DOCSLIB.ORG

Additional Tables.Xlsx

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Additional Tables.Xlsx Additional Table 1 Enriched pathways of upregulated DEGs by the phosphorylation deficient of CRMP2 (P <0.05, q <0.05) Database Description Ratio of DEGs Ratio of universe P -value P adjust q -value Gene name GO structural constituent of ribosome 77/880 170/11165 1.97E-40 1.30E-37 1.25E-37 Mrpl17/Gm10036/Rpl36- ps3/Gm10263/Mrpl11/Rps15a/Rps20/Mrpl51/Gm10073/Mrpl2/Mrpl52/Rpl22/M rpl54/Mrps34/Gm2000/Mrpl4/Mrps24/Mrpl36/Rpl28/Mrpl34/Mrpl55/Rpl29/Rpl 37rt/Rpl23a- ps3/Mrps18a/Mrpl12/Rpl23a/Rpl18/Rpl35a/Mrpl33/Mrpl41/Mrps12/Rps9/Rps1 8/Rps25/Rps5/Mrps18c/Rps27a/Rps26/Rplp2/Rpl14/Mrpl20/Rps3/Rps4x/Rps16 /Rpl37/Rpl37a/Rps8/Mrps21/Rpl36/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl3 1/Rpl39/Rps13/Rps11/Rpl8/Fau/Rps21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/ Rpl41/Rpl24/Rpl19/Rps14/Ndufa7/Rps27/Rplp1/Rps29 GO ribosome 91/907 248/11442 2.51E-38 1.41E-35 1.29E-35 Malsu1/Mrpl17/Zfp622/Gm10036/Rpl36- ps3/Gm10263/Gm10269/Mrpl11/Mrps28/Gm9493/Rpl13- ps3/Rps15a/Mrpl58/Rps20/Mrpl51/Gm10073/Mrpl2/Mrpl52/Rpl22/Mrpl54/Mrp s34/Gm2000/Mrpl4/Mrps24/Mrpl36/Rpl28/Mrpl34/Mrpl55/Rpl29/Rpl37rt/Rpl23 a- ps3/Rack1/Mrps18a/Mrps33/Mrpl12/Rpl23a/Rpl18/Rpl35a/Aurkaip1/Mrpl33/Btf 3/Mrpl41/Mrps12/Rpl36a/Rps9/Rps18/Rps25/Rps5/Mrps18c/Rps27a/Rps26/Rpl p2/Rpl14/Mrpl20/Rps3/Ndufab1/Rps4x/Rps16/Rpl37/Rpl37a/Rps8/Mrps21/Rpl 36/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl8/Fau/ Rps21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/Uba52/Rpl41/Rpl24/Rpl19/Rps1 4/Ndufa7/Rps27/Rplp1/Rps29 GO ribosomal subunit 84/907 215/11442 8.01E-38 2.26E-35 2.07E-35 Malsu1/Mrpl17/Zfp622/Gm10036/Rpl36- ps3/Gm10263/Gm10269/Mrpl11/Mrps28/Gm9493/Rpl13- ps3/Rps15a/Mrpl58/Rps20/Mrpl51/Gm10073/Mrpl2/Mrpl52/Rpl22/Mrpl54/Mrp s34/Mrpl4/Mrps24/Mrpl36/Rpl28/Mrpl34/Mrpl55/Rpl29/Rpl23a- ps3/Rack1/Mrps18a/Mrpl12/Rpl23a/Rpl18/Rpl35a/Mrpl33/Mrpl41/Mrps12/Rpl3 6a/Rps9/Rps18/Rps25/Rps5/Mrps18c/Rps27a/Rps26/Rplp2/Rpl14/Mrpl20/Rps3 /Ndufab1/Rps4x/Rps16/Rpl37/Rpl37a/Rps8/Mrps21/Rpl36/Rpl11/Rps7/Rps17/R pl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl8/Fau/Rps21/Rps19/Rpl9/Rpl3 8/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps14/Rps27/Rplp1/Rps29 KEGG Ribosome 63/374 118/4117 3.60E-36 8.88E-34 8.82E-34 Mrpl17/Mrpl11/Rps15a/Rps20/Rpl34/Rpl34- ps1/Gm4705/Mrpl2/Rpl22/Rps27/Rps27rt/Mrpl4/Mrpl36/Rpl28/Mrpl34/Rpl29/ Gm8210/Rpl37/Rpl37rt/Mrps18a/Mrpl12/Rpl23a/Rpl18/Rpl35a/Mrpl33/Mrps12/ Rpl36a/Rpl36al/Rps9/Rps18/Rps25/Rps5/Mrps18c/Rps27a/Rps26/Rplp2/Rpl14/ Mrpl20/Rps3/Rps4x/Rps16/Rpl37a/Rps8/Mrps21/Rpl36/Rpl11/Rps7/Rps17/Rpl3 5/Rpl27/LOC108167922/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl8/Fau/Rps21/Rps 19/Rpl9/Rpl38/Rpl26/Rpl13a/Uba52/Rpl41/Rpl24/Rps14/Rplp1/Rps29 Reactome SRP-dependent cotranslational 52/460 84/5641 2.25E-36 1.49E-33 1.30E-33 Rps15a/Rps20/Rpl34- protein targeting to membrane