{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["511145"],"full_dataset_link":["https://pax-db.org/dataset/511145/1076937984"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["After hundreds of generations of adaptive evolution at exponential growth, Escherichia coli grows as predicted using flux balance analysis (FBA) on genome-scale metabolic models (GEMs). However, it is not known whether the predicted pathway usage in FBA solutions is consistent with gene and protein expression in the wild-type and evolved strains. Here, we report that >98% of active reactions from FBA optimal growth solutions are supported by transcriptomic and proteomic data. Moreover, when E. coli adapts to growth rate selective pressure, the evolved strains upregulate genes within the optimal growth predictions, and downregulate genes outside of the optimal growth solutions. In addition, bottlenecks from dosage limitations of computationally predicted essential genes are overcome in the evolved strains. We also identify regulatory processes that may contribute to the development of the optimal growth phenotype in the evolved strains, such as the downregulation of known regulons and stringent response suppression. Thus, differential gene and protein expression from wild-type and adaptively evolved strains supports observed growth phenotype changes, and is consistent with GEM-computed optimal growth states."],"pubmed_title":["Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models."],"pubmed_authors":["Lewis Nathan E NE, Hixson Kim K KK, Conrad Tom M TM, Lerman Joshua A JA, Charusanti Pep P, Polpitiya Ashoka D AD, Adkins Joshua N JN, Schramm Gunnar G, Purvine Samuel O SO, Lopez-Ferrer Daniel D, Weitz Karl K KK, Eils Roland R, König Rainer R, Smith Richard D RD, Palsson Bernhard Ø BØ"],"data_synonyms":["Add, DmelCG43443, ADD, ADD-87, Hts-RC, data, AU023367, Data Set, protein complex, supply, Proteins, Ovhts, Gene, HtsRC, CG9325, protein, neutral molecular compounds, protein-containing complex, Dmel_CG9325, Xt, Peptide, 1B1, add, Polypeptides, anon-EST:Posey9, protein polypeptide chains, native protein, peptido, htsRC, GLI3-190, natural protein, polypeptide chain, Add-hts, Protein, CG43443, Gene Products, l(2)k14523, Dmel_CG34197, l(2)00634, median, Ovhts-RC, background, supply and distribution, protein aggregate, all_pairs, molecule, Bph, molecula, Random selection by shearing, oligonucleotide random primer, proportion, HTS-R1, HTS, Hts, molecules, peptides, l(2)k06121, adducin, GLI3FL, distribution, AI854843, proportionality, add-like, HTS-RC, rate, proteins, Molekuel, Pdn, sample population, introduction, Protein Gene Products, Gene Proteins, Adducin, RANDOM, 10^[-6], ppm, sample, supply., quotient, Peptid, peptidos, Polypeptide, Attention Deficit Hyperactivity Disorder, l(2)01103, EST D, CG34197, HtsF, ratio"],"description_synonyms":["D-lactose, beta-Gal1, LPH, G, milk sugar, H2N-CH2-COOH, 4-O-beta-D-galactopyranosyl-D-glucose, Aminoessigsaeure, Hgly, LPH1, lac, Aminoacetic