{"database":"GPMDB","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":22,"searchCount":6},"additional":{"omics_type":["Other"],"submitter":["Yang W, et al."],"instrument_platform":["Instrument"],"disease":["Not Available"],"brenda_tissue":["Not available"],"species":["Homo_sapiens_viruses, Human"],"publication":["25080971"],"submitter_mail":["omician@gmail.com"],"submitter_affiliation":["Cedars-Sinai Medical Center"],"model":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002751","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002752","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002753","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002754","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002755","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002734","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002757","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002735","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002758","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002736","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002750","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002737","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002759","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002738","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002739","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002740","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002762","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002741","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002763","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002742","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002743","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002744","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002745","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002746","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002747","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002760","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002761","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002748","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002749"],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_abstract":["Platelet-derived growth factor-BB (PDGF-BB) has been implicated in the proliferation, migration and synthetic activities of smooth muscle cells that characterize physiologic and pathologic tissue remodeling in hollow organs. However, neither the molecular basis of PDGFR-regulated signaling webs, nor the extent to which specific components within these networks could be exploited for therapeutic benefit has been fully elucidated.","Expression profiling and quantitative proteomics analysis of PDGF-treated primary human bladder smooth muscle cells identified 1,695 genes and 241 proteins as differentially expressed versus non-treated cells. Analysis of gene expression data revealed MYC, JUN, EGR1, MYB, RUNX1, as the transcription factors most significantly networked with up-regulated genes. Forty targets were significantly altered at both the mRNA and protein levels. Proliferation, migration and angiogenesis were the biological processes most significantly associated with this signature, and MYC was the most highly networked master regulator. Alterations in master regulators and gene targets were validated in PDGF-stimulated smooth muscle cells in vitro and in a model of bladder injury in vivo. Pharmacologic inhibition of MYC and JUN confirmed their role in SMC proliferation and migration. Network analysis identified the diaphanous-related formin 3 as a novel PDGF target regulated by MYC and JUN, which was necessary for PDGF-stimulated lamellipodium formation.","These findings provide the first systems-level analysis of the PDGF-regulated transcriptome and proteome in normal smooth muscle cells. The analyses revealed an extensive cohort of PDGF-dependent biological processes and connected key transcriptional effectors to their regulation, significantly expanding current knowledge of PDGF-stimulated signaling cascades. These observations also implicate MYC as a novel target for pharmacological intervention in fibroproliferative expansion of smooth muscle, and potentially in cancers in which PDGFR-dependent signaling or MYC activation promote tumor progression.","Platelet-derived growth factor-BB (PDGF-BB) has been implicated in the proliferation, migration and synthetic activities of smooth muscle cells that characterize physiologic and pathologic tissue remodeling in hollow organs. However, neither the molecular basis of PDGFR-regulated signaling webs, nor the extent to which specific components within these networks could be exploited for therapeutic benefit has been fully elucidated.Expression profiling and quantitative proteomics analysis of PDGF-treated primary human bladder smooth muscle cells identified 1,695 genes and 241 proteins as differentially expressed versus non-treated cells. Analysis of gene expression data revealed MYC, JUN, EGR1, MYB, RUNX1, as the transcription factors most significantly networked with up-regulated genes. Forty targets were significantly altered at both the mRNA and protein levels. Proliferation, migration and angiogenesis were the biological processes most significantly associated with this signature, and MYC was the most highly networked master regulator. Alterations