Table 2. Functional enrichment analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene ontology (GO) analysis of differentially expressed genes from RNA-sequencing data.
List of selected pathways characterize the signaling response in RAW264.7 osteoclastic cells exposed for 24h to media with low [Na+] (120 mmol/l) compared with expression from cells in normal [Na+] (140 mmol/l). Results from RNA-sequencing data revealed that the lysosomal pathway was disproportionately affected by low [Na+] exposure, with over 18-fold enrichment. Results also show high impacts on the PI3K/AKT/mTOR pathway, MAP-kinase pathway, and NF-kappa-B pathway, and regulation of mitochondrial energy production, actin cytoskeleton, and ascorbate metabolism. Gene expression drives regulatory changes inducing osteoclast functions including motility, adhesion, acid and proteinase secretion, and autophagy. P-value stands for the fisher exact test value of the term and FDR stands for the false discovery rate of the term, using Benjamini and Hochberg (1995) method.
| p-value | FDR | Enrichment | genes | |
|---|---|---|---|---|
|
| ||||
| Kegg pathway term | ||||
| Lysosome | 2.73108242969185E-19 | 8.05669316759095E-17 | 18.5636651917606 | Ap1g1//Ap3m2//Ap3s1//Ap4e1//Arsa//Arsg//Asah1//Atp6v0a1//Cd164//Cd68//Cln5//Cltc//Ctns//Ctsa//Ctsb//Ctsc//Ctsd//Ctse//Ctsl//Ctso//Ctss//Ctsz//Gaa//Galc//Gba//Gla//Gnptg//Gns//Gusb//Ids//Lamp1//Lamp2//Laptm4a//Laptm4b//Lgmn//Lipa//Litaf//Man2b1//Mcoln1//Naglu//Neu1//Npc1//Pla2g15//Ppt1//Psap//Slc11a1//Sort1//Sumf1//Tpp1 |
| Osteoclast_differentiation | 0.000139855166622009 | 0.00275048494356618 | 3.85432148500228 | Akt3//Fcgr1//Fcgr2b//Fcgr3//Fyn//Gab2//Gm14548//Gm15448//Il1a//Irf9//Jak1//Jun//Lilra6//Lilrb4a//Mapk12//Pik3cb//Pirb//Pparg//Ppp3r1//Sirpa//Sirpb1a//Sirpb1b//Stat2//Tgfb1//Tgfbr2//Tyk2 |
| MAPK_signaling_pathway | 0.000233069190293451 | 0.00404443594920989 | 3.63251513261368 | Akt3//Braf//Cacna1a//Cacna1b//Cd14//Crkl//Ddit3//Dusp1//Dusp16//Dusp3//Dusp4//Dusp6//Dusp7//Fas//Fgf13//Flnc//Gadd45a//Gna12//Gng12//Il1a//Jun//Map3k1//Map3k2//Map3k20//Map3k3//Map4k1//Mapk12//Mknk1//Nf1//Pla2g4a//Ppp3r1//Prkacb//Rapgef2//Rasa1//Rasgrp3//Rps6ka2//Sos1//Sos2//Taok1//Taok3//Tgfb1//Tgfbr2 |