acid, CT24921, Gly, WURCS=2.0/2, Milchzucker, 4-Glc, Glyzin, Milk sugar, aminoethanoic acid, lactobiose, CG12369, beta-D-Galp-(1->4)-D-Glcp, Laktobiose, Glycin, bulb, beta-D-Gal-(1->4)-D-Glc, Glycocoll, Glykokoll, 4-(beta-D-galactosido)-D-glucose, l(2)k11012b, 1-beta-D-Galactopyranosyl-4-D-glucopyranose, Lac, LAC, l(2)k11012., 2, Leimzucker, DmelCG12369, 1/[a2122h-1x_1-5][a2112h-1b_1-5]/1-2/a4-b1, (Gal)1 (Glc)1, (+)-lactose, Laktose, Galbeta1-4Glc"],"pubmed_title_synonyms":["development, data, scale tissue, Bacterium coli, Escherichia/Shigella coli, Bacterium coli commune, scale, growth pattern, Genomes, Bacillus coli, non-developmental growth, plant peltate hair, postnatal development, postnatal growth, Enterococcus coli, growth and development, whole genome, scales, peltate hair., growth, E. coli"],"name_synonyms":["D-lactose, beta-Gal1, multi-cellular organism, H2N-CH2-COOH, mol, CG4482, body, Aminoessigsaeure, lac, Aminoacetic acid, l(2)35Bb, CT24921, nip, whole body, Gly, Milchzucker, 4-Glc, Milk sugar, aminoethanoic acid, DmelCG4482, lactobiose, CG12369, organism, Laktobiose, LEW/CrlBR, bulb, l(2)br3, l35Bb, 4-(beta-D-galactosido)-D-glucose, l(2)k11012b, B1, l(2)SH1330, 2, DmelCG12369, animal, 1/[a2122h-1x_1-5][a2112h-1b_1-5]/1-2/a4-b1, (Gal)1 (Glc)1, (+)-lactose, Galbeta1-4Glc, l(2)k11012, l(2)br23, l(2)SH2 1330., LPH, G, milk sugar, whole organism, 4-O-beta-D-galactopyranosyl-D-glucose, Hgly, LPH1, LEW/Crl, 35Bb, WURCS=2.0/2, CG15268, Glyzin, br3, beta-D-Galp-(1->4)-D-Glcp, Glycin, beta-D-Gal-(1->4)-D-Glc, Glycocoll, MDC-01-40, Glykokoll, Koerper, 1-beta-D-Galactopyranosyl-4-D-glucopyranose, Lac, LAC, Leimzucker, NIP, BG:DS01219.1, Laktose, LEW"],"pubmed_abstract_synonyms":["FBA, Fba, scale tissue, AW546347, Gems, Materials, postnatal development., single-organism developmental process, determination, anon-EST:Liang-1.63, 1200002G09Rik, postnatal development, peltate hair, A4, bacterium E3, Gene, l(2)k14019, growth and development, CG6058, protein, Progress Reports, protein-containing complex, TYPE, limitations, protrusion, DAGA4, protein polypeptide chains, 1700026K02Rik, Investigative, polypeptide chain, Summary Report, Escherchia coli, Gem, Gene Products, Alleviating interaction, Enteroinvasive Escherichia coli, Enterococcus coli, protein aggregate, MAM, study limitations, SCG3, Sprains, Summary Reports, CT15952, Escherichia/Shigella coli, Genetic, Genomes, Progress Report, plant peltate hair, gem, E coli, proteins, suppressive genetic interaction (sensu inequality), E. coli, Solution, T4, Enteroaggregative Escherichia coli, Eschericia coli, T6, Progress, T7, DmelCG4974, Field Reports, CG3183, l(3)SG18, BcDNA:LP07735, anon-WO0257455.1, Dm Geminin, GL2-EXPRESSION MODULATOR, T12, Strains, clone 1.63, Investigative Reports, ALD, l(3)06464, CG3459, Alkalescens-Dispar Group, data, Bacterium coli, anatomical protrusion, protein complex, DmelCG30011, Proteins, Sprain, Dm geminin, v(2)k09107, EAggEC, ald, Enteroaggregative E. coli, Cistrons, predicted, LGMD2C, CG30011, development, DmelCG6058, native