Impact of the chemical modification of tRNAs anticodon loop on the variability and evolution of codon usage in proteobacteriadoi:10.34691/UCHILE/AYDRZLRepositorio de datos de investigación de la Universidad de Chile2024-03-063Sebastian Delgado; Álvaro Armijo; Verónica Bravo; Omar Orellana; Juan Carlos Salazar; Assaf Katz, 2024, "Impact of the chemical modification of tRNAs anticodon loop on the variability and evolution of codon usage in proteobacteria", https://doi.org/10.34691/UCHILE/AYDRZL, Repositorio de datos de investigación de la Universidad de Chile, V3, UNF:6:H4RkW4KY33+u8SKNSXXA8A== [fileUNF]Impact of the chemical modification of tRNAs anticodon loop on the variability and evolution of codon usage in proteobacteriadoi:10.34691/UCHILE/AYDRZLSebastian DelgadoÁlvaro ArmijoVerónica BravoOmar OrellanaJuan Carlos SalazarAssaf KatzRepositorio de datos de investigación de la Universidad de ChileKatz, AssafKatz, Assaf2024-03-04Medicine, Health and Life SciencesCodon usageProteobacteriatRNAtRNA modifiaction enzymeN6-threonylcarbamoyladenosineglutamyl-queuosine2-lysidine2-thiouridineGenome evolutionThe data presented here corresponds to the supplementary data of the article entitled "Impact of the chemical modification of tRNAs anticodon loop on the variability and evolution of codon usage in proteobacteria" by Delgado et al. It contains supplementary figures, supplemntary tables and scripts including: - Relations between codon usage and GC% in proteobacteria - Phylogenetic trees coupled to bar graphs showing codon usage in proteobacteria - Relations between codon usage and the number of genes coding for tRNAs in proteobacteria - Relations between the presence of genes coding for tRNA modification enzymes and codon usage or GC% - Scripts required to perform the analyzes presented in the article and this supplementary dataPublication in review.Table_S10-Genes_coding_for_tRNAs.tab148467text/tab-separated-valuesUNF:6:HmAzkR8a99szs+OCJnRS9g==Table_S2.tab359218text/tab-separated-valuesUNF:6:pKcK/V3hph5rx13Vse2D4w==Table_S9.tab148410text/tab-separated-valuesUNF:6:Wxc4E386AXyXDr7n6nwPhw==genomaUNF:6:cf4HZDs3noEdCv2eakbREg==Ala-AGC0.00134770889487869371.00.00.036698775495457320.00.0.1484.0UNF:6:TghnnFGHeB6RfpHzCEAMIw==Ala-GGC0.80917986425518150.01484.01.40296495956873210.06.0.1.0UNF:6:h6HREi9Hnuz1cIxGiohUcg==Ala-TGC0.00.0.3.02493261455525183.01.583818523319130411.01484.0UNF:6:BHYnUL1ieRsJMOkPUvOryg==Ala-CGC0.51848751356011860.0.1484.03.00.00.37196765498652260.0UNF:6:vKwWY7hSH/nOJRCHHyK4DA==Arg-ACG1.97439353099730512.01.01.4700945502360632.1484.00.00.0UNF:6:7RQmh/lLFaar0XnMwfNvJA==Arg-GCG1484.00.00.212073399817166750.01.00.0.0.04716981132075463UNF:6:3llkLwA6be3VdraY27EfOQ==Arg-TCG1484.02.00.00.0.0.121293800539082740.332715097966226