Table 6 Differentially expressed pathways in POLR3B mutant patients using ToppGene
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 |