PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK2000ProteomicsChristian von Mering10090https://pax-db.org/dataset/10090/8657263mering@imls.uzh.chUniversity of ZurichPAXDBFor the rescaling, the datasets are first parsed or processed such that the data reflect proportional abundances of whole protein molecules (i.e. proportionality to counts of complete, individual protein molecules, not to molecular weights, protein volumes, or digested peptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up to one million; this means the abundance of each protein of interest is finally expressed in (parts per million,) relative to all other proteins in a sample. For a given protein abundance dataset, we then compute the absolute log abundance ratios of all pairs of proteins annotated to be functionally linked. The median of these absolute log abundance ratios represents an indirect quality metric: the closer it is to zero, the better (i.e. the more there is consistency between abundance values and functional annotations such as protein complexes or pathways). We then compute a background expectation for this metric, by permuting the abundance values in a given dataset randomly, and recomputing the median log abundance ratios. The permutation is repeated several times, yielding a distribution of medians. The actually observed median is then expressed as a Z-score distance to the random distribution ofmedians—this distance is termed the interaction consistency score.Genes are pleiotropic and getting a better knowledge of their function requires a comprehensive characterization of their mutants. Here, we generated multi-level data combining phenomic, proteomic and metabolomic acquisitions from plasma and liver tissues of two C57BL/6 N mouse models lacking the Lat (linker for activation of T cells) and the Mx2 (MX dynamin-like GTPase 2) genes, respectively. Our dataset consists of 9 assays (1 preclinical, 2 proteomics and 6 metabolomics) generated with a fully non-targeted and standardized approach. The data and processing code are publicly available in the ProMetIS R package to ensure accessibility, interoperability, and reusability. The dataset thus provides unique molecular information about the physiological role of the Lat and Mx2 genes. Furthermore, the protocols described herein can be easily extended to a larger number of individuals and tissues. Finally, this resource will be of great interest to develop new bioinformatic and biostatistic methods for multi-omics data integration.ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis.Imbert Alyssa A, Rompais Magali M, Selloum Mohammed M, Castelli Florence F, Mouton-Barbosa Emmanuelle E, Brandolini-Bunlon Marion M, Chu-Van Emeline E, Joly Charlotte C, Hirschler Aurélie A, Roger Pierrick P, Burger Thomas T, Leblanc Sophie S, Sorg Tania T, Ouzia Sadia S, Vandenbrouck Yves Y, Médigue Claudine C, Junot Christophe C, Ferro Myriam M, Pujos-Guillot Estelle E, de Peredo Anne Gonzalez AG, Fenaille François F, Carapito Christine C, Herault Yann Y, Thévenot Etienne A EAAdd, 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, ratioMus musculus, determination, Laboratory, Peptidomics, Swiss, mice, Mus domesticus, mouse, Swiss Mouse, Metabonomic, chemical analysis., House Mice, Swiss Mice, Metabonomics, House Mouse, mice C57BL/6xCBA/CaJ hybrid, domesticus, Mus muscaris, Laboratory Mice, House, Mus, Mus musculus domesticus, Mouse, assay, house mouse, Metabolomic, Mice, Laboratory MousePlasma, Fresh, Frozen Plasmas, Fresh Frozen Plasmas, Fresh Frozen, blood plasm, portion of blood plasma, Blood Plasma, Frozen Plasma, Fresh Frozen Plasma, musculus, Blood Plasmas, Blood, portion of plasma, muscle, Plasmas, muscle element, plasma.Panomics, Fresh, big, DmelCG4088, GTP, Materials, Fresh Frozen Plasma, Procedures, Laboratory, Peptidomics, Blood, Mus domesticus, number, Metabonomic, Gene, Metabonomics, 36 kDa phospho-tyrosine adapter protein, PP2030, House Mouse, AI528743, Guanosine Triphosphate, jecur, Multi-Omics, large, Techniques, GTPases, House, Method, nrs, Studies, Mus musculus domesticus, Phenomic, Metabolomic, Mice, CG14225, Technique, INSL3R, Guanosine Triphosphate Phosphohydrolases, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, ORC3L, Genetic, Gpr106, AI327394, Swiss, Tissue, Triphosphate Phosphohydrolases, vr-6, iecur, Swiss Mice, ORC3, Orc3, RXFPR2, pp36, procedures, Omics, Study, GREAT, HSpin1, Methodological Studies, data., Blood Plasmas, great, Great, Band25, Pan-Omics, house mouse, LATHEO, GPR106, plasma, GTPase, LAT, data, Frozen Plasma, Guanosine, Integrative-Omics, Data Set, Guanosinetriphosphatases, GTP Phosphohydrolase, l(2)vr6, mouse, Mx-2, function, SPIN1, AI227039, p36-38, Procedure, Integrative Omics, Cistrons, Plasmas, Cell, mice C57BL/6xCBA/CaJ hybrid, lat, gtl11, Mus muscaris, Frozen