450.0UNF:6:A0sozqC/m9UgQAKW9ZodUw==Arg-CCG1.00.976415094339623.0.00.340732747660551344.01484.00.0UNF:6:+QLQCS+rI06VXFeEdrj+0A==Arg-TCT0.01.0.0.24429669588434870.01484.03.01.0485175202156334UNF:6:qCsszblmwnKQw7T+Jjn2oQ==Arg-CCT0.01.01484.03.00.91846361185983820.00.3571201371198533.UNF:6:EHxWlIzg820SYAXQU4PoHg==Asn-ATT1484.0.1.00.00.00.00134770889487871320.00.03669877549545738UNF:6:Mnlwjj7BUrkyqA9/s2uUug==Asn-GTT.0.02.02762803234501731.34877563686228992.01484.00.09.0UNF:6:bHA9Poz6qKwIEWO9nOc4ww==Asp-ATC0.044931470332939880.01.01484.00.00.002021563342318070.0.UNF:6:kjOuLBNDT8brEkZyk8iurQ==Asp-GTC0.013.01.4229120186356241484.02.00.0.2.38274932614555UNF:6:kHIpvuPF2gB0tKnyRUs1uQ==Cys-ACA0.0013477088948787020.01.0.0.00.01484.00.036698775495457525UNF:6:3R79IDV9K44UgDk8ajsDUA==Cys-GCA7.00.00.55906159666372611.1826145552560651.0.1484.00.0UNF:6:uJA8NCVwAV0F941he44xPA==Gln-TTG1.01.56064690026954160.01484.00.0.1.032036324147515710.0UNF:6:jArcdMfm3viRs73aQvd9gg==Gln-CTG0.50269541778975783.00.00.00.6666050187814571484.00.0.UNF:6:au+YugqGYY5fDNmSK4LO1Q==Glu-TTC1.709887010237050313.02.52762803234501780.0.1484.00.02.0UNF:6:VE8w7kCdMBIwLu3xGHUMoQ==Glu-CTC0.04.0.0.00.01484.00.26549865229110520.5031214306406147UNF:6:pz9BWvHMj1pyyEW+IC2iMw==Gly-ACC0.0040431266846361350.097077112503466463.00.01484.0.0.00.0UNF:6:JQlENnBS+myLEz3cvcLJ5g==Gly-GCC2.01484.02.56334231805929361.872007987607366.16.00.00.0UNF:6:twStkyw8dW64p8Xh7yWWlw==Gly-TCC0.01484.01.01.0828840970350404.4.00.00.3568095457879511UNF:6:74vWotHCJEliEdT7RP+xWg==Gly-CCC1484.00.68800539083557970.0.2.01.00.4903289220083150.0UNF:6:65S2TzwSF6NOX2gXMStnww==His-ATG0.00.02.0.1484.00.00.0026954177897574160.06354984519707722UNF:6:TpKh7od1igTGoXKlWd138g==His-GTG1.00.00.40386208450506081484.00.01.16846361185983844.0.UNF:6:UNWSmccDh1s2n7hqFrzMng==Ile-AAT0.0013477088948787040.0.1484.01.00.00.036698775495457690.0UNF:6:qauzTMSaodO93Ic9MUXjIg==Ile-GAT1484.00.01.57649500766371942.97102425876010611.03.0.0.0UNF:6:ITCAdZCqhw3z2begZoEnUA==Ile-TAT2.00.00.0148247978436657850.01484.0.0.12634670227440230.0UNF:6:Tb5++Q2c5bwibPjUHgo4/A==Leu-TAA.1.00.62079768300835241.10849056603773580.05.00.01484.0UNF:6:lDFJeyO9RCJT0A6B0FwAgQ==Leu-CAA.3.00.01.01886792452830231484.00.25898773082056031.00.0UNF:6:M6efWvMRHdQsDM9V+yGj/w==Leu-AAG0.093216005062000260.00.0087601078167115890.01.0.1484.00.0UNF:6:QrSNWzDz+LhoGB30N5kJYQ==Leu-GAG0.00.0.1.00.29913049916620624.01.0747978436657681484.0UNF:6:U9ZuXPvmdLttPjnHqokwRw==Leu-TAG1.30660377358490590.017.01.00.01484.01.246842345610334.UNF:6:4Awk6g1Ss4evvTCL7eMN6A==Leu-CAG0.01.55053908355795071.00.01.30231640938904031484.0.6.0UNF:6:K3q7ASM/WMOrF9YUDGzRPQ==Lys-TTT1484.00.01.02.11320754716981171.81716197257578750.017.0.UNF:6:s0Y5l0FLTyt325fucdgZbw==Lys-CTT4.00.6293800539083555.0.69394793909755