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um=GPM32310021144</model><model>http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310021145</model><model>http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310021146</model><submitter_affiliation>Imperial College, London</submitter_affiliation><cell_type>Not available</cell_type><repository>GPMDB</repository><pubmed_abstract>Tyrosine kinases (TKs) are central regulators in cellular activities and perturbations of TK signaling contribute to oncogenesis. However, less than half of the TKs have been thoroughly studied and a global functional analysis of their proteomic portrait is lacking. Here we conducted a combined approach of RNA interference (RNAi) and stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics to decode the TK-regulated proteome and associated signaling dynamics. As a result, a broad proteomic repertoire modulated by TKs was revealed, upon silencing of the 65 TKs expressed in MCF7 breast cancer cells. This yielded 10 new distinctive TK clusters according to similarity in TK-regulated proteome, each characterized by a unique signaling signature in contrast to previous classifications. We provide functional analyses and identify critical pathways for each cluster based on their common downstream targets. Analysis of different breast cancer subtypes showed distinct correlations of each cluster with clinical outcome. From the significantly up- and down-regulated proteins, we identified a number of markers of drug sensitivity and resistance. These data supports the role of TKs in regulating major aspects of cellular activity, but also reveals redundancy in signaling, explaining why kinase inhibitors alone often fail to achieve their clinical aims. The TK-SILACepedia provides a comprehensive resource for studying the global function of TKs in cancer.</pubmed_abstract><pubmed_title>Characterization of the Tyrosine Kinase-Regulated Proteome in Breast Cancer by Combined use of RNA interference (RNAi) and Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) Quantitative Proteomics.</pubmed_title><pubmed_authors>Stebbing Justin J,Zhang Hua H,Xu Yichen Y,Grothey Arnhild A,Ajuh Paul P,Angelopoulos Nicos N,Giamas Georgios G,</pubmed_authors><pubmed_authors>Stebbing Justin J, Zhang Hua H, Xu Yichen Y, Grothey Arnhild A, Ajuh Paul P, Angelopoulos Nicos N, Giamas Georgios G</pubmed_authors><name_synonyms>Human Mammary Neoplasm, Carcinoma, para Tyrosine, Carcinoma of breast NOS, use, Breast Neoplasms, Neoplasms, 2-Amino-3-(p-hydroxyphenyl)propionic acid, posttranscriptional gene silencing by siRNA, number, Human Mammary Neoplasms, para-Tyrosine, Tumor, presence, Phosphotransferases, Tyrosine, Human, RNAi, count in organism, count, tirosina, Mammary Carcinomas, Breast Tumor, BREAST NEOPL, Neoplasm, Human Mammary Carcinoma, Carcinoma of the Breast, Kinase, Mammary carcinoma, Carcinomas, BC, Mammary Neoplasms, Transphosphorylases, Breast Neoplasm, Human Mammary, Kinases, NEOPL BREAST, Mammary Neoplasm, Carcinoma of breast NOS (disorder), 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, Mammary Carcinoma, carcinoma OF breast, L-isomer, Human Mammary Carcinomas, C9H11NO3, Cancer of the Breast, L isomer, CA - Carcinoma of breast, presence or absence in organism., L Tyrosine, Tyr, Breast Tumors, Breast Cancer, Carcinoma of breast (disorder), Cancer of Breast, L-Tyrosine, Tyrosin, quantitative, ATP Phosphotransferases, Breast, Proteomes, ATP, Tumors, Cancer</name_synonyms><description_synonyms>data, para Tyrosine, biological signaling, Tksk, determination, mol, AP-1, Aminokarbonsaeure, Aminosaeure, c-jun, 