| Phosphatidylinositol_signaling_system | 0.000632673874945795 | 0.00927122293124602 | 3.19882009852826 | Cds2//Dgka//Dgkd//Dgkh//Dgkq//Inpp4a//Inppl1//Itpkb//Itpr2//Mtm1//Mtmr3//Mtmr4//Mtmr6//Pi4ka//Pik3cb//Pikfyve//Pip4k2a//Pip4k2c//Plcg1//Pten |
| NF-kappa_B_signaling_pathway | 0.0014036206756552 | 0.0128213499059841 | 2.85275024315196 | Atm//Bcl2//Bcl2a1a//Bcl2a1b//Bcl2a1d//Bcl2l1//Ccl4//Cd14//Cd40//Cflar//Cxcl2//Ddx58//Irak1//Malt1//Plcg1//Ptgs2//Ripk1//Tab3//Ticam2//Trim25 |
| Ascorbate_and_aldarate_metabolism | 0.0115647164809968 | 0.0631776178128528 | 1.93686500986681 | Aldh2//Ugdh//Ugt1a1//Ugt1a2//Ugt1a6a//Ugt1a6b//Ugt1a7c |
| Regulation_of_actin_cytoskeleton | 0.0123605023966884 | 0.0662972401276922 | 1.90796387684629 | Arhgap35//Arhgef7//Braf//Cd14//Cfl2//Crkl//Cyfip2//Diaph1//Dock1//Ezr//Fgf13//Gna12//Gng12//Iqgap1//Itga7//Itgam//Itgax//Itgb1//Msn//Pfn2//Pik3cb//Pikfyve//Pip4k2a//Pip4k2c//Rock2//Slc9a1//Sos1//Sos2//Ssh1//Ssh2//Vav3 |
| Gene Ontology (GO) term biological processes | ||||
| regulation_of_cell_motility | 3.47370660338332E-20 | 3.81481320263358E-18 | 19.4592068657716 | Abhd6//Acvr1b//Adam15//Adam17//Adam9//Ago2//Aif1//Akt3//Aldoa//Amotl1//Anxa3//App//Atp7a//Atp8a1//Bcl2//Bmpr1a//Bmpr2//Braf//Bst1//C3ar1//C5ar1//Calr//Ccbe1//Ccl4//Cd274//Cd40//Cd74//Cd81//Ceacam1//Col18a1//Cpeb1//Cpne3//Cxcr4//Dab2//Dag1//Ddx58//Diaph1//Dock1//Dock10//Dock4//Ecm1//Evl//Flcn//Fpr2//Gab2//Gas6//Gna12//Gpnmb//Gsk3b//Hdac4//Igf1//Igsf8//Il1a//Il6st//Insr//Iqgap1//Itgb1//Jag1//Jun//Kitl//Lgals3//Lgals9//Lgmn//Lrp1//Macf1//Map3k1//Map3k3//Mia3//Mink1//Mmp12//Mospd2//Mpp1//Msn//Myo1f//Myo5a//Nf1//Nfe2l2//Nipbl//Nod2//Nrp1//Osbpl8//P2rx4//P2ry6//Pdpn//Pfn2//Plcg1//Pld2//Plk2//Plpp3//Plxna1//Plxna2//Plxna3//Plxnc1//Ppard//Pparg//Prcp//Prkce//Prkd2//Prkx//Ptafr//Pten//Ptgs2//Ptk2b//Ptpn23//Ptprc//Rab5a//Rap2a//Rap2b//Rapgef2//Rhob//Rhoc//Rhod//Rhoj//Rock2//Rreb1//S1pr1//Sash1//Sdc3//Sdcbp//Selenok//Sema4c//Slc8a1//Slk//Smad3//Spag9//Spry2//Srgap2//Ssh1//Ssh2//Stap1//Stat3//Stk24//Sun2//Tgfb1//Tgfbr2//Trf//Trp53inp1//Trpv4//Vegfb |