ps1/Rpl22/Rps27rt/Rpl28/Rpl29/Rpl37rt/Rpl23a/Rpl18/Rpl35a/Rpl36a/Rps9/Rps 18/Rps25/Rps5/Rps27a/Rps26/Rplp2/Rpl14/Rps3/Rps4x/Rps16/Rpl37/Rps8/Rpl 36al/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl8/Sr p14/Rps21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps14/ Rps27/Rplp1/Rps29 Reactome Nonsense Mediated Decay (NMD) 52/460 85/5641 5.38E-36 1.78E-33 1.55E-33 Rps15a/Pabpc1/Rps20/Rpl34- independent of the Exon Junction ps1/Rpl22/Rps27rt/Rpl28/Rpl29/Rpl37rt/Rpl23a/Rpl18/Rpl35a/Rpl36a/Rps9/Rps Complex (EJC) 18/Rps25/Rps5/Rps27a/Rps26/Rplp2/Rpl14/Rps3/Rps4x/Rps16/Rpl37/Rps8/Rpl 36al/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl8/Rp s21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps14/Rps27/ Rplp1/Rps29 GO mitochondrial protein complex 86/907 241/11442 3.63E-35 6.82E-33 6.23E-33 Malsu1/Mrpl17/Mrpl11/Mrps28/Mrpl58/Mtx2/Mrpl51/Sdhc/Mtx1/Timm10b/Mr pl2/Mrpl52/Mrpl54/Mrps34/Mrpl4/Bax/Etfb/Mrps24/Mrpl36/Dnajc19/Dmac1/T omm6/Mrpl34/Mrpl55/Uqcc3/Ndufa11/Pam16/Mrps18a/Mrpl12/Mrpl33/Timm 13/Timm10/Pink1/Tomm7/Mrpl41/Mrps12/Gm10250/Ndufb2/Mrps18c/Ndufa6 /Ndufb4/Mrpl20/Chchd6/Ndufab1/Ndufb11/Ndufb7/Ndufc1/Mrps21/Romo1/T omm5/Ndufs7/Ndufs6/Smdt1/Ndufa5/Ndufv3/Ndufb3/Ndufa8/Ndufb5/Park7/ Ndufa13/Atp5j2/Atp5l/Ndufb10/Uqcrq/Atp5e/Ndufa3/Ndufa7/Atp5k/Cox5a/At p5d/Ndufa2/Ndufa1/Atp5g3/Atp5o/Ndufb8/Ndufs5/Ndufa4/Ndufc2/Atp5h/Ch chd10/Uqcr10/Uqcrh/Ndufb6/Ndufb9/Cox4i1/Cox6a1 Reactome Translation 80/460 216/5641 2.47E-34 5.45E-32 4.73E-32 Mrpl17/Mrpl11/Trmt112/Mrps28/Eif2b2/Rps15a/Mrpl58/Pabpc1/Rps20/Mrpl51 /Rpl34- ps1/Mrpl2/Mrpl52/Rpl22/Mrpl54/Mrps34/Rps27rt/Mrpl4/Mrps24/Mrpl36/Rpl28 /Eif3f/Mrpl34/Mrpl55/Rpl29/Rpl37rt/Mrps18a/Mrps33/Mrpl12/Rpl23a/Rpl18/Rp l35a/Aurkaip1/Mrpl33/Mrpl41/Mrps12/Rpl36a/Rps9/Rps18/Rps25/Rps5/Mrps18 c/Rps27a/Rps26/Rplp2/Rpl14/Mrpl20/Rps3/Rps4x/Rps16/Rpl37/Rps8/Rpl36al/ Mrps21/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl8 /Srp14/Rps21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps1 4/Rps27/Rplp1/Rps29 Reactome Formation of a pool of free 40S 52/460 93/5641 3.15E-33 5.23E-31 4.54E-31 Rps15a/Rps20/Rpl34- subunits ps1/Rpl22/Rps27rt/Rpl28/Eif3f/Rpl29/Rpl37rt/Rpl23a/Rpl18/Rpl35a/Rpl36a/Rps 9/Rps18/Rps25/Rps5/Rps27a/Rps26/Rplp2/Rpl14/Rps3/Rps4x/Rps16/Rpl37/Rps 8/Rpl36al/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl 8/Rps21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps14/Rp s27/Rplp1/Rps29 GO cytosolic ribosome 60/907 132/11442 1.28E-31 1.80E-29 1.65E-29 Zfp622/Gm10036/Rpl36-ps3/Gm10263/Gm10269/Gm9493/Rpl13- ps3/Rps15a/Rps20/Gm10073/Rpl22/Rpl28/Rpl29/Rpl23a- ps3/Rack1/Rpl23a/Rpl18/Rpl35a/Rpl36a/Rps9/Rps18/Rps25/Rps5/Rps27a/Rps2 6/Rplp2/Rpl14/Rps3/Rps4x/Rps16/Rpl37/Rpl37a/Rps8/Rpl36/Rpl11/Rps7/Rps17 /Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl8/Fau/Rps21/Rps19/Rpl9/Rp l38/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps14/Rps27/Rplp1/Rps29 Reactome L13a-mediated translational 53/460 103/5641 2.10E-31 2.79E-29 2.42E-29 Rps15a/Pabpc1/Rps20/Rpl34- silencing