GPMDB003813OtherHuenten S, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Humanheiko.hermeking@med.uni-muenchen.de.26183718http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017010http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016954http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016953http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016956http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017008http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017009http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016955http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016958http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016957http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016959http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017002http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017003http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017000http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017001http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016950http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017006http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017007http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017004http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016952http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016951http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017005http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017020http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017021http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016965http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016964http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016967http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017019http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016966http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016969http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016968http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017013http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017014http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017011http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017012http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016961http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017017http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016960http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017018http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016963http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017015http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016962http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017016http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017031http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017032http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017030http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016975http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016978http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016977http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016979http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017024http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017025http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017022http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016970http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017023http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016972http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017028http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016971http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017029http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017026http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016974http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016973http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017027http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016987http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016986http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016989http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016988http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017035http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017036http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016981http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017033http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017034http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016980http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016983http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016982http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017037http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016985http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016984http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016918http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016919http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016998http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016997http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016999http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016990http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016992http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016991http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016994http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016993http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016996http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016995http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016929http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016928http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016921http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016920http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016923http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016922http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016925http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016924http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016927http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016926http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016939http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016932http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016931http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016934http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016933http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016936http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016935http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016938http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016937http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016930http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016943http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016942http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016945http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016944http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016947http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016946http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016949http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016948http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016941http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016940Ludwig-Maximilians-University Munich, et al.Not availableGPMDBWe determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics (pulsed stable isotope labeling with amino acids in cell culture/pSILAC) in the colorectal cancer cell line SW480. This was combined with mRNA and noncoding RNA expression analyses by next generation sequencing (RNA-, miR-Seq). Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated proteins (542 up, 569 down), mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down) and lncRNAs (270 up, 123 down). Changes in protein and mRNA expression levels showed a positive correlation (r = 0.50, p < 0.0001). In total, we detected 133 direct p53 target genes that were differentially expressed and displayed p53 occupancy in the vicinity of their promoter. More transcriptionally induced genes displayed occupied p53 binding sites (4.3% mRNAs, 7.2% miRNAs, 6.3% lncRNAs, 5.9% proteins) than repressed genes (2.4% mRNAs, 3.2% miRNAs, 0.8% lncRNAs, 1.9% proteins), suggesting indirect mechanisms of repression. Around 50% of the down-regulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3'-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed up-regulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibits proliferation in SW480 cells. Furthermore, KLF12, HMGB1 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486-5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of KLF12, HMGB1 and CIT was detected in advanced stages of cancer. In conclusion, the integration of multiple omics methods allowed the comprehensive identification of direct and indirect effectors of p53 that provide new insights and leads into the mechanisms of p53-mediated tumor suppression.p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses.Hünten Sabine S,Kaller Markus M,Drepper Friedel F,Oeljeklaus Silke S,Bonfert Thomas T,Erhard Florian F,Dueck Anne A,Eichner Norbert N,Friedel Caroline C CC,Meister Gunter G,Zimmer Ralf R,Warscheid Bettina B,Hermeking Heiko H,Hünten Sabine S, Kaller Markus M, Drepper Friedel F, Oeljeklaus Silke S, Bonfert Thomas T, Erhard Florian F, Dueck Anne A, Eichner Norbert N, Friedel Caroline C CC, Meister Gunter G, Zimmer Ralf R, Warscheid Bettina B, Hermeking Heiko Hsmall temporal RNA, INSDC_qualifier:miRNA., protein_coding_transcript, BCC7, mRNA, antigen NY-CO-13, stRNA, p53, messenger RNA, micro RNA, proteins, LFS1, INSDC_feature:ncRNA, Tp53, polypeptide, template RNA, Trp53, bbl, P53, phosphoprotein p53, p44, INSDC_feature:mRNA, bhy, bfy, TRP53, microRNA, tumor suppressor p53, TP53protein translation, Ribonucleic, Large Bowel Carcinoma, Colorectal Cancer, antigen NY-CO-13, p53, Aminosaeure, number, Aminocarbonsaeure, Gene, Isotope-Coded Affinity, IDOL, LFS1, Large Intestine Carcinoma, presence, Tp53, Colorectal, bbl, Gene Products, Line, Carcinoma of Large Intestine, Isotopically-Coded Affinity, MIR, Mir, tumor suppressor p53, Non Polyadenylated, TP53, Isotopically-Coded Affinity Tagging, RNA Gene Products, Large Bowel Cancer, Cancer of Large Bowel, amino acids, MONDOA, Large Intestine Cancer, BCC7, Scrb1, messenger RNA, cell line cell, proteins, cell line, Non-Polyadenylated RNA, SW480., template RNA, Trp53, Myosin regulatory light chain-interacting protein, Stable, vartul, Isotope-Coded Affinity Tagging, phosphoprotein p53, TRP53, bHLHe36, Tagging, Idol, Stable Isotope Labeling, Cancer, 9430057C20Rik, data, protein anabolism, RNA, protein biosynthetic process, ribose nucleic acid, Myosin regulatory light chain interacting protein, 6.3.2.