| cell_death | 2.65730168296323E-19 | 2.57989332958996E-17 | 18.5755591374194 | 1600012H06Rik//Aatk//Acvr1b//Aktip//Als2//Anxa6//App//Asah2//Atm//Atn1//Atp7a//Bbc3//Bcl2//Bcl2a1a//Bcl2a1b//Bcl2a1d//Bcl2l1//Birc6//Bmpr2//C5ar1//Cacna1a//Cadm1//Casp2//Cd24a//Cd5l//Cflar//Clu//Csrnp2//Ctsc//Cxcl2//Cyfip2//Dab2//Dapk1//Ddit3//Dnajc10//Dock1//Dram2//Ep300//Ercc6//Ern1//Ero1l//Fas//Fem1b//Fgf13//Fnip2//Fzd5//Gas6//Gclm//Gpr65//Gsk3b//Hcar2//Hip1//Hipk1//Hipk3//Htatip2//Ifi204//Ifi27l2a//Igf1//Ikbke//Il1a//Irak3//Jun//Kank2//Kitl//Lamp1//Lcn2//Lgals1//Lsp1//Magi1//Malt1//Map3k1//Map3k9//Mgea5//Mknk1//Naip2//Naip5//Naip6//Nf1//Nlrc4//Nlrp1b//Ogt//Oxr1//P2rx4//P2rx7//Pacs2//Parp4//Pdcd6ip//Pea15a//Phlda3//Pik3cg//Pmp22//Ppard//Ppp1r15a//Prkcd//Prkd2//Prune2//Pten//Rabep1//Rb1//Rhbdd1//Rhob//Ripk1//Rnf130//Rnf144b//Rock2//Rps6ka2//Rtn3//Rybp//Selenok//Serpinb9//Sgk1//Sgms1//Sgpl1//Sgpp1//Sirt2//Slc9a1//Slk//Smad3//Sort1//Sp110//Stk24//Susd6//Taok1//Tax1bp1//Tctn3//Tgfb1//Tgfbr2//Them4//Tlr3//Tmem173//Tnfrsf10b//Tnfrsf1b//Tnfsf12//Trim35//Trp53bp2//Trp53inp1//Trpm7//Vps35//Zfp385a//Zmat3 |
| regulation_of_GTPase_activity | 5.73246345857646E-13 | 3.39838696539856E-11 | 12.2416587049869 | Acap3//Adap2//Als2//Als2cl//Arfgap3//Arfgef1//Arhgap12//Arhgap17//Arhgap22//Arhgap35//Arhgef7//Asap1//Cav2//Ccl3//Ccl4//Ccl6//Cd40//Chm//Chml//Dock1//Dock10//Dock11//Dock2//Dock4//Evi5//Fam13b//Gpr65//Gpsm1//Gsk3b//Iqgap1//Itgb1//Jun//Myo9a//Myo9b//Nf1//Nrp1//Pkp4//Plxna1//Plxna2//Plxna3//Plxnc1//Ptk2b//Rab3gap2//Rabep1//Ralgapb//Ranbp2//Rap1gds1//Rapgef2//Rasa1//Rasgrp3//Rgs1//Rgs18//Rictor//Rin2//S1pr1//Sbf1//Snx13//Snx18//Spry2//Srgap2//Stard8//Stxbp5//Syngap1//Tbc1d16//Tbc1d2//Tbc1d20//Tbc1d22a//Tbc1d4//Tbc1d8b//Tbc1d9//Tbc1d9b//Tsc1//Vav3 |
| regulation_of_cell_adhesion | 8.87547800076692E-13 | 5.17015888062066E-11 | 12.0518082481314 | Adam15//Adam9//Aif1//Arg2//Ass1//Bcl2//Braf//Bst1//Calr//Cask//Cblb//Cd24a//Cd274//Cd276//Cd36//Cd74//Ceacam1//Crkl//Dab2//Dag1//Dock1//Dusp3//Emilin2//Flcn//Flot2//Fzd7//Gpam//Gpnmb//Gsk3b//H2-M3//H2-T23//Hfe//Hlx//Igf1//Il6st//Il7r//Iqgap1//Itgb1//Itpkb//Jag1//Kifap3//L1cam//Lgals1//Lgals3//Lgals9//Macf1//Malt1//Mia3//Mink1//Myo1f//Nck2//Nf1//Nfkbiz//Nrp1//Pag1//Pdpn//Peak1//Pik3cb//Pik3r6//Pkd1//Pld2//Plpp3//Plxna1//Plxna2//Plxna3//Plxnc1//Prkcd//Prkce//Prkd2//Prkx//Ptafr//Pten//Ptk2b//Ptpn23//Ptprc//Rasa1//Rc3h1//Rc3h2//Rhod//Rreb1//S1pr1//Selenok//Sirpa//Slk//Smad3//Spp1//Stat5b//Stx3//Tarm1//Tgfb1//Tgfbr2//Tnfsf9//Trpv4//Tsc1//Utrn//Vav3//Zmiz1 |