of Ceruloplasmin ps1/Rpl22/Rps27rt/Rpl28/Eif3f/Rpl29/Rpl37rt/Rpl23a/Rpl18/Rpl35a/Rpl36a/Rps expression 9/Rps18/Rps25/Rps5/Rps27a/Rps26/Rplp2/Rpl14/Rps3/Rps4x/Rps16/Rpl37/Rps 8/Rpl36al/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl 8/Rps21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps14/Rp s27/Rplp1/Rps29 Reactome Nonsense-Mediated Decay 53/460 104/5641 3.97E-31 3.76E-29 3.27E-29 Rps15a/Pabpc1/Rps20/Rpl34- (NMD) ps1/Eif4a3/Rpl22/Rps27rt/Rpl28/Rpl29/Rpl37rt/Rpl23a/Rpl18/Rpl35a/Rpl36a/Rp s9/Rps18/Rps25/Rps5/Rps27a/Rps26/Rplp2/Rpl14/Rps3/Rps4x/Rps16/Rpl37/Rp s8/Rpl36al/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/R pl8/Rps21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps14/R ps27/Rplp1/Rps29 Reactome Nonsense Mediated Decay (NMD) 53/460 104/5641 3.97E-31 3.76E-29 3.27E-29 Rps15a/Pabpc1/Rps20/Rpl34- enhanced by the Exon Junction ps1/Eif4a3/Rpl22/Rps27rt/Rpl28/Rpl29/Rpl37rt/Rpl23a/Rpl18/Rpl35a/Rpl36a/Rp Complex (EJC) s9/Rps18/Rps25/Rps5/Rps27a/Rps26/Rplp2/Rpl14/Rps3/Rps4x/Rps16/Rpl37/Rp s8/Rpl36al/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/R pl8/Rps21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps14/R ps27/Rplp1/Rps29 GO inner mitochondrial membrane 54/907 108/11442 3.22E-31 3.63E-29 3.32E-29 Sdhc/Timm10b/Dnajc19/Dmac1/Uqcc3/Ndufa11/Pam16/Timm10/Gm10250/Nd protein complex ufb2/Ndufa6/Ndufb4/Chchd6/Ndufab1/Ndufb11/Ndufb7/Ndufc1/Romo1/Nduf s7/Ndufs6/Smdt1/Ndufa5/Ndufv3/Ndufb3/Ndufa8/Ndufb5/Park7/Ndufa13/Atp 5j2/Atp5l/Ndufb10/Uqcrq/Atp5e/Ndufa3/Ndufa7/Atp5k/Cox5a/Atp5d/Ndufa2/ Ndufa1/Atp5g3/Atp5o/Ndufb8/Ndufs5/Ndufa4/Ndufc2/Atp5h/Chchd10/Uqcr1 0/Uqcrh/Ndufb6/Ndufb9/Cox4i1/Cox6a1 Reactome Eukaryotic Translation Initiation 54/460 111/5641 2.26E-30 1.67E-28 1.45E-28 Eif2b2/Rps15a/Pabpc1/Rps20/Rpl34- ps1/Rpl22/Rps27rt/Rpl28/Eif3f/Rpl29/Rpl37rt/Rpl23a/Rpl18/Rpl35a/Rpl36a/Rps 9/Rps18/Rps25/Rps5/Rps27a/Rps26/Rplp2/Rpl14/Rps3/Rps4x/Rps16/Rpl37/Rps 8/Rpl36al/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl 8/Rps21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps14/Rp s27/Rplp1/Rps29 Reactome Cap-dependent Translation 54/460 111/5641 2.26E-30 1.67E-28 1.45E-28 Eif2b2/Rps15a/Pabpc1/Rps20/Rpl34- Initiation ps1/Rpl22/Rps27rt/Rpl28/Eif3f/Rpl29/Rpl37rt/Rpl23a/Rpl18/Rpl35a/Rpl36a/Rps 9/Rps18/Rps25/Rps5/Rps27a/Rps26/Rplp2/Rpl14/Rps3/Rps4x/Rps16/Rpl37/Rps 8/Rpl36al/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl 8/Rps21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps14/Rp s27/Rplp1/Rps29 Reactome GTP hydrolysis and joining of the 52/460 104/5641 5.11E-30 3.39E-28 2.94E-28 Rps15a/Rps20/Rpl34- 60S ribosomal subunit ps1/Rpl22/Rps27rt/Rpl28/Eif3f/Rpl29/Rpl37rt/Rpl23a/Rpl18/Rpl35a/Rpl36a/Rps 9/Rps18/Rps25/Rps5/Rps27a/Rps26/Rplp2/Rpl14/Rps3/Rps4x/Rps16/Rpl37/Rps 8/Rpl36al/Rpl11/Rps7/Rps17/Rpl35/Rpl27/Rps28/Rpl31/Rpl39/Rps13/Rps11/Rpl 8/Rps21/Rps19/Rpl9/Rpl38/Rpl26/Rps15/Rpl13a/Uba52/Rpl24/Rpl19/Rps14/Rp s27/Rplp1/Rps29 KEGG Oxidative phosphorylation 51/374 