protein, natural protein, Investigative Report, Diffusely Adherent E. coli, Bacillus coli, chemical analysis, Protein, Research Reports, Strain, dCP2, Genetic Materials, KIR, FBX3, scales, Genetic Material, DmelCG3183, Diffusely Adherent Escherichia coli, CG11867, Enteroinvasive E. coli, scale, DMDA1, growth pattern, non-developmental growth, coiled body, postnatal growth, Field, CG4974, Regulons, INSDC_feature:gene, whole genome, Dally, Geminin, AV020497, Protein Gene Products, Gene Proteins, Phenotypes, BcDNA:HL07889, Report, DMDA, Bacterium coli commune, Pressures, Reports, Material, spine, SCARMD2, Cistron, assay, geminin, Summary, growth, Strains and Sprains, Gemini of coiled bodies, Field Report, anon-AE003830.1, AI046358"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"E.coli - Whole organism, Gly and lac substrate, SC (Lewis,mol_syst_biol,2010)","description":"abundance based on Spectral counting, Gly and Lac substrate, Interaction consistency score: 6.5, Coverage: 21","dates":{"publication":"2010"},"accession":"1076937984","cross_references":{"pubmed":["20664636"],"uniprot":["RS19_ECOLI","BAMA_ECOLI","GMHA_ECOLI","OPGG_ECOLI","CHEA_ECOLI","ILVD_ECOLI","KPRS_ECOLI","YCBX_ECOLI","AEGA_ECOLI","GCSH_ECOLI","MAO2_ECOLI","CH10_ECOLI","GNSB_ECOLI","POTD_ECOLI","YECF_ECOLI","RRF_ECOLI","ASNB_ECOLI","ISCU_ECOLI","ARCA_ECOLI","DACA_ECOLI","MUKB_ECOLI","LPXA_ECOLI","UCPA_ECOLI","GLGA_ECOLI","HCXB_ECOLI","RS14_ECOLI","TOLA_ECOLI","THRC_ECOLI","PTSN_ECOLI","YICC_ECOLI","PHOP_ECOLI","CUSB_ECOLI","RL25_ECOLI","LUXS_ECOLI","RPE_ECOLI","YEBC_ECOLI","YBIS_ECOLI","GLRX1_ECOLI","RECJ_ECOLI","GLTB_ECOLI","YDCS_ECOLI","A2MG_ECOLI","LEUC_ECOLI","PGM_ECOLI","SYE_ECOLI","RS6_ECOLI","PUR9_ECOLI","ZNUA_ECOLI","PANZ_ECOLI","PNTB_ECOLI","YQJH_ECOLI","MGLA_ECOLI","ATPE_ECOLI","YBJQ_ECOLI","THIE_ECOLI","FABD_ECOLI","MSRA_ECOLI","ZINT_ECOLI","RL20_ECOLI","APT_ECOLI","HIS8_ECOLI","HSLU_ECOLI","GALM_ECOLI","HLDE_ECOLI","IHFB_ECOLI","HINT_ECOLI","GLMS_ECOLI","YHAJ_ECOLI","GUAC_ECOLI","CYSM_ECOLI","DHAK_ECOLI","GLPD_ECOLI","DSBC_ECOLI","CASC_ECOLI","SYS_ECOLI","CLPB_ECOLI","METC_ECOLI","UBIG_ECOLI","HPRT_ECOLI","MNMA_ECOLI","PPIA_ECOLI","SDHB_ECOLI","ILVI_ECOLI","CPDB_ECOLI","FKBA_ECOLI","RL17_ECOLI","DNAK_ECOLI","PPIB_ECOLI","ODP1_ECOLI","AROC_ECOLI","YHFA_ECOLI","FIMB_ECOLI","ISPG_ECOLI","THIS_ECOLI","RL4_ECOLI","YDJA_ECOLI","GCH1_ECOLI","RL21_ECOLI","DPO1_ECOLI","KTHY_ECOLI","DEF_ECOLI","NLPA_ECOLI","EFG_ECOLI","YEEZ_ECOLI","PPNP_ECOLI","UGPQ_ECOLI","PYRI_ECOLI","RNC_ECOLI","CISY_ECOLI","UDG_ECOLI","TIG_ECOLI","RBSD_ECOLI","YAHO_ECOLI","CATE_ECOLI","SRMB_ECOLI","GLNQ_ECOLI","FOLX_ECOLI","FABI_ECOLI","AK1H_ECOLI","FUMC_ECOLI","BIOD2_ECOLI","IOJAP_ECOLI","YEAO_ECOLI","GSHB_ECOLI","TOLB_ECOLI","YBIT_ECOLI","FMT_ECOLI","RL13_ECOLI","NARL_ECOLI","THTM_ECOLI","OMPX_ECOLI","PYRD_ECOLI","PFKA_ECOLI","SYD_ECOLI","LPXB_ECOLI","PURR_ECOLI","YFIF_ECOLI","PEPD_ECOLI","THIO_ECOLI","CYSN_ECOLI","FABH_ECOLI","ATPD_ECOLI","SSB_ECOLI","SKP_ECOLI","NADE_ECOLI","CSPE_ECOLI","YQIK_ECOLI","MAP1_ECOLI","