in master regulators and gene targets were validated in PDGF-stimulated smooth muscle cells in vitro and in a model of bladder injury in vivo. Pharmacologic inhibition of MYC and JUN confirmed their role in SMC proliferation and migration. Network analysis identified the diaphanous-related formin 3 as a novel PDGF target regulated by MYC and JUN, which was necessary for PDGF-stimulated lamellipodium formation.These findings provide the first systems-level analysis of the PDGF-regulated transcriptome and proteome in normal smooth muscle cells. The analyses revealed an extensive cohort of PDGF-dependent biological processes and connected key transcriptional effectors to their regulation, significantly expanding current knowledge of PDGF-stimulated signaling cascades. These observations also implicate MYC as a novel target for pharmacological intervention in fibroproliferative expansion of smooth muscle, and potentially in cancers in which PDGFR-dependent signaling or MYC activation promote tumor progression.","<h4>Background</h4>Platelet-derived growth factor-BB (PDGF-BB) has been implicated in the proliferation, migration and synthetic activities of smooth muscle cells that characterize physiologic and pathologic tissue remodeling in hollow organs. However, neither the molecular basis of PDGFR-regulated signaling webs, nor the extent to which specific components within these networks could be exploited for therapeutic benefit has been fully elucidated.<h4>Results</h4>Expression profiling and quantitative proteomics analysis of PDGF-treated primary human bladder smooth muscle cells identified 1,695 genes and 241 proteins as differentially expressed versus non-treated cells. Analysis of gene expression data revealed MYC, JUN, EGR1, MYB, RUNX1, as the transcription factors most significantly networked with up-regulated genes. Forty targets were significantly altered at both the mRNA and protein levels. Proliferation, migration and angiogenesis were the biological processes most significantly associated with this signature, and MYC was the most highly networked master regulator. Alterations in master regulators and gene targets were validated in PDGF-stimulated smooth muscle cells in vitro and in a model of bladder injury in vivo. Pharmacologic inhibition of MYC and JUN confirmed their role in SMC proliferation and migration. Network analysis identified the diaphanous-related formin 3 as a novel PDGF target regulated by MYC and JUN, which was necessary for PDGF-stimulated lamellipodium formation.<h4>Conclusions</h4>These findings provide the first systems-level analysis of the PDGF-regulated transcriptome and proteome in normal smooth muscle cells. The analyses revealed an extensive cohort of PDGF-dependent biological processes and connected key transcriptional effectors to their regulation, significantly expanding current knowledge of PDGF-stimulated signaling cascades. These observations also implicate MYC as a novel target for pharmacological intervention in fibroproliferative expansion of smooth muscle, and potentially in cancers in which PDGFR-dependent signaling or MYC activation promote tumor progression."],"pubmed_title":["Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells."],"pubmed_authors":["Yang Wei W,Ramachandran Aruna A,You Sungyong S,Jeong HyoBin H,Morley Samantha S,Mulone Michelle D MD,Logvinenko Tanya T,Kim Jayoung J,Hwang Daehee D,Freeman Michael R MR,Adam Rosalyn M RM,","Yang Wei W, Ramachandran Aruna A, You Sungyong S, Jeong HyoBin H, Morley Samantha S, Mulone Michelle D MD, Logvinenko Tanya T, Kim Jayoung J, Hwang Daehee D, Freeman Michael R MR, Adam Rosalyn M RM"],"name_synonyms":["c-myc, PDGFR binding, Homo sapients, human being, smooth muscle, platelet-derived growth factor, AU016757, PDGF receptor binding, Humo sapiens, involuntary muscle, textus muscularis levis, MYC, textus muscularis nonstriatus, non-striated muscle, Homo sapiense, man, Homo sapines, human, Myc2, B430311C09Rik, Niard, Homo spaiens, c-Myc, Homo spiens, visceral muscle, \"human\" EXACT genbank_common_name [], Homo sapien, adult visceral muscle., MYCC, Nird, RNCMYC, Homo sapience, Homo sapian, visceral muscle tissue, Homo sampiens, Homo sapians, NOP, ARC, Nop30, platelet-derived growth factor receptor ligand, PDGF, Homo sapeins, mMyc, MRTL, bHLHe39, Home sapiens"],"description_synonyms":["extent, bladder non-striated muscle, Ngf1, c-myb_CDS, biological signaling, PDGFR binding, artificial sequence, human being, Materials, platelet-derived growth factor, determination, Myocytes, AP-1, Myocyte, number, egr, Gene, ETR103, MYC, JTK12, Homo sapiense, non-striated muscle of bladder, Transcription Factor, presence, B430311C09Rik, Krox-1, Homo spaiens, c-Myc, bladder smooth muscle, Cbfa2, Homo sapien, MYCC, zif-268, Homo sapians, Gene Products, Krox-24, ARC, Nop30, Cmyb, Growth Factor, synthetic genetic interaction (sensu inequality), Muscle Cell, IBGC4, Platelet-Derived, smooth muscle tissue of urinary bladder, Junc, c-myc, Pebp2a2, Transcription, c-myb, Homo sapients, Genetic, Gene Expressions, Pdgfr, AMLCR1, cell, AI528809, PDGFR1, synthetic genetic interaction defined by inequality, proteins, PDGFR, AT225, Muscle Cells, A530045N19Rik, man, Expressions, TIS8, CD140b, smooth muscle tissue of bladder, Zenk, urinary bladder non-striated muscle, non-striated muscle of urinary bladder, AI550390, Nird, RNCMYC, Egr-1, Homo sapience, Zfp-6, Mature Muscle Cell, Pebpa2b, signaling