2-Amino-3-(p-hydroxyphenyl)propionic acid, posttranscriptional gene silencing by siRNA, Aminocarbonsaeure, number, para-Tyrosine, Isotope-Coded Affinity, Labeling, presence, Cell, Tyrosine, RNAi, Isotope, count in organism, count, tirosina, Stable Isotope, chemical analysis, Sik, Isotopically-Coded Affinity, Isotope Coded Affinity Tagging, Isotopically-Coded Affinity Tagging, Junc, amino acids, cell, 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, L-isomer, C9H11NO3, Isotope Labeling, Amino, Affinity Tagging, Isotopically-Coded, tks, signalling, L isomer, AP1, signalling process, L Tyrosine, Stable, Tyr, signaling process, Isotope-Coded Affinity Tagging, c-Jun, Isotope-Coded, L-Tyrosine, Acids, assay, Tyrosin, quantitative, associated, Tagging, BRK, Proteomes, Stable Isotope Labeling, single organism signaling., single organism signaling, presence or absence in organism</description_synonyms><pubmed_title_synonyms>para Tyrosine, Carcinoma of breast NOS, Breast Neoplasms, Neoplasms, Aminosaeure, Aminocarbonsaeure, number, Human Mammary Neoplasms, Tumor, Isotope-Coded Affinity, presence, Human, Breast Tumor, BREAST NEOPL, Post Transcriptional, Carcinoma of the Breast, Kinase, Isotopically-Coded Affinity, Isotopically-Coded Affinity Tagging, BC, Mammary Neoplasms, Human Mammary, amino acids, Mammary Neoplasm, Carcinoma of breast NOS (disorder), 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, Mammary Carcinoma, Human Mammary Carcinomas, Cosuppression, Cancer of the Breast, CA - Carcinoma of breast, Gene Silencings, L Tyrosine, Stable, Tyr, Isotope-Coded Affinity Tagging, Carcinoma of breast (disorder), Tyrosin, ATP Phosphotransferases, Breast, Tagging, Stable Isotope Labeling, ATP, Tumors, Cancer, Human Mammary Neoplasm, Carcinoma, RNA, use, Aminokarbonsaeure, 2-Amino-3-(p-hydroxyphenyl)propionic acid, posttranscriptional gene silencing by siRNA, para-Tyrosine, Labeling, Phosphotransferases, Tyrosine, RNAi, Isotope, count in organism, Interference, count, tirosina, Mammary Carcinomas, Stable Isotope, Neoplasm, Human Mammary Carcinoma, Mammary carcinoma, RNA Silencing, Silencing, Isotope Coded Affinity Tagging, Post-Transcriptional Gene, Carcinomas, Post-Transcriptional Gene Silencings, Transphosphorylases, Breast Neoplasm, Kinases, NEOPL BREAST, Posttranscriptional, Posttranscriptional Gene Silencing, carcinoma OF breast, L-isomer, C9H11NO3, Isotope Labeling, Amino, Co Suppression, Affinity Tagging, Isotopically-Coded, Post Transcriptional Gene Silencing, L isomer, Post-Transcriptional, presence or absence in organism., Gene Silencing, Breast Tumors, Breast Cancer, Isotope-Coded, Cancer of Breast, L-Tyrosine, Acids, quantitative, Co-Suppression, Post-Transcriptional Gene Silencing, Proteomes</pubmed_title_synonyms><pubmed_abstract_synonyms>para Tyrosine, biological signaling, Carcinoma of breast NOS, Tksk, determination, Breast Neoplasms, Clinical Paths, Neoplasms, Aminosaeure, Aminocarbonsaeure, number, RCB1904, Gene, Human Mammary Neoplasms, Critical Path, broad, Tumor, Isotope-Coded Affinity, presence, Clinical Pathways, Human, Classifications, Roles, Breast Tumor, BREAST NEOPL, resistance, Post Transcriptional, Gene Products, Critical Paths, Concepts, Carcinoma of the Breast, Kinase, Isotopically-Coded Affinity, Clinical Path, malignant tumour, Isotopically-Coded Affinity Tagging, BC, Mammary Neoplasms, Critical Pathway, Human Mammary, Taxonomy, amino acids, Clinical, Mammary Neoplasm, Carcinoma of breast NOS (disorder), 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, Mammary Carcinoma, Human Mammary Carcinomas, malignant neoplasia, Pathways, proteins, number