MODA_ECOLI","MINE_ECOLI","DPPF_ECOLI","METH_ECOLI","DMSA_ECOLI","RS15_ECOLI","GLRX2_ECOLI","MALE_ECOLI","YECJ_ECOLI","YCIT_ECOLI","ILVN_ECOLI","OMPT_ECOLI","SYY_ECOLI","NFUA_ECOLI","SPEB_ECOLI","OTC2_ECOLI","PNP_ECOLI","FUMB_ECOLI","EMRA_ECOLI","GLN1B_ECOLI","GSA_ECOLI","YEDD_ECOLI","CSPC_ECOLI","PDXH_ECOLI","YBFF_ECOLI","PT1_ECOLI","UVRY_ECOLI","YGIN_ECOLI","FOLD_ECOLI","PUR4_ECOLI","ACEA_ECOLI","ENO_ECOLI","RUVB_ECOLI","NUSA_ECOLI","TESB_ECOLI","RNH2_ECOLI","RS18_ECOLI","TOP1_ECOLI","TESA_ECOLI","CSPD_ECOLI","KDSA_ECOLI","ATPA_ECOLI","ALF1_ECOLI","DKGA_ECOLI","NIRB_ECOLI","GCVR_ECOLI","TPX_ECOLI","YQJD_ECOLI","RF1_ECOLI","SYA_ECOLI","EX7S_ECOLI","TALA_ECOLI","AROB_ECOLI","RL11_ECOLI","KHSE_ECOLI","IHFA_ECOLI","YGIB_ECOLI","THIF_ECOLI","YAHF_ECOLI","PTHP_ECOLI","UDP_ECOLI","ARGB_ECOLI","UPP_ECOLI","YIBF_ECOLI","SUCD_ECOLI","POLOX_ECOLI","MASZ_ECOLI","PTNAB_ECOLI","YCDX_ECOLI","RS21_ECOLI","SURA_ECOLI","MREB_ECOLI","RS7_ECOLI","HTPG_ECOLI","THIO2_ECOLI","YACC_ECOLI","TTDA_ECOLI","PHOE_ECOLI","QOR1_ECOLI","DEGP_ECOLI","FIU_ECOLI","AROG_ECOLI","IMDH_ECOLI","PXPC_ECOLI","PRMA_ECOLI","PTGA_ECOLI","HDFR_ECOLI","RL30_ECOLI","IDH_ECOLI","HFLC_ECOLI","NAGB_ECOLI","PUR8_ECOLI","RODZ_ECOLI","YCCU_ECOLI","FADR_ECOLI","DBHB_ECOLI","NADC_ECOLI","RL3_ECOLI","RIR1_ECOLI","RL18_ECOLI","SELB_ECOLI","XGPT_ECOLI","OBG_ECOLI","ENGB_ECOLI","DPS_ECOLI","YDFG_ECOLI","ACSA_ECOLI","FUR_ECOLI","NPD_ECOLI","ZNTA_ECOLI","GAL1_ECOLI","OMPA_ECOLI","RECA_ECOLI","SRP54_ECOLI","PARC_ECOLI","UVRD_ECOLI","ILVH_ECOLI","CRP_ECOLI","DNAJ_ECOLI","OMPN_ECOLI","YEED_ECOLI","YAHK_ECOLI","LIVG_ECOLI","YHCB_ECOLI","YIIQ_ECOLI","RL16_ECOLI","ARGD_ECOLI","SUHB_ECOLI","AROD_ECOLI","GUDP_ECOLI","ODP2_ECOLI","GPMA_ECOLI","ACP_ECOLI","YCAO_ECOLI","PHOL_ECOLI","DUT_ECOLI","KPYK1_ECOLI","FADI_ECOLI","RL5_ECOLI","ISCR_ECOLI","ACNA_ECOLI","SYGA_ECOLI","GLNB_ECOLI","CSQR_ECOLI","SEQA_ECOLI","NUOB_ECOLI","RIDA_ECOLI","SDHA_ECOLI","OPGH_ECOLI","MCP2_ECOLI","FTSY_ECOLI","RS9_ECOLI","INGK_ECOLI","YEJL_ECOLI","OPDA_ECOLI","YGGE_ECOLI","6PGL_ECOLI","HIS1_ECOLI","UUP_ECOLI","F16PA_ECOLI","OPPA_ECOLI","MURA_ECOLI","YRAP_ECOLI","ASSY_ECOLI","RL19_ECOLI","SELD_ECOLI","ILVB_ECOLI","AROK_ECOLI","NUOG_ECOLI","RS4_ECOLI","RISA_ECOLI","SRA_ECOLI","EFEO_ECOLI","THID_ECOLI","MRR_ECOLI","YEGD_ECOLI","PURE_ECOLI","METQ_ECOLI","GREA_ECOLI","GLPA_ECOLI","LIVK_ECOLI","MPRA_ECOLI","HIS7_ECOLI","TRXB_ECOLI","MTLD_ECOLI","PSIF_ECOLI","CPXR_ECOLI","RS5_ECOLI","RIBB_ECOLI","HFLK_ECOLI","NDK_ECOLI","CH60_ECOLI","THIC_ECOLI","SAD_ECOLI","SUFC_ECOLI","YIIM_ECOLI","CYCA_ECOLI","PTA_ECOLI","RL7_ECOLI","PSPE_ECOLI","MENB_ECOLI","HIS6_ECOLI","YEEN_ECOLI","AROF_ECOLI","HIS2_ECOLI","MIAB_ECOLI","CYOA_ECOLI","THIB_ECOLI","ILVC_ECOLI","RS3_ECOLI","OSMY_ECOLI","RPIA_ECOLI","OMPF_ECOLI","RISB_ECOLI","SSPA_ECOLI","YQGE_ECOLI","RHO_ECOLI","EFTS_ECOLI","NUOF_ECOLI","PBPA_ECOLI","GAL7_ECOLI","TALB_ECOLI","DEDA_ECOLI","BTUE_ECOLI","RL35_ECOLI","OXYR_ECOLI","AAEB_ECOLI","ARTI_ECOLI","RS1_ECOLI","FABZ_ECOLI","RL32_ECOLI","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