440.01484.00.01.0UNF:6:vIBPfPqlae4xR4wfJID3OQ==fMet-CAT1484.00.02.0.1.58668213628375351.011.02.43935309973046UNF:6:hb1NKs/jBl/fqYtmn5SpYw==Met-CAT0.62959762925115810.01484.01.0.0.05.01.355121293800539UNF:6:m5WHGaMPynKsBO11OmAtgA==Phe-AAA0.140784649723056380.00.01484.00.00.0202156334231805881.0.UNF:6:+9vRLjR0kEAYbnY59t3WSA==Phe-GAA11.0.1484.01.01.38746630727762880.75090723878823070.00.0UNF:6:504t1prKqX3UDRclIIr9lA==Pro-AGG0.01484.00.00.00202156334231805460.0.0.044931470332939831.0UNF:6:bFS6W88Jc9FvMJUl6YVSaA==Pro-GGG0.410284849174350541484.00.01.00.91644204851751993.00.0.UNF:6:u6BRlu9EFni3FiLkGwAfEQ==Pro-TGG1484.00.0.8.00.01.34770889487870550.66942785639489271.0UNF:6:x/BlEJrPFSMiLRH3qSm02w==Pro-CGG0.01484.0.0.56835073461631680.01.03.00.6556603773584906UNF:6:RBJwIJyXbO6Yqwx+jNACJA==Pyl-CTA.0.00.01484.00.00.00.00.0UNF:6:3pYGJT7LvyFQyrohLzqxqQ==Sec-TCA1484.02.00.0.0.00.330188679245282950.49009580246788740.0UNF:6:qfWhOwUibq3i9trz0+2UYg==Ser-AGA0.00.00.07324882226465011.1484.00.00.0053908355795148241.0UNF:6:PJIurGxUo3OKIM344DaNYQ==Ser-GGA0.409288560564037.1484.00.00.01.01.14353099730458353.0UNF:6:V7Xc5bNErvDvJ4sHzpgCkw==Ser-TGA0.01484.00.00.85446111669244521.01.323450134770889411.0.UNF:6:g5jpuvdMiZiUCzvO/AWPIQ==Ser-CGA0.7318059299191376.5.01484.00.01.00.61189532339185380.0UNF:6:3HQSi0qgfKhdpqI7+3pOSQ==Ser-ACT0.0366987754954572960.00134770889487869980.0.1.00.01484.00.0UNF:6:DdyOBM3gj1LtiITNatrEMA==Ser-GCT1.04.01.07816711590296490.00.01484.0.0.29939545128082UNF:6:HRjDws/cCgP4GDgLz4xmZw==Thr-AGT0.00.00.00336927223719676830.05796709857384237.0.01.01484.0UNF:6:G6TfwUmw/JSvUPKUQ6uXCw==Thr-GGT0.01.18800539083557970.41429814233999741484.01.00.03.0.UNF:6:VwLovHX4hAiAZxrePs/RSg==Thr-TGT1484.00.7833173371712763.0.01.29716981132075420.01.08.0UNF:6:g6/pakRbWR8XlADtzepfxg==Thr-CGT.1.01484.02.00.48568456528732850.00.00.7190026954177902UNF:6:V9CkowexurPkZH+sKa2p8Q==Trp-CCA0.01.12331536388140130.37489786283573880.01.0.4.01484.0UNF:6:G6HO1vwDCD/clCnOzMclXw==Tyr-ATA0.073248822264649830.0053908355795148330.00.0.0.01484.01.0UNF:6:XYJijcCWI9C7c5I/p2lYiQ==Tyr-GTA1484.00.01.00.0.9.01.5060646900269541.1440265033868804UNF:6:/GagIOX6G5m/Mp202C+iMQ==Val-AAC.1.00.01484.00.0366987754954581360.00.00.0013477088948787024UNF:6:HyZClWcmCmfZSRBNbEEb2w==Val-GAC0.00.0.1.01484.01.38881401617250936.00.7375189004828524UNF:6:23jDGebienfY9I6PxtYQrg==Val-TAC0.0.23.01.687658571162271.00.01484.02.0094339622641493UNF:6:ARyj8BcGvbQES5VkrZ84nQ==Val-CAC0.01484.0.0.00.62241170605368120.48180592991913785.00.0UNF:6:JaEcf0cHVBB9AVM5ZArStg==TOTAL0.0201.020.993453311110981484.0.14.054.060.561994609164394UNF:6:0nrmVDZaOgWWq24REBID3Q==notesUNF:6:WwL6t52HJ3WhtTC8EWcBaQ==GeneUNF:6:fPkV5Ko7/iNV+nuh1NWkuA==Non-unique Gene