95/4117 1.98E-29 2.45E-27 2.43E-27 Sdhc/Ndufa11/Ndufb2/Atp6v1d/Ndufa6/Ndufb4/Ndufb4c/Ndufb4b/Ndufab1/ Ndufb11/Ndufb7/Ndufc1/Atp6v1g1/Cox17/Ndufs7/Ndufs6/Ndufv3/Ndufb3/N dufa8/Ndufb5/Ndufa13/Atp5j2/Atp5l/Ndufb10/Uqcrq/Atp6v1f/Atp5e/Cox7c/N dufa3/Ndufa7/Atp5k/Cox5a/Ndufa2/Ndufa1/Atp5g3/Uqcr11/Atp5o/Ndufs5/Nd ufa4/Ndufc2/Cox7b/Cox7a2/Atp6v0b/Atp5h/Uqcr10/Cox5b/Uqcrh/Ndufb6/Nd ufb9/Cox4i1/Cox6b1/Cox6a1/Cox8a GO respiratory chain 42/907 69/11442 3.32E-29 3.12E-27 2.86E-27 Sdhc/Dmac1/Uqcc3/Ndufa11/Ndufb2/Ndufa6/Ndufb4/Ndufab1/Ndufb11/Nduf b7/Ndufc1/Ndufs7/Ndufs6/Ndufa5/Ndufv3/Ndufb3/Ndufa8/Ndufb5/Park7/Nd ufa13/Ndufb10/Uqcrq/Ndufa3/Ndufa7/Cox5a/Ndufa2/Ndufa1/Uqcr11/Ndufb8 /Ndufs5/Ndufa4/Ndufc2/Cox7b/Cox7a2/Uqcr10/Uqcrh/Ndufb6/Ndufb9/Cox4i1 /Cox6b1/Cox6a1/Cox8a GO respiratory chain complex 40/907 63/11442 6.57E-29 5.29E-27 4.84E-27 Sdhc/Dmac1/Uqcc3/Ndufa11/Ndufb2/Ndufa6/Ndufb4/Ndufab1/Ndufb11/Nduf
Load more

Recommended publications
  • Supplementary Materials: Evaluation of Cytotoxicity and Α-Glucosidase Inhibitory Activity of Amide and Polyamino-Derivatives of Lupane Triterpenoids
    Supplementary Materials: Evaluation of cytotoxicity and α-glucosidase inhibitory activity of amide and polyamino-derivatives of lupane triterpenoids Oxana B. Kazakova1*, Gul'nara V. Giniyatullina1, Akhat G. Mustafin1, Denis A. Babkov2, Elena V. Sokolova2, Alexander A. Spasov2* 1Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences, 71, pr. Oktyabrya, 450054 Ufa, Russian Federation 2Scientific Center for Innovative Drugs, Volgograd State Medical University, Novorossiyskaya st. 39, Volgograd 400087, Russian Federation Correspondence Prof. Dr. Oxana B. Kazakova Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences 71 Prospeсt Oktyabrya Ufa, 450054 Russian Federation E-mail: [email protected] Prof. Dr. Alexander A. Spasov Scientific Center for Innovative Drugs of the Volgograd State Medical University 39 Novorossiyskaya st. Volgograd, 400087 Russian Federation E-mail: [email protected] Figure S1. 1H and 13C of compound 2. H NH N H O H O H 2 2 Figure S2. 1H and 13C of compound 4. NH2 O H O H CH3 O O H H3C O H 4 3 Figure S3. Anticancer screening data of compound 2 at single dose assay 4 Figure S4. Anticancer screening data of compound 7 at single dose assay 5 Figure S5. Anticancer screening data of compound 8 at single dose assay 6 Figure S6. Anticancer screening data of compound 9 at single dose assay 7 Figure S7. Anticancer screening data of compound 12 at single dose assay 8 Figure S8. Anticancer screening data of compound 13 at single dose assay 9 Figure S9. Anticancer screening data of compound 14 at single dose assay 10 Figure S10.
    [Show full text]
  • MRPL11 Antibody A