| regulation_of_cytoskeleton_organization | 7.53047540398149E-13 | 4.42514515186597E-11 | 12.1231776056308 | Add3//Akap13//Arfgef1//Arhgap17//Arhgap35//Atf5//Avil//Braf//Bst1//Bst2//Camsap1//Cep192//Cfl2//Chmp1b//Clip1//Cltc//Ctnnb1//Ctsl//Dctn1//Diaph1//Dst//Dync1h1//Ep300//Eps8//Evl//Fgf13//Gda//Gmfg//Gpr65//Gsk3b//Il1a//Kank2//Lats1//Lima1//Lrp1//Map3k1//Mtpn//Mtss1//Mycbp2//Myo1f//Nck2//Nin//Nrp1//Pdcd6ip//Pdlim4//Pfn2//Pkd1//Plek//Plk2//Plxna3//Ppfia1//Prkcd//Prkce//Psrc1//Ptk2b//Rasa1//Rhob//Rhoc//Rhod//Rhoj//Rhoq//Rhov//Rictor//Rock2//S1pr1//Sgk1//Sh3pxd2b//Smad3//Spire1//Spire2//Sptan1//Sptbn1//Ssh1//Ssh2//Stag1//Stap1//Stau2//Taok1//Tgfb1//Tmod1//Togaram1//Tpr//Trpv4//Tsc1//Tubb4a |
| positive_regulation_of_secretion | 1.80558349995658E-09 | 5.92921758147506E-08 | 8.7433824226446 | Aacs//Acsl3//Acvr2a//Adam9//Ap1g1//Arhgef7//Atg7//Bcl2l1//Bglap2//Cacna1b//Cadm1//Cadps//Cask//Ccl3//Cd14//Cd274//Cd276//Cd300c2//Cd36//Ceacam1//Clec4e//Dab2//Ddx58//Dtnbp1//Ep300//Exoc2//Ezr//Fcer1g//Fzd5//Gab2//Glul//H2-T23//Hcar2//Hfe//Ifih1//Igf1//Il1a//Il1rl1//Itgam//Kif5b//Lamp1//Lgals3//Lgals9//Lpl//Mcu//Mgea5//Mmp12//Nlgn2//Nod2//Nucb2//P2rx7//Panx1//Pdcd6ip//Pld2//Ppard//Prkce//Ptafr//Ptpn23//Rab5a//Rhbdd1//Sdcbp//Sec24a//Selenok//Spp1//Sptbn1//Stxbp5//Tgfb1//Tlr1//Tlr8//Trpv4//Vamp7//Vps35//Wls |
| proteolysis | 1.30353087110097E-08 | 3.56422583898179E-07 | 7.88487867911779 | Adam15//Adam17//Adam9//Adamts1//Amz1//Anpep//Aph1b//Aph1c//Asph//Ate1//Atg4c//C1ra//C1rb//Capn1//Capn15//Casp2//Cbl//Ccdc47//Cd5l//Cfb//Cflar//Cln5//Clock//Cndp2//Cpd//Ctsa//Ctsb//Ctsc//Ctsd//Ctse//Ctsl//Ctso//Ctss//Ctsz//Cul9//Cyfip2//Dag1//Ddit3//Derl1//Dnajb9//Dnajc10//Dnajc3//Dpep2//Dpp7//Dpp8//Dtx3l//Edem1//Edem2//Edem3//Erap1//Ero1lb//F10//Fbxl17//Fbxl5//Fbxw4//Foxred2//Ggh//Hectd3//Herc2//Hp//Hsp90b1//Hspa13//Ift172//Kctd17//Kctd21//Kctd6//Lgmn//Lnpep//Malt1//