process, Homo sampiens, c-Jun, bladder involuntary muscle, Expression, M16449, G0S30, smooth muscle of urinary bladder, bHLHe39, Ngfi, Home sapiens, urinary bladder involuntary muscle, KROX-24, single organism signaling, CD140B, data, Krox24, CBF-alpha-2, AU016757, completeness, Aml1, AML1, Proteins, c-jun, Platelet Derived Growth Factor, urinary bladder muscle, artificial gene, Factor, Zif268, synthetic DNA, Cistrons, Cell, Mature Muscle Cells, polypeptide, count in organism, count, EVI-1, PEBP2aB, Homo sapian, chemical analysis, Protein, NOP, smooth muscle layer of bladder, synthetic, Genetic Materials, Platelet-Derived Growth, Homo sapeins, mMyc, Genetic Material, smooth muscle of bladder, AML1-EVI-1, urinary bladder smooth muscle tissue, PDGFR-1, Factors, PDGF receptor binding, Humo sapiens, NGFI-A, CBFA2, Mature, synthetic constructs, Homo sapines, ZNF225, human, signalling, Myc2, Protein Gene Products, Gene Proteins, AP1, SYNTHETIC CONSTRUCT sequences, Niard, Homo spiens, \"human\" EXACT genbank_common_name [], efg, signalling process, involuntary muscle of urinary bladder, NGFIA, Material, ZIF-268, IMF1, involuntary muscle of bladder, artificial, bladder smooth muscle tissue, Cistron, platelet-derived growth factor receptor ligand, assay, PDGF, quantitative, Genetic Material., MRTL, NGF1-A, presence or absence in organism"],"pubmed_title_synonyms":["c-myc, PDGFR binding, Homo sapients, human being, smooth muscle, platelet-derived growth factor, AU016757, PDGF receptor binding, Humo sapiens, involuntary muscle, textus muscularis levis, MYC, textus muscularis nonstriatus, non-striated muscle, Homo sapiense, man, Homo sapines, human, Myc2, B430311C09Rik, Niard, Homo spaiens, c-Myc, Homo spiens, visceral muscle, \"human\" EXACT genbank_common_name [], Homo sapien, adult visceral muscle., MYCC, Nird, RNCMYC, Homo sapience, Homo sapian, visceral muscle tissue, Homo sampiens, Homo sapians, NOP, ARC, Nop30, platelet-derived growth factor receptor ligand, PDGF, Homo sapeins, mMyc, MRTL, bHLHe39, Home sapiens"],"pubmed_abstract_synonyms":["extent, biological signaling, PDGFR binding, PDGFR-1, artificial sequence, smooth muscle, platelet-derived growth factor, Pdgfr, PDGF receptor binding, completeness., adult visceral muscle, AI528809, PDGFR1, Platelet Derived Growth Factor, involuntary muscle, textus muscularis levis, synthetic genetic interaction defined by inequality, artificial gene, textus muscularis nonstriatus, Factor, non-striated muscle, JTK12, PDGFR, synthetic DNA, synthetic constructs, signalling, CD140b, SYNTHETIC CONSTRUCT sequences, visceral muscle, signalling process, visceral muscle tissue, signaling process, IMF1, synthetic, artificial, Growth Factor, platelet-derived growth factor receptor ligand, PDGF, Platelet-Derived Growth, synthetic genetic interaction (sensu inequality), IBGC4, single organism signaling, Platelet-Derived, CD140B"],"view_count":["22"],"citation_count":["0"],"search_count":["6"],"full_dataset_link":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002736"],"search_domains":["dbgap_ncbi~0","patentfamilies~0","rfam~0","merops~0","complex-portal~0","uniprot~0","wormbaseparasite~0","embl-covid19~0","reactome~0","emdb~0","wgs_masters~0","ebiweb_resources~0","opentargets_genetics~0","biomodels_all~0","ipd-mhc~0","ebiweb_teams~0","taxonomy~0","genome_assembly~0","sc-experiments~0","ebiweb_people~0","enzymeportal_enzymes~0","ipd-nhkir~0","cellosaurus~0","pdbe~0","chebi~0","patentproteins~0","interpro7~0","uniref~0","chembl~0","pdbekb~0","gpcrdb~0","hgnc~0","sc-genes~0","intact~0","rhea~0","ebiweb_training~0","alphafold~0","imgt-hla~0","patentnucleotides~0","ensemblroot~0","eva_studies~0","non-coding~0","europepmc~0","pubmed~1","identifiers_registry~0","pdbechem~0","hpa-covid19~0","eva-variants-covid19~0","biosamples~0","gwas_catalog~0","biotools~0","tls_masters~0","mesh~0","coding~0","sra~0","opentargets~0","efo~0","embl-pathogen~0","pride~1","human_diseases~0","geo_datasets~0","embl~0","treefam~0","project~1","uniparc~0","ols~0","dgva~0","intenz~0","go~0","tsa_masters~0","biosamples-covid19~0","ebiweb_corporate~0","omim~0","lrg~0","earlycause-molecular-sequences~0","ipd-kir~0","empiar~0","rnacentral~0","orcid_data_claims~0","gpmdb~2","lineage-covid19~0","metagenomics~0","pfam~0","pride 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File: WY_R103.mzml. Published as part of Cell Commun Signal. 2014 Aug 1;12(1):44  . From the Abstract: {{i}} ... Platelet-derived growth factor-BB (PDGF-BB) has been implicated in the proliferation, migration and synthetic activities of smooth muscle cells that characterize physiologic and pathologic tissue remodeling in hollow organs. However, neither the molecular basis of PDGFR-regulated signaling webs, nor the extent to which specific components within these networks could be exploited for therapeutic benefit has been fully elucidated.ResultsExpression [sic] profiling and quantitative proteomics analysis of PDGF-treated primary human bladder smooth muscle cells identified 1,695 genes and 241 proteins as differentially expressed versus non-treated cells. Analysis of gene expression data revealed MYC, JUN, EGR1, MYB, RUNX1, as the transcription factors most significantly networked with up-regulated genes ... {{/i}}","dates":{"submission":"2014-08-04"},"accession":"GPM32310002736","cross_references":{"pubmed":["25080971"],"Pride":["PXD000624"],"pride":[],"Pride Archive":["PXD000624"]}}