    Revision 1 C 0 2 - t MRPL11 Antibody a e r o t S Orders: 877-616-CELL (2355) [email protected] Support: 877-678-TECH (8324) 9 9 Web: [email protected] 1 www.cellsignal.com 2 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source: UniProt ID: Entrez-Gene Id: WB, IP H Mk Endogenous 21 Rabbit Q9Y3B7 65003 Product Usage Information Application Dilution Western Blotting 1:1000 Immunoprecipitation 1:50 Storage Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA and 50% glycerol. Store at –20°C. Do not aliquot the antibody. Specificity / Sensitivity MRPL11 Antibody detects endogenous levels of total MRPL11 protein. Species Reactivity: Human, Monkey Source / Purification Polyclonal antibodies are produced by immunizing animals with a synthetic peptide corresponding to the sequence of human MRPL11. Antibodies are purified by peptide affinity chromatography. Background A subset of mitochondrial proteins are synthesized on the ribosomes within mitochondria (1). The 55S mammalian mitochondrial ribosomes are composed of a 28S small subunit and a 39S large subunit (1). Over 40 protein components have been identified from the large subunit of the human mitochondrial ribosome (1). The mitochondrial ribosomal protein L11 (MRPL11) is one such component (1). In animals, plants and fungi, this protein is translated from a gene in the nuclear genome (2). 1. Koc, E.C. et al. (2001) J Biol Chem 276, 43958-69. 2. Handa, H. et al. (2001) Mol Genet Genomics 265, 569-75.
    [Show full text]
  • Analysis of Gene Expression Data for Gene Ontology
    ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins.
    [Show full text]
  • Organ Level Protein Networks As a Reference for the Host Effects of the Microbiome
    Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press 1 Organ level protein networks as a reference for the host effects of the microbiome 2 3 Robert H. Millsa,b,c,d, Jacob M. Wozniaka,b, Alison Vrbanacc, Anaamika Campeaua,b, Benoit 4 Chassainge,f,g,h, Andrew Gewirtze, Rob Knightc,d, and David J. Gonzaleza,b,d,# 5 6 a Department of Pharmacology, University of California, San Diego, California, USA 7 b Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 8 California, USA 9 c Department of Pediatrics, and Department of Computer Science and Engineering, University of 10 California, San Diego California, USA 11 d Center for Microbiome Innovation, University of California, San Diego, California, USA 12 e Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State 13 University, Atlanta, GA, USA 14 f Neuroscience Institute, Georgia State University, Atlanta, GA, USA 15 g INSERM, U1016, Paris, France. 16 h Université de Paris, Paris, France. 17 18 Key words: Microbiota, Tandem Mass Tags, Organ Proteomics, Gnotobiotic Mice, Germ-free Mice, 19 Protein Networks, Proteomics 20 21 # Address Correspondence to: 22 David J. Gonzalez, PhD 23 Department of Pharmacology and Pharmacy 24 University of California, San Diego 25 La Jolla, CA 92093 26 E-mail: [email protected] 27 Phone: 858-822-1218 28 1 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press 29 Abstract 30 Connections between the microbiome and health are rapidly emerging in a wide range of 31 diseases.