of, Cosuppression, Paths, Cancer of the Breast, MCF7 cell, Path, CA - Carcinoma of breast, Gene Silencings, L Tyrosine, Stable, Tyr, signaling process, has or lacks parts of type, Role Concepts, Isotope-Coded Affinity Tagging, Carcinoma of breast (disorder), Tyrosin, associated, Tagging, Breast, ATP Phosphotransferases, Stable Isotope Labeling, ATP, single organism signaling, MCF 7 cell, MCF-7 cell, Tumors, Cancer, Human Mammary Neoplasm, Carcinoma, RNA, data, Pathway, wide/broad, Malignant Neoplasm, Critical, Cancer., Aminokarbonsaeure, Proteins, 2-Amino-3-(p-hydroxyphenyl)propionic acid, posttranscriptional gene silencing by siRNA, Systematics, extra or missing physical or functional parts, function, para-Tyrosine, Labeling, Cell, Phosphotransferases, Tyrosine, Concept, mereological quality, RNAi, polypeptide, Isotope, Taxonomies, count in organism, Interference, Role Concept, count, Clinical Pathway, tirosina, Mammary Carcinomas, Stable Isotope, chemical analysis, Protein, Neoplasm, Role, Human Mammary Carcinoma, Sik, RNA Silencing, Mammary carcinoma, Silencing, Isotope Coded Affinity Tagging, Post-Transcriptional Gene, Post-Transcriptional Gene Silencings, Carcinomas, Transphosphorylases, Breast Neoplasm, distinct, Posttranscriptional, NEOPL BREAST, Kinases, Posttranscriptional Gene Silencing, carcinoma OF breast, L-isomer, Cancers, C9H11NO3, Isotope Labeling, Amino, Co Suppression, Affinity Tagging, Isotopically-Coded, malignant tumor, tks, signalling, Post Transcriptional Gene Silencing, L isomer, Protein Gene Products, Gene Proteins, MCF7, wide, Post-Transcriptional, Gene Silencing, signalling process, Breast Tumors, Breast Cancer, cardinality, Isotope-Coded, Cancer of Breast, L-Tyrosine, Acids, assay, quantitative, Co-Suppression, Post-Transcriptional Gene Silencing, BRK, Proteomes, presence or absence in organism</pubmed_abstract_synonyms><view_count>29</view_count><citation_count>0</citation_count><search_count>5</search_count><full_dataset_link>http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016092</full_dataset_link><search_domains>dbgap_ncbi~0</search_domains><search_domains>patentfamilies~0</search_domains><search_domains>rfam~0</search_domains><search_domains>merops~0</search_domains><search_domains>complex-portal~0</search_domains><search_domains>uniprot~0</search_domains><search_domains>wormbaseparasite~0</search_domains><search_domains>embl-covid19~0</search_domains><search_domains>reactome~0</search_domains><search_domains>emdb~0</search_domains><search_domains>wgs_masters~0</search_domains><search_domains>ebiweb_resources~0</search_domains><search_domains>opentargets_genetics~0</search_domains><search_domains>biomodels_all~0</search_domains><search_domains>ipd-mhc~0</search_domains><search_domains>ebiweb_teams~0</search_domains><search_domains>taxonomy~0</search_domains><search_domains>genome_assembly~0</search_domains><search_domains>sc-experiments~0</search_domains><search_domains>ebiweb_people~0</search_domains><search_domains>enzymeportal_enzymes~0</search_domains><search_domains>ipd-nhkir~0</search_domains><search_domains>cellosaurus~0</search_domains><search_domains>pdbe~0</search_domains><search_domains>chebi~0</search_domains><search_domains>patentproteins~0</search_domains><search_domains>interpro7~0</search_domains><search_domains>uniref~0</search_domains><search_domains>chembl~0</search_domains><search_domains>pdbekb~0</search_domains><search_domains>gpcrdb~0</search_domains><search_domains>hgnc~0</search_domains><search_domains>sc-genes~0</search_domains><search_domains>intact~0</search_domains><search_domains>rhea~0</search_domains><search