-, Aminokarbonsaeure, SCRIB1, Proteins, ribonucleic acids, Cell Lines, Cancer of Large Intestine, RNS, cell_line, Labeling, Cell, polypeptide, AW228700, Isotope, count in organism, count, Stable Isotope, yeast nucleic acid, Ribonukleinsaeure, Protein, protein formation, INSDC_feature:mRNA, protein biosynthesis, pentosenucleic acids, bfy, Ribonucleic acids, CRC, Crc, Colorectal Cancers, activation, Isotope Coded Affinity Tagging, Carcinoma of Large Bowel, Lines, ribonucleic acid, Acid, protein_coding_transcript, mRNA, Non Polyadenylated RNA, Non-Polyadenylated, Inducible degrader of the LDL-receptor, Ribonucleic Acid, Cancers, CRIB, Isotope Labeling, Amino, Affinity Tagging, Isotopically-Coded, Protein Gene Products, Gene Proteins, protein synthesis, P53, p44, Isotope-Coded, bhy, Acids, quantitative, mKIAA0147, Malignant Colorectal Neoplasm, AI118201, presence or absence in organismantigen NY-CO-13, stRNA, Aminokarbonsaeure, p53, Aminocarbonsaeure, micro RNA, Isotope-Coded Affinity, LFS1, Labeling, Tp53, polypeptide, Isotope, Stable Isotope, bbl, INSDC_feature:mRNA, bfy, Isotopically-Coded Affinity, tumor suppressor p53, Isotope Coded Affinity Tagging, TP53, Isotopically-Coded Affinity Tagging, small temporal RNA, amino acids, protein_coding_transcript, BCC7, mRNA, messenger RNA, proteins, Isotope Labeling, Amino, Affinity Tagging, INSDC_feature:ncRNA, Isotopically-Coded, INSDC_qualifier:miRNA, Aminosaeure., template RNA, Trp53, Stable, P53, Isotope-Coded Affinity Tagging, phosphoprotein p53, p44, Isotope-Coded, bhy, Acids, TRP53, Tagging, microRNA, Stable Isotope Labelingprotein translation, Co-Immunoprecipitations, Ribonucleic, Materials, PLXN4, MTSP1, PLXN3, Aminosaeure, B130052C06Rik, known_ncrna, D530033K05Rik, GRO:0005339, Tumor, IDOL, Tp53, Co Immunoprecipitation, noncoding RNA, exact), Method, bbl, MIR, Mir, tumor suppressor p53, Non Polyadenylated, Chromatins, TP53, Isotopically-Coded Affinity Tagging, RNA Gene Products, seed, amino acids, BCC7, Genomes, Identification, Co-Immunoprecipitation, Precipitation, Plant Embryo, MT-SP1, proteins, elevated, procedures, Immune, Methodological Studies, HSSEXGENE, chromosome scaffold, phosphoprotein p53, HAI, Precipitations, Tagging, Idol, 6.3, Stable Isotope Labeling, I-mfa, Tumors, 9430057C20Rik, close to, protein anabolism, XAP-6, protein biosynthetic process, wide/broad, ribose nucleic acid, 6.3.2.-, Aminokarbonsaeure, DS, ribonucleic acids, Up-Regulation (Physiology), Procedure, tumours, 種子 (Japanese, W91638, mislocalized, count, PRSS14, Ribonukleinsaeure, Hmg1, HMG1, CIT, protein formation, HMG3, precocious, pentosenucleic acids, Genetic Materials, bfy, Ribonucleic acids, high mobility group protein 1, Seed, activation, Genetic Material, suppressive genetic interaction (sensu inequality)., C030025P15Rik, Acid, protein_coding_transcript, Upregulation, p30, AP2REP, Plant, Identifications (Psychology), Plant Zygote, Inducible degrader of the LDL-receptor, HDS, whole genome, Methodological, Methodological Study, early, TADG15, loss of, wide, amphoterin, protein synthesis, Material, Cit-k, P53, p44, bhy, Cistron, Acids, advanced, Procedures, ectopic, antigen NY-CO-13, Neoplasms, p53, diaspore (broad), number, Aminocarbonsaeure, Gene, broad, Isotope-Coded Affinity, LFS1, presence, HMG-1, NEOPL, Ac2-008, AI315654, Gene Products, Immune Precipitations, Studies, Isotopically-Coded Affinity, ARCI11, Immune Precipitation, malignant tumour, RP59, Epididymis tissue protein Li 189m, MONDOA, Genetic, Receptor Up-Regulation, Up Regulation, plasmid binding, malignant neoplasia, messenger RNA, Zygote, tumour, Hmgb1, 2.5.1.87, Non-Polyadenylated RNA, Study, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), template RNA, 2700063E05Rik, Trp53, microtubule/chromatin interaction, Myosin regulatory light chain-interacting protein, Stable, CRC cell line, Cis-IPTase, TMPRSS14, Isotope-Coded Affinity Tagging, Zygotes, TRP53, bHLHe36, high elevation, Neoplastic Growth, Cancer, AP-2rep, CRIK-SK, RNA, structure-specific DNA binding, CPT, Malignant Neoplasm, Myosin regulatory light chain interacting protein, HMGB1, Cis-isoprenyltransferase, Proteins, RNS, function, Cistrons, Labeling, Cell, near to, AW228700, polypeptide, Isotope, count in organism, Stable Isotope, yeast nucleic acid, Embryos, Protein, INSDC_feature:mRNA, structure specific DNA binding, protein biosynthesis, techniques, Isotope Coded Affinity Tagging, I-MF, RGD1560271, ribonucleic acid, Embryo, SNC19, mRNA, Non Polyadenylated RNA, CRIK, Non-Polyadenylated, INSDC_qualifier:other, Ribonucleic Acid, Cancers, Isotope Labeling, Amino, Plant Embryos, Affinity Tagging, Isotopically-Coded, malignant tumor, Protein Gene Products, Gene Proteins, DEF, 3222401G21Rik, semilla (Spanish, Plant Zygotes, approaches, AI225908, vicinity of, Isotope-Coded, SW480, SBP-1, quantitative, NEOPLASMS BENIGN, Neoplasia, methodology, presence or absence in organism, pyrene (narrow)38013http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017018dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0opentargets~0sra~3efo~0embl-pathogen~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0project~4ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~1orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.0117211597779148681.00.0falsep53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses.Data from ProteomeXchange, PXD ID: PXD001976. File: ELITE-RSLC001392.mzml. Published as part of . From the Abstract: {{i}} We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics of newly synthesized proteins (pulsed stable isotope labeling with amino acids in cell culture, pSILAC) in combination with mRNA and non-coding RNA expression analyses by next generation sequencing (RNA-, miR-Seq) in the colorectal cancer (CRC) cell line SW480 ... {{/i}}2015-07-26GPM3232001701826183718PXD001976PXD001976