March6//Mbtps2//Mindy1//Mindy2//Mmp12//Mmp19//Ncstn//Nfe2l2//Nhlrc3//Ogt//Os9//P2rx7//Pdcd6ip//Pdia3//Prcp//Psen2//Psma8//Psme4//Ptpn23//Rhbdd1//Rhbdf2//Rnf11//Rnf115//Rnf144b//Rnf213//Scpep1//Sdf2l1//Sel1l//Senp5//Sirt2//Smurf1//Sppl2a//St14//Stt3b//Taf1//Tgfb1//Tollip//Tpp1//Trim25//Trip12//Trp53inp2//Trrap//Ttc3//Uba6//Uba7//Ube4a//Ubr3//Ubr4//Uggt1//Usp18//Usp24//Usp31//Usp32//Usp33//Usp9x//Vcpip1//Vps35//Wdr81//Wfs1//Wwp1 |
| positive_regulation_of_autophagy | 1.96916314294321E-07 | 4.29688074741909E-06 | 6.70571830156381 | Atg7//Dapk1//Flcn//Gba//Gnai3//Gpsm1//Gsk3b//Irgm1//Irgm2//Nod2//Optn//Pip4k2a//Pip4k2c//Plk2//Rab12//Rab3gap2//Smcr8//Smurf1//Tfeb//Tlr9//Trim21//Trp53inp1//Trp53inp2//Tsc1 |
| positive_regulation_of_cell_proliferation | 3.57035860223322E-07 | 7.42789822247215E-06 | 6.44728816171702 | Adam17//Aif1//Akt3//Atf3//Atp7a//Bcl2//Bcl2l1//Birc6//Bmpr1a//Bmpr2//Bst1//C3ar1//C5ar1//Cacul1//Calr//Cav2//Ccng1//Ccpg1//Cd24a//Cd274//Cd276//Cd40//Cd74//Cd81//Ceacam1//Cflar//Clu//Col18a1//Crkl//Ctnnb1//Ctsz//Ecm1//Ern1//Fabp4//Fbxw4//Fndc3b//Foxj2//Fzd7//Gab2//Gas6//Glul//Gnai3//Gpam//Grn//Gsk3b//H2-T23//Hdac4//Hipk1//Hlx//Hmga2//Hpse//Id2//Igf1//Il11ra1//Il6st//Il7r//Insr//Irak1//Itgb1//Jun//Kii3a//Kitl//Kmt2c//Kmt2d//Lgals3//Lgmn//Map3k3//Mmp12//Nampt//Nck2//Nf1//Nlgn2//Nod2//Notch2//Nqo2//Optn//Pggt1b//Pla2g4a//Plcg1//Ppard//Prkd2//Ptafr//Pten//Ptgs2//Ptk2b//Ptprc//Rab5a//Rasa1//Rictor//Rreb1//Runx2//S1pr1//Scg2//Sdcbp//Selenok//Selenon//Slc39a10//Stat3//Stat5b//Stx3//Syne1//Tgfb1//Tgfbr2//Tlr9//Tnfsi9//Trf//Ufl1//Vav3//Vegfb//Zmiz1 |
| vacuolar_acidification | 0.00110116049065754 | 0.008557626597349 | 2.95814937936846 | Atp6v0a1//Cln5//Dmxl1//Dmxl2//Ppt1//Slc11a1 |
| positive_regulation_of_ATP_biosynthetic_process | 0.00685437248156771 | 0.0355123288894215 | 2.16403229875441 | Bcl2l1//Entpd5//Igf1//Insr//P2rx7//Stat3 |
| positive_regulation_of_TOR_signaling | 0.0102227149011714 | 0.0490207352347509 | 1.99043375097056 | Akt3//Flcn//Gas6//Rictor//Rragc//Rragd//Smcr8 |
| osteoclast_differentiation | 0.0111237823954741 | 0.0520475125816834 | 1.95374751543618 | Cd300lf//Ctnnb1//Fam20c//Fcer1g//Gab2//Ostm1//Tgfb1//Trf |