nameUNF:6:Sdz7G+9iUe7cgZNCOX/5hw==AnnotationUNF:6:hR+cGVOn4Nho4NuDIdBKIw==Number_pos_present_in3592.00.08.00.04.82173284970345625.09.579064587973225.UNF:6:fMXqfzIvBOVWwUp37arSfg==Number_neg_present_in0.03592.025.0.0.02.93592296223126330.01.1937639198218204UNF:6:fxbFQI2XxlJmrkrP6sxooQ==Number_pos_not_present_in4.821732849703456.15.42093541202677525.00.017.03592.00.0UNF:6:BAth38jc78Z6Gz6iDJQFbQ==Number_neg_not_present_in0.023.806236080178180.0.2.93592296223126425.03592.025.0UNF:6:5kD4WcNxa35FUPlR0Vu4Og==Sensitivity0.032.0.0.03592.019.286931398813824100.038.3162583518929UNF:6:JTF9iifh/5W6o5HErq1+aQ==Specificity100.011.7436918489250573592.0100.00.00.0.95.22494432071272UNF:6:2LaEjuUxvVgOR2aSiC5W8A==Odds_ratio3592.00.0NaN.NaNNaNInfinity0.0UNF:6:t28nvCl5nWRM0KZWOjJPTw==Naive_p3592.0.0.0040291227822153160.00.0107020641169632160.048797153695718840.009429494411315681.5821457204897244E-14UNF:6:HTWjQYuQ86D4rH0sI038Eg==Bonferroni_p3592.01.00.94343285037593921.00.21543679913286311.2207361735582567E-90.0.UNF:6:ozzV+VhFNJMgnt7aTG2qKg==Benjamini_H_p2.4414723471165137E-100.00.242326460448399843592.00.163532365337920680.7841086094917842.0.2102666719820398UNF:6:GuG5eH7TQaEl6Nuwv7LhXQ==Max_Pairwise_comparisons.1.01.00.03592.01.01.00.0UNF:6:YxlafifurvWxc3inu7zlhQ==Max_supporting_pairs0.01.00.01.00.9716035634743877.3592.00.16612574164429877UNF:6:SGKcsEs9eg1kdDRhBUKIIg==Max_opposing_pairs3592.01.0.0.248051224944321660.00.00.43194184355862710.0UNF:6:Jz2h7mZ5OcXTkm1m76jXOA==Best_pairwise_comp_p0.00.01.0.1.01.03592.01.0UNF:6:YxlafifurvWxc3inu7zlhQ==Worst_pairwise_comp_p.1.01.01.00.03592.00.01.0UNF:6:YxlafifurvWxc3inu7zlhQ==#GenomeUNF:6:cf4HZDs3noEdCv2eakbREg==A_count917835.0.332712.841110458828012.00.0935460.63072776261484.02195410.0UNF:6:GH+dvwd8HG3dCzJru1SgHg==C_count1263088.12803234650.01484.01245406.04649278.09300.0670144.9066948249.UNF:6:UeBePcvFMY7srHlW1hsO8w==G_count1245257.50.01484.01262507.0114555254653678.0.669629.02277560819316.0UNF:6:GXacekFLRWt5N3mO9lOh8Q==T_count332867.91772405175935185.4730458222209004.029182.00.01484.0.919601.5UNF:6:Arh960wfonQz0ryP60/lYw==A_frac0.2125484408444720.228432018034637590.058072513049085721484.0.0.4104578197106160.125235694732450.0UNF:6:rsFUJ77mPJ8LNunEKgvm1g==C_frac0.3745309813119561484.00.287537038133701460.2716607858901129.0.058148458988677290.08301273754585780.0UNF:6:ycTgsKM3CtYO1vtYPoquxg==G_frac0.057867109965473396.0.00.083155555158840.28745471204734050.3738758566407041484.00.2715997901953958UNF:6:tN+Q1+JWzOOBj3xcD11ydQ==T_frac0.00.21284178177984950.228307405879853680.126357467314891484.00.0579050623600653460.423373887584686.UNF:6:8N98Vdj37F02yvlg+tyXng==GC_frac0.54326057608550870.1661682927046980.5743167248168711484.00.115955649719030110.0.0.74840683795266UNF:6:WSdb9kA8NPaS8k+d8bL9CQ==AGCT_count_V2.plapplication/octet-streamCodon_counter-V1.plapplication/octet-streamCodon_statistics-V2.plapplication/octet-streamCompiled_supplementary_figures.pdfA