    [Show full text]
  • Effects of Stressors on Differential Gene Expression And
    EFFECTS OF STRESSORS ON DIFFERENTIAL GENE EXPRESSION AND SECONDARY METABOLITES BY AXINELLA CORRUGATA by Jennifer Grima A Thesis Submitted to the Faculty of Charles E. Schmidt College of Science in Partial Fulfillment of the Requirements for the Degree of Master of Science Florida Atlantic University Boca Raton, Florida May 2013 ACKNOWLEDGEMENTS This thesis was made possible by the help and support of my mentors and friends. Without their guidance and expertise, I would not have been able to accomplish all that I have. Their belief and encouragement in my efforts have motivated and inspired me along through this journey and into a new era in my life. First and foremost, I am grateful to Dr. Shirley Pomponi for taking on the role as my advisor and giving me the opportunity to experience life as a researcher. Not only has she guided me in my scientific studies, she has become a wonderful, lifelong friend. Dr. Pomponi and Dr. Amy Wright have also provided financial support that enabled me to conduct the research and complete this thesis. I would also like to acknowledge Dr. Amy Wright for her willingness to tender advice on all things chemistry related as well as providing me with the space, equipment, and supplies to conduct the chemical analyses. I am grateful to Dr. Esther Guzman who not only served as a committee member, but has also been readily available to help me in any endeavor, whether it be research or personal related. She is truly one of kind with her breadth of knowledge in research and her loyal and caring character.
    [Show full text]
  • Allele-Specific Expression of Ribosomal Protein Genes in Interspecific Hybrid Catfish
    Allele-specific Expression of Ribosomal Protein Genes in Interspecific Hybrid Catfish by Ailu Chen A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama August 1, 2015 Keywords: catfish, interspecific hybrids, allele-specific expression, ribosomal protein Copyright 2015 by Ailu Chen Approved by Zhanjiang Liu, Chair, Professor, School of Fisheries, Aquaculture and Aquatic Sciences Nannan Liu, Professor, Entomology and Plant Pathology Eric Peatman, Associate Professor, School of Fisheries, Aquaculture and Aquatic Sciences Aaron M. Rashotte, Associate Professor, Biological Sciences Abstract Interspecific hybridization results in a vast reservoir of allelic variations, which may potentially contribute to phenotypical enhancement in the hybrids. Whether the allelic variations are related to the downstream phenotypic differences of interspecific hybrid is still an open question. The recently developed genome-wide allele-specific approaches that harness high- throughput sequencing technology allow direct quantification of allelic variations and gene expression patterns. In this work, I investigated allele-specific expression (ASE) pattern using RNA-Seq datasets generated from interspecific catfish hybrids. The objective of the study is to determine the ASE genes and pathways in which they are involved. Specifically, my study investigated ASE-SNPs, ASE-genes, parent-of-origins of ASE allele and how ASE would possibly contribute to heterosis. My data showed that ASE was operating in the interspecific catfish system. Of the 66,251 and 177,841 SNPs identified from the datasets of the liver and gill, 5,420 (8.2%) and 13,390 (7.5%) SNPs were identified as significant ASE-SNPs, respectively.
    [Show full text]
  • Role of Mitochondrial Ribosomal Protein S18-2 in Cancerogenesis and in Regulation of Stemness and Differentiation
    From THE DEPARTMENT OF MICROBIOLOGY TUMOR AND CELL BIOLOGY (MTC) Karolinska Institutet, Stockholm, Sweden ROLE OF MITOCHONDRIAL RIBOSOMAL PROTEIN S18-2 IN CANCEROGENESIS AND IN REGULATION OF STEMNESS AND DIFFERENTIATION Muhammad Mushtaq Stockholm 2017 All previously published papers were reproduced with permission from the publisher. Published by Karolinska Institutet. Printed by E-Print AB 2017 © Muhammad Mushtaq, 2017 ISBN 978-91-7676-697-2 Role of Mitochondrial Ribosomal Protein S18-2 in Cancerogenesis and in Regulation of Stemness and Differentiation THESIS FOR DOCTORAL DEGREE (Ph.D.) By Muhammad Mushtaq Principal Supervisor: Faculty Opponent: Associate Professor Elena Kashuba Professor Pramod Kumar Srivastava Karolinska Institutet University of Connecticut Department of Microbiology Tumor and Cell Center for Immunotherapy of Cancer and Biology (MTC) Infectious Diseases Co-supervisor(s): Examination Board: Professor Sonia Lain Professor Ola Söderberg Karolinska Institutet Uppsala University Department of Microbiology Tumor and Cell Department of Immunology, Genetics and Biology (MTC) Pathology (IGP) Professor George Klein Professor Boris Zhivotovsky Karolinska Institutet Karolinska Institutet Department of Microbiology Tumor and Cell Institute of Environmental Medicine (IMM) Biology (MTC) Professor Lars-Gunnar Larsson Karolinska Institutet Department of Microbiology Tumor and Cell Biology (MTC) Dedicated to my parents ABSTRACT Mitochondria carry their own ribosomes (mitoribosomes) for the translation of mRNA encoded by mitochondrial DNA. The architecture of mitoribosomes is mainly composed of mitochondrial ribosomal proteins (MRPs), which are encoded by nuclear genomic DNA. Emerging experimental evidences reveal that several MRPs are multifunctional and they exhibit important extra-mitochondrial functions, such as involvement in apoptosis, protein biosynthesis and signal transduction. Dysregulations of the MRPs are associated with severe pathological conditions, including cancer.
