9
  Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 1.53E−09 3.47E−06 16 100 RPL26,RPL27,RPL31,RPL34,RPL39,RPL41,RPS16,RPS17,RPS21,RPS24,RPS27,RPS27A,LOC101929876,RPL35,RPL7,RPL9
  rRNA processing 2.71E−05 6.17E−02 16 203 RPL26,RPL27,RPL31,RPL34,RPL39,RPL41,RPS16,RPS17,RPS21,RPS24,RPS27,RPS27A,LOC101929876,RPL35,RPL7,RPL9
  Spliceosomal snRNP assembly 1.44E−06 7.61E−03 9 53 RNU6ATAC,RNU5E-1,RNU5B-1,RNU4-2,RNU4-1,SMN2,SNRPD2,SNRPG,STRAP
  Innate Immune System 2.14E−06 4.86E−03 58 1312 TRAF3,ABCA13,RPS27A,LY96,CHI3L1,ADCY9,S100A8,TUBB4B,MGST1,MAVS,MME,MMP8,MMP9,HSP90AA1,ADGRG3,ANGPT1,DEFA1B,ITLN1,CEP290,ICAM3,GMFG,OLFM4,PYCARD,IRS2,VAMP8,IL3RA,IL5RA,CLEC4C,CXCR1,PROS1,CYBA,ATP6V1A,ATP6V0B,SPTAN1,ITGA2B,ITGB3,CLEC12A,CFD,VNN1,NFKBIA,C3AR1,C4BPA,CRISPLD2,DUSP1,CAMP,DUSP2,RAB44,RNASE2,CD3G,RNASE6,ATP6V0D1,CD14,P2RX7,GZMM,CD180,HBB,CDC34,HERC5
Molecular function
GO:0,003,735 Structural constituent of ribosome 1.82E−08 1.93E−05 19 183 RPL26,RPL27,RPL31,RPL34,RPL39,RPL41,RPS16,RPS17,RPS21,RPS24,RPS27,RPS27A,MRPL35,MRPL22,MRPS33,RPL35,RPL7,RSL24D1,RPL9
GO:0,004,601 Peroxidase activity 2.93E−05 3.10E−02 8 57 MGST1,PRDX5,ALOX5AP,PTGS1,HBA2,HBM,HBB,HBQ1
GO:0,016,209 Antioxidant activity 2.99E−05 3.17E−02 10 92 S100A8,MGST1,PRDX5,ALOX5AP,SRXN1,PTGS1,HBA2,HBM,HBB,HBQ1
GO:0,031,720 Haptoglobin binding 4.09E−05 4.33E−02 4 10 HBA2,HBM,HBB,HBQ1
Biological process
GO:0,000,387 Spliceosomal snRNP assembly 1.44E−06 7.61E−03 9 53 RNU6ATAC,RNU5E-1,RNU5B-1,RNU4-2,RNU4-1,SMN2,SNRPD2,SNRPG,STRAP
GO:0,045,087 Innate immune response 1.85E−06 9.78E−03 46 1045 TRAF3,RPL39,HLA-DQA2,HLA-DRB5,ZNF683,LY96,S100A8,TUBB4B,MAVS,IFITM3,FES,CCL3,HSP90AA1,ANXA1,DEFA1B,ICAM3,SAMHD1,RAB20,IFI27,NLRP2,NLRP6,RSAD2,PIK3R6,PYCARD,CD24,XAF1,VAMP8,CLEC4C,MX1,CYBA,IFIT5,TRIM14,NDUFS4,CFD,GBP4,VNN1,C4BPA,APOBEC3C,IGHV4-39,CAMP,RNASE2,RNASE6,CD14,GZMM,CD180,HERC5
GO:0,022,613 Ribonucleoprotein complex biogenesis 4.62E−06 2.44E−02 27 484 RPL26,RPL27,RPS16,RPS17,RPS21,RPS24,RPS27,RNU6ATAC,RNU11,RNVU1-14,RNVU1-4,RNU5E-1,RNU5B-1,RNU4-2,RNU4-1,HSP90AA1,EIF2S3B,NIFK,MRPL22,SMN2,SNRPD2,SNRPG,RRP1B,STRAP,RPL35,RPL7,RSL24D1