file that compiles all supplementary figures of the paper in a single fileapplication/pdfCompiled_supplementary_tables.odsSingle file including the data of all supplementary tables of the paperapplication/vnd.oasis.opendocument.spreadsheetFig_S1.pdfapplication/pdfFig_S10.pdfapplication/pdfFig_S11.pdfapplication/pdfFig_S12.pdfapplication/pdfFig_S13.pdfapplication/pdfFig_S14.pdfapplication/pdfFig_S15.pdfapplication/pdfFig_S16.pdfapplication/pdfFig_S17.pdfapplication/pdfFig_S18A.pdfapplication/pdfFig_S18B.pdfapplication/pdfFig_S19.pdfapplication/pdfFig_S2.pdfapplication/pdfFig_S20.pdfapplication/pdfFig_S21.pdfapplication/pdfFig_S22.pdfapplication/pdfFig_S23.pdfapplication/pdfFig_S24A.pdfapplication/pdfFig_S24B.pdfapplication/pdfFig_S25.pdfapplication/pdfFig_S3.pdfapplication/pdfFig_S4.pdfapplication/pdfFig_S5.pdfapplication/pdfFig_S6.pdfapplication/pdfFig_S7.pdfapplication/pdfFig_S8.pdfapplication/pdfFig_S9.pdfapplication/pdfHistogram-all-columns-compare-all_vs_high-bars.plapplication/octet-streamLegends for supplementary figures and tables.pdfContains a list of figures and tables included in the dataset with their corresponding description. Please refer to "README.pdf" for a list and description of the scripts included in this dataset.application/pdfMANIFEST.TXTtext/plainREADME.pdfContains a list and description of the scripts included in this dataset. Please refer to "Legends for supplementary figures and tables.pdf" for a list of figures and tables included in the dataset with their corresponding description.application/pdfRPSB-criteria-example.txttext/plainTable_S1.odsapplication/vnd.oasis.opendocument.spreadsheetTable_S3.odsapplication/vnd.oasis.opendocument.spreadsheetTable_S4.pdfapplication/pdfTable_S5.odsapplication/vnd.oasis.opendocument.spreadsheetTable_S6.odsapplication/vnd.oasis.opendocument.spreadsheetTable_S7-Codon_usage_considering_all_genes.txttext/plainTable_S8-Codon_usage_considering_high_expression_genes.txttext/plainbatch-separate_file_by_gene_presence_and_plot_histograms-Wilcoxon.plapplication/octet-streambatch-separate_file_by_gene_presence_and_plot_histograms.plapplication/octet-streamcodon_usage_by_gene_presence-ALL-V3.1.plapplication/octet-streamcodon_usage_by_gene_presence-ALL-Wilcoxon-V3.1.plapplication/octet-streamcodons.txttext/plaincount_trnascan.plapplication/octet-streamplot-codonusage-vs-GC-V3-High_expression-vs-all-genes.plapplication/octet-streamplot-codonusage-vs-tRNAgenes-V3.plapplication/octet-streamrpsblast-summary-V4.plapplication/octet-streamseparate_file_by_gene_presence-v2.plapplication/octet-streamstatistics-all-columns-V2.plapplication/octet-streamtrnascan_all_v2.plapplication/octet-stream