    [Show full text]
  • DNA·RNA Triple Helix Formation Can Function As a Cis-Acting Regulatory
    DNA·RNA triple helix formation can function as a cis-acting regulatory mechanism at the human β-globin locus Zhuo Zhoua, Keith E. Gilesa,b,c, and Gary Felsenfelda,1 aLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; bUniversity of Alabama at Birmingham Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL 35294; and cDepartment of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294 Contributed by Gary Felsenfeld, February 4, 2019 (sent for review January 4, 2019; reviewed by James Douglas Engel and Sergei M. Mirkin) We have identified regulatory mechanisms in which an RNA tran- of the criteria necessary to establish the presence of a triplex script forms a DNA duplex·RNA triple helix with a gene or one of its structure, we first describe and characterize triplex formation at regulatory elements, suggesting potential auto-regulatory mecha- the FAU gene in human erythroid K562 cells. FAU encodes a nisms in vivo. We describe an interaction at the human β-globin protein that is a fusion containing fubi, a ubiquitin-like protein, locus, in which an RNA segment embedded in the second intron of and ribosomal protein S30. Although fubi function is unknown, the β-globin gene forms a DNA·RNA triplex with the HS2 sequence posttranslational processing produces S30, a component of the within the β-globin locus control region, a major regulator of glo- 40S ribosome. We used this system to refine methods necessary bin expression. We show in human K562 cells that the triplex is to detect triplex formation and to distinguish it from R-loop stable in vivo.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • CD8 T Cell Memory Transition and Maintenance of Functional Foxo1
    FoxO1 Controls Effector-to-Memory Transition and Maintenance of Functional CD8 T Cell Memory This information is current as Melba Marie Tejera, Eui Ho Kim, Jeremy A. Sullivan, Erin of October 1, 2021. H. Plisch and M. Suresh J Immunol 2013; 191:187-199; Prepublished online 3 June 2013; doi: 10.4049/jimmunol.1300331 http://www.jimmunol.org/content/191/1/187 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2013/06/03/jimmunol.130033 Material 1.DC1 http://www.jimmunol.org/ References This article cites 52 articles, 7 of which you can access for free at: http://www.jimmunol.org/content/191/1/187.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on October 1, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology FoxO1 Controls Effector-to-Memory Transition and Maintenance of Functional CD8 T Cell Memory Melba Marie Tejera, Eui Ho Kim, Jeremy A.
    [Show full text]
  • Supplementary Figures 1-14 and Supplementary References
    SUPPORTING INFORMATION Spatial Cross-Talk Between Oxidative Stress and DNA Replication in Human Fibroblasts Marko Radulovic,1,2 Noor O Baqader,1 Kai Stoeber,3† and Jasminka Godovac-Zimmermann1* 1Division of Medicine, University College London, Center for Nephrology, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK. 2Insitute of Oncology and Radiology, Pasterova 14, 11000 Belgrade, Serbia 3Research Department of Pathology and UCL Cancer Institute, Rockefeller Building, University College London, University Street, London WC1E 6JJ, UK †Present Address: Shionogi Europe, 33 Kingsway, Holborn, London WC2B 6UF, UK TABLE OF CONTENTS 1. Supplementary Figures 1-14 and Supplementary References. Figure S-1. Network and joint spatial razor plot for 18 enzymes of glycolysis and the pentose phosphate shunt. Figure S-2. Correlation of SILAC ratios between OXS and OAC for proteins assigned to the SAME class. Figure S-3. Overlap matrix (r = 1) for groups of CORUM complexes containing 19 proteins of the 49-set. Figure S-4. Joint spatial razor plots for the Nop56p complex and FIB-associated complex involved in ribosome biogenesis. Figure S-5. Analysis of the response of emerin nuclear envelope complexes to OXS and OAC. Figure S-6. Joint spatial razor plots for the CCT protein folding complex, ATP synthase and V-Type ATPase. Figure S-7. Joint spatial razor plots showing changes in subcellular abundance and compartmental distribution for proteins annotated by GO to nucleocytoplasmic transport (GO:0006913). Figure S-8. Joint spatial razor plots showing changes in subcellular abundance and compartmental distribution for proteins annotated to endocytosis (GO:0006897). Figure S-9. Joint spatial razor plots for 401-set proteins annotated by GO to small GTPase mediated signal transduction (GO:0007264) and/or GTPase activity (GO:0003924).