GO:0,006,413 Translational initiation 5.12E−06 2.70E−02 16 199 RPL26,RPL27,RPL31,RPL34,RPL39,RPL41,RPS16,RPS17,RPS21,RPS24,RPS27,RPS27A,EIF2S3B,RPL35,RPL7,RPL9
GO:0,045,291 mRNA trans splicing, SL addition 3.66E−05 1.93E−01 4 10 RNU5E-1,RNU5B-1,RNU4-2,RNU4-1
GO:0,000,353 Formation of quadruple SL/U4/U5/U6 snRNP 3.66E−05 1.93E−01 4 10 RNU5E-1,RNU5B-1,RNU4-2,RNU4-1
GO:0,000,365 mRNA trans splicing, via spliceosome 3.66E−05 1.93E−01 4 10 RNU5E-1,RNU5B-1,RNU4-2,RNU4-1
GO:0,000,244 Spliceosomal tri-snRNP complex assembly 1.51E−04 7.95E−01 5 25 RNU6ATAC,RNU5E-1,RNU5B-1,RNU4-2,RNU4-1
GO:0,000,395 mRNA 5'-splice site recognition 1.47E−03 1.00E + 00 4 24 RNU6ATAC,RNU11,RNVU1-14,RNVU1-4
Cellular component
GO:0,005,840 Ribosome 8.00E−08 5.29E−05 22 269 RPL26,RPL27,RPL31,RPL34,RPL39,RPL41,RPS16,RPS17,RPS21,RPS24,RPS27,RPS27A,MRPL35,MRPL22,MRPS33,LARP4,AURKAIP1,RPL35,HBA2,RPL7,RSL24D1,RPL9
GO:1,990,904 Ribonucleoprotein complex 4.88E−05 3.22E−02 34 768 RPL26,RPL27,RPL31,RPL34,RPL39,RPL41,RPS16,RPS17,RPS21,RPS24,RPS27,RPS27A,MRPL35,RNU6ATAC,RNU11,RNVU1-14,RNVU1-4,RNU5E-1,RNU5B-1,RNU4-2,RNU4-1,VBP1,MRPL22,MRPS33,SNRPD2,SNRPG,MKRN3,RRP1B,LARP4,RPL35,HBA2,RPL7,RSL24D1,RPL9
GO:0,034,719 SMN-Sm protein complex 6.07E−04 4.01E−01 4 19 SMN2,SNRPD2,SNRPG,STRAP
GO:0,005,925 Focal adhesion 8.12E−04 5.37E−01 20 424 RPL27,RPL31,RPS16,RPS17,FES,MME,FHL1,ANXA1,SNTB1,CYBA,GAK,ITGA2B,ITGB3,MRC2,DPP4,RDX,AFAP1,CD151,RPL7,RPL9
GO:0,062,023 Collagen-containing extracellular matrix 1.07E−03 7.09E−01 22 498 ACHE,PF4,F13A1,S100A8,FBN2,CLC,MMP8,MMP9,PLOD1,SDC2,HSP90AA1,COL1A2,ANGPT1,ANXA1,DEFA1B,ITLN1,CCDC80,MMRN1,MXRA7,CD151,EGFL7,HCFC1
GO:0,005,687 U4 snRNP 3.72E−03 1.00E + 00 6 70 RNU5E-1,RNU5B-1,RNU4-2,RNU4-1,SNRPD2,SNRPG
GO:0,097,525 Spliceosomal snRNP complex 4.01E−03 1.00E + 00 10 173 RNU6ATAC,RNU11,RNVU1-14,RNVU1-4,RNU5E-1,RNU5B-1,RNU4-2,RNU4-1,SNRPD2,SNRPG
  1. “Hit Count in Query List” is the number of genes in our list of differentially expressed genes which involved in a specific pathway and “Hit Count in Genome” is the number of all genes involved in this specific pathway