Plasmas, Mus, ET, Multi-Omic, LAT1, Pan Omics, Genetic Materials, DmORC3, l(2)49Fd, DmOrc3, CG4088, techniques, Genetic Material, activation, Plasma, ORC, Mus musculus, MgcRacGAP, LGR8, Multi Omics, Epistemology, portion of blood plasma, Lgr8, DmelCG14225, mice, Swiss Mouse, expanded, Integrative, portion of plasma, House Mice, Methodological, LGR8.1, Methodological Study, domesticus, Laboratory Mice, Phosphohydrolases, Livers, blood plasm, Phosphohydrolase, enlarged, Material, cardinality, 36 kDa phosphotyrosine adapter protein, Cistron, Mouse, MXB, mKIAA1478, Laboratory Mouse, vr6, SPINL, methodology2falseM.musculus - Plasma, SC (Imbertetal,scidata2021)abundance based on Spectral counting, Interaction consistency score: 4.5, Coverage: 22021865726334862403TSP4_MOUSEHINT1_MOUSERET4_MOUSEPEPD_MOUSEFETUA_MOUSESAA1_MOUSEDHR11_MOUSEUROM_MOUSEFIBB_MOUSEK22O_MOUSECO8B_MOUSEGSTM1_MOUSEKPYM_MOUSESPA3M_MOUSEAPOB_MOUSETBB4B_MOUSETITIN_MOUSETRFL_MOUSEPAFA_MOUSECAH2_MOUSECO8G_MOUSEFIBG_MOUSEPSB8_MOUSEPGK1_MOUSEB4GT1_MOUSEAMBP_MOUSECS1B_MOUSECOR1B_MOUSEPHLD_MOUSEPROC_MOUSEQSOX1_MOUSEMYH3_MOUSECO1A2_MOUSESODC_MOUSEC1QA_MOUSEOBP1A_MOUSECSF1R_MOUSEADH1_MOUSEK2C5_MOUSEGELS_MOUSEIBP2_MOUSEMASP1_MOUSENDKA_MOUSEANT3_MOUSESPA3C_MOUSEHSP74_MOUSEACE_MOUSEPSB3_MOUSECHLE_MOUSECOL11_MOUSEACBP_MOUSEIF5A1_MOUSEMDHC_MOUSECO5_MOUSEACTN4_MOUSECCL8_MOUSEF13B_MOUSESEPR_MOUSEHBA_MOUSEEST2E_MOUSEAFAM_MOUSEFGL1_MOUSEGP1BA_MOUSEITIH4_MOUSECLC11_MOUSECATE_MOUSEVWF_MOUSEVINC_MOUSEA1AT1_MOUSENCAM1_MOUSEMUG1_MOUSEB2MG_MOUSEHSP7C_MOUSECBPQ_MOUSEFA20C_MOUSEPIP_MOUSEIBP4_MOUSEPSA3_MOUSETBB1_MOUSEPSB1_MOUSEBLVRB_MOUSEFBLN3_MOUSEEST1_MOUSEPLMN_MOUSEAL3A1_MOUSEAPOA4_MOUSEICA_MOUSELYVE1_MOUSEPON1_MOUSEMYL6_MOUSEGSH0_MOUSEEST2C_MOUSEAMPL_MOUSERAP1A_MOUSEAPOD_MOUSEPPIA_MOUSEMBL1_MOUSEPSA5_MOUSESODE_MOUSETIMP3_MOUSESBSN_MOUSEITIH2_MOUSETLN1_MOUSEMA1A1_MOUSEMA2B1_MOUSEHEMO_MOUSEIGF1_MOUSECBG_MOUSEPRDX1_MOUSECD44_MOUSEUN13D_MOUSEPLSL_MOUSESAP_MOUSEMMP2_MOUSECTRB1_MOUSESIAE_MOUSEAPOA2_MOUSEFA10_MOUSEAPOE_MOUSEANGT_MOUSEA2AP_MOUSEA1AG2_MOUSEALDOA_MOUSEBMX_MOUSECO9_MOUSECBPB2_MOUSEDSG2_MOUSEILK_MOUSEPEBP1_MOUSEGGH_MOUSERAB32_MOUSEPSA1_MOUSEAL1A1_MOUSEAPOA1_MOUSEPLEK_MOUSECFAI_MOUSEMASP2_MOUSEDEST_MOUSEMOES_MOUSECOL10_MOUSEGSTA4_MOUSEPROP_MOUSEPLTP_MOUSEPMGE_MOUSEPRDX2_MOUSEPPIC_MOUSESAMP_MOUSEIGJ_MOUSEHPT_MOUSEPI16_MOUSECLUS_MOUSESPAT7_MOUSEFA11_MOUSECO1A1_MOUSEA1AG1_MOUSECD5L_MOUSECATB_MOUSETCO2_MOUSEGPX3_MOUSEFCN1_MOUSESBP1_MOUSEDSPP_MOUSEPXDC2_MOUSECYC_MOUSEPSME1_MOUSEPARK7_MOUSEFA12_MOUSEA2MG_MOUSEURP2_MOUSETFR1_MOUSEPTPRG_MOUSESPRL1_MOUSEACTN1_MOUSEPGRP2_MOUSELUM_MOUSEPRDX6_MOUSEANGL3_MOUSECADH1_MOUSEZA2G_MOUSEADIPO_MOUSELONM_MOUSEPEDF_MOUSEHS90B_MOUSELIPC_MOUSEACTB_MOUSEUBA1_MOUSEAPEH_MOUSE1433G_MOUSEACTC_MOUSECYT1_MOUSEMFAP4_MOUSEENPL_MOUSEALDOB_MOUSETKT_MOUSEPMEL_MOUSEVGFR3_MOUSECD97_MOUSEHRG_MOUSECATA_MOUSEMUG2_MOUSECATZ_MOUSEKLKB1_MOUSEHBE_MOUSEAPOH_MOUSEOBP1B_MOUSEGSTO1_MOUSELAMP1_MOUSEIBP3_MOUSEPROS_MOUSETBB5_MOUSEPNPH_MOUSELCAT_MOUSEPSB2_MOUSEMERTK_MOUSECOF1_MOUSEGDIB_MOUSETCTP_MOUSEHGFA_MOUSEITIH3_MOUSEGPX1_MOUSELGUL_MOUSETTHY_MOUSEENOB_MOUSEA1BG_MOUSEAPOC4_MOUSEISG15_MOUSEVTNC_MOUSELYAM1_MOUSEFLNA_MOUSES2B24_MOUSEA1AT2_MOUSEAPOM_MOUSESIA7A_MOUSEGDIR1_MOUSECS1A_MOUSEALS_MOUSEECM1_MOUSECEL2A_MOUSECOR1A_MOUSEMMRN1_MOUSEICAM1_MOUSENOE1_MOUSEPOSTN_MOUSEB3AT_MOUSECAH1_MOUSETENA_MOUSEPZP_MOUSEARFG2_MOUSECADH5_MOUSEC4BPA_MOUSERETNG_MOUSETERA_MOUSETPIS_MOUSEARPC4_MOUSEPSA6_MOUSETHOC7_MOUSECAP1_MOUSEPRVA_MOUSEVTDB_MOUSECFAH_MOUSECYTC_MOUSETYB4_MOUSEITIH1_MOUSEIC1_MOUSEK2C79_MOUSEIL1R2_MOUSECTL2A_MOUSE1433Z_MOUSEMYL9_MOUSESEPP1_MOUSEFETUB_MOUSEAPOF_MOUSECO8A_MOUSETHIO_MOUSEILEUA_MOUSESLPI_MOUSEK1C18_MOUSETBA1B_MOUSEEF1A1_MOUSECSKI2_MOUSEG3P_MOUSEPSA4_MOUSEFIBA_MOUSEIBP5_MOUSEF13A_MOUSETETN_MOUSEBIP_MOUSEFRPD1_MOUSETBA4A_MOUSEBGH3_MOUSELIFR_MOUSEICOSL_MOUSERAN_MOUSEK2C1_MOUSECRP_MOUSEIFT80_MOUSEHEPC_MOUSEPIGR_MOUSEHEP2_MOUSEMBL2_MOUSECFAD_MOUSEFBLN1_MOUSEMIF_MOUSETSP1_MOUSEAPOC2_MOUSELYZ2_MOUSEBTD_MOUSEZBT43_MOUSESAP25_MOUSETAGL2_MOUSEESTD_MOUSEHABP2_MOUSEPSB5_MOUSESYUA_MOUSEDHSO_MOUSEHA11_MOUSEALBU_MOUSETPM4_MOUSEABRAL_MOUSEMUP2_MOUSETRML1_MOUSEC1QC_MOUSESAA4_MOUSECPN2_MOUSEFAT4_MOUSECO3A1_MOUSEFA9_MOUSEPROF1_MOUSEPSB4_MOUSECO3_MOUSEC1QB_MOUSECERU_MOUSEKNG1_MOUSEMYG_MOUSEPSA7_MOUSEMINP1_MOUSEMUP3_MOUSEEST1C_MOUSESRGN_MOUSEEGFR_MOUSESPP24_MOUSEPPAC_MOUSELBP_MOUSEIDHC_MOUSEIKKB_MOUSECELA1_MOUSELDHA_MOUSETHRB_MOUSEGPV_MOUSEAMYP_MOUSEPPGB_MOUSEHBB1_MOUSEOAF_MOUSEVCAM1_MOUSE4F2_MOUSEZPI_MOUSEGCAB_MOUSECO2_MOUSEENOA_MOUSEHA10_MOUSEKCRM_MOUSELAC2_MOUSEMYH9_MOUSEVCIP1_MOUSETRFE_MOUSECALM1_MOUSEC1RA_MOUSES10A9_MOUSEPLF4_MOUSEA1AT4_MOUSEGRN_MOUSEAPOC3_MOUSEAMY1_MOUSEFA7_MOUSEV2R1_MOUSEUBB_MOUSECBPN_MOUSESPA3N_MOUSECFAB_MOUSETHBG_MOUSESPA3K_MOUSEHGFL_MOUSEFINC_MOUSETEBP_MOUSEIGS10_MOUSEA1AT5_MOUSEMAOX_MOUSES2B20_MOUSEWDR1_MOUSEH4_MOUSERAC1_MOUSEFA5_MOUSEINAR2_MOUSECO4B_MOUSEPCYOX_MOUSEAPOC1_MOUSEAGRF5_MOUSEPROZ_MOUSENAPSA_MOUSEPSB6_MOUSE