_domains>ebiweb_training~0</search_domains><search_domains>alphafold~0</search_domains><search_domains>imgt-hla~0</search_domains><search_domains>patentnucleotides~0</search_domains><search_domains>ensemblroot~0</search_domains><search_domains>eva_studies~0</search_domains><search_domains>non-coding~0</search_domains><search_domains>europepmc~0</search_domains><search_domains>pubmed~1</search_domains><search_domains>identifiers_registry~0</search_domains><search_domains>pdbechem~0</search_domains><search_domains>hpa-covid19~0</search_domains><search_domains>eva-variants-covid19~0</search_domains><search_domains>biosamples~0</search_domains><search_domains>gwas_catalog~0</search_domains><search_domains>biotools~0</search_domains><search_domains>tls_masters~0</search_domains><search_domains>mesh~0</search_domains><search_domains>coding~0</search_domains><search_domains>sra~0</search_domains><search_domains>opentargets~0</search_domains><search_domains>efo~0</search_domains><search_domains>embl-pathogen~0</search_domains><search_domains>project~0</search_domains><search_domains>pride~1</search_domains><search_domains>human_diseases~0</search_domains><search_domains>geo_datasets~0</search_domains><search_domains>embl~0</search_domains><search_domains>treefam~0</search_domains><search_domains>uniparc~0</search_domains><search_domains>ols~0</search_domains><search_domains>dgva~0</search_domains><search_domains>intenz~0</search_domains><search_domains>go~0</search_domains><search_domains>tsa_masters~0</search_domains><search_domains>biosamples-covid19~0</search_domains><search_domains>ebiweb_corporate~0</search_domains><search_domains>omim~0</search_domains><search_domains>lrg~0</search_domains><search_domains>earlycause-molecular-sequences~0</search_domains><search_domains>ipd-kir~0</search_domains><search_domains>empiar~0</search_domains><search_domains>rnacentral~0</search_domains><search_domains>orcid_data_claims~0</search_domains><search_domains>gpmdb~2</search_domains><search_domains>lineage-covid19~0</search_domains><search_domains>metagenomics~0</search_domains><search_domains>pfam~0</search_domains><search_domains>pride archive~1</search_domains><search_domains>varsite~0</search_domains><reanalysis_count>0</reanalysis_count><submitter_keywords>Resource Reanalysis</submitter_keywords><citation_count_scaled>0.0</citation_count_scaled><reanalysis_count_scaled>0.0</reanalysis_count_scaled><view_count_scaled>0.008945095619987662</view_count_scaled><download_count_scaled>0.0</download_count_scaled><normalized_connections>1.0</normalized_connections></additional><is_claimable>false</is_claimable><name>Reprogramming of the tyrosine kinase-regulated proteome in breast cancer by combined use of RNAi and SILAC quantitative proteomics</name><description>Data from ProteomeXchange, PXD ID: PXD002065. File: GS-45.mzml. Published as part of Mol Cell Proteomics. 2015 Jun 18  . From the Abstract: {{i}} ... Tyrosine kinases (TKs) are central regulators in cellular activities and perturbations of TK signaling contribute to oncogenesis. However, less than half of the TKs have been thoroughly studied and a global functional analysis of their proteomic portrait is lacking. Here we conducted a combined approach of RNAi and stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics to decode the TK-regulated proteome and associated signaling dynamics ... {{/i}}</description><dates><submission>2015-06-27</submission></dates><accession>GPM32320016092</accession><cross_references><pubmed>26089344</pubmed><Pride>PXD002065</Pride><Pride Archive>PXD002065</Pride Archive></cross_references></HashMap>