    [Show full text]
  • 1 AGING Supplementary Table 2
    SUPPLEMENTARY TABLES Supplementary Table 1. Details of the eight domain chains of KIAA0101. Serial IDENTITY MAX IN COMP- INTERFACE ID POSITION RESOLUTION EXPERIMENT TYPE number START STOP SCORE IDENTITY LEX WITH CAVITY A 4D2G_D 52 - 69 52 69 100 100 2.65 Å PCNA X-RAY DIFFRACTION √ B 4D2G_E 52 - 69 52 69 100 100 2.65 Å PCNA X-RAY DIFFRACTION √ C 6EHT_D 52 - 71 52 71 100 100 3.2Å PCNA X-RAY DIFFRACTION √ D 6EHT_E 52 - 71 52 71 100 100 3.2Å PCNA X-RAY DIFFRACTION √ E 6GWS_D 41-72 41 72 100 100 3.2Å PCNA X-RAY DIFFRACTION √ F 6GWS_E 41-72 41 72 100 100 2.9Å PCNA X-RAY DIFFRACTION √ G 6GWS_F 41-72 41 72 100 100 2.9Å PCNA X-RAY DIFFRACTION √ H 6IIW_B 2-11 2 11 100 100 1.699Å UHRF1 X-RAY DIFFRACTION √ www.aging-us.com 1 AGING Supplementary Table 2. Significantly enriched gene ontology (GO) annotations (cellular components) of KIAA0101 in lung adenocarcinoma (LinkedOmics). Leading Description FDR Leading Edge Gene EdgeNum RAD51, SPC25, CCNB1, BIRC5, NCAPG, ZWINT, MAD2L1, SKA3, NUF2, BUB1B, CENPA, SKA1, AURKB, NEK2, CENPW, HJURP, NDC80, CDCA5, NCAPH, BUB1, ZWILCH, CENPK, KIF2C, AURKA, CENPN, TOP2A, CENPM, PLK1, ERCC6L, CDT1, CHEK1, SPAG5, CENPH, condensed 66 0 SPC24, NUP37, BLM, CENPE, BUB3, CDK2, FANCD2, CENPO, CENPF, BRCA1, DSN1, chromosome MKI67, NCAPG2, H2AFX, HMGB2, SUV39H1, CBX3, TUBG1, KNTC1, PPP1CC, SMC2, BANF1, NCAPD2, SKA2, NUP107, BRCA2, NUP85, ITGB3BP, SYCE2, TOPBP1, DMC1, SMC4, INCENP. RAD51, OIP5, CDK1, SPC25, CCNB1, BIRC5, NCAPG, ZWINT, MAD2L1, SKA3, NUF2, BUB1B, CENPA, SKA1, AURKB, NEK2, ESCO2, CENPW, HJURP, TTK, NDC80, CDCA5, BUB1, ZWILCH, CENPK, KIF2C, AURKA, DSCC1, CENPN, CDCA8, CENPM, PLK1, MCM6, ERCC6L, CDT1, HELLS, CHEK1, SPAG5, CENPH, PCNA, SPC24, CENPI, NUP37, FEN1, chromosomal 94 0 CENPL, BLM, KIF18A, CENPE, MCM4, BUB3, SUV39H2, MCM2, CDK2, PIF1, DNA2, region CENPO, CENPF, CHEK2, DSN1, H2AFX, MCM7, SUV39H1, MTBP, CBX3, RECQL4, KNTC1, PPP1CC, CENPP, CENPQ, PTGES3, NCAPD2, DYNLL1, SKA2, HAT1, NUP107, MCM5, MCM3, MSH2, BRCA2, NUP85, SSB, ITGB3BP, DMC1, INCENP, THOC3, XPO1, APEX1, XRCC5, KIF22, DCLRE1A, SEH1L, XRCC3, NSMCE2, RAD21.
    [Show full text]