{"database":"GPMDB","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":42,"searchCount":5},"additional":{"omics_type":["Other"],"submitter":["Deeb SJ, et al."],"instrument_platform":["Instrument"],"disease":["Not Available"],"brenda_tissue":["Not available"],"species":["Homo_sapiens_viruses, Human"],"submitter_mail":["mmann@biochem.mpg.de"],"publication":["26311899"],"model":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017943","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017936","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017929","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017964","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017950"],"submitter_affiliation":["Max-Planck Institute of Biochemistry, et al."],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_abstract":["Characterization of tumors at the molecular level has improved our knowledge of cancer causation and progression. Proteomic analysis of their signaling pathways promises to enhance our understanding of cancer aberrations at the functional level, but this requires accurate and robust tools. Here, we develop a state of the art quantitative mass spectrometric pipeline to characterize formalin-fixed paraffin-embedded tissues of patients with closely related subtypes of diffuse large B-cell lymphoma. We combined a super-SILAC approach with label-free quantification (hybrid LFQ) to address situations where the protein is absent in the super-SILAC standard but present in the patient samples. Shotgun proteomic analysis on a quadrupole Orbitrap quantified almost 9,000 tumor proteins in 20 patients. The quantitative accuracy of our approach allowed the segregation of diffuse large B-cell lymphoma patients according to their cell of origin using both their global protein expression patterns and the 55-protein signature obtained previously from patient-derived cell lines (Deeb, S. J., D'Souza, R. C., Cox, J., Schmidt-Supprian, M., and Mann, M. (2012) Mol. Cell. Proteomics 11, 77-89). Expression levels of individual segregation-driving proteins as well as categories such as extracellular matrix proteins behaved consistently with known trends between the subtypes. We used machine learning (support vector machines) to extract candidate proteins with the highest segregating power. A panel of four proteins (PALD1, MME, TNFAIP8, and TBC1D4) is predicted to classify patients with low error rates. Highly ranked proteins from the support vector analysis revealed differential expression of core signaling molecules between the subtypes, elucidating aspects of their pathobiology."],"pubmed_title":["Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles."],"pubmed_authors":["Deeb Sally J SJ,Tyanova Stefka S,Hummel Michael M,Schmidt-Supprian Marc M,Cox Juergen J,Mann Matthias M,","Deeb Sally J SJ, Tyanova Stefka S, Hummel Michael M, Schmidt-Supprian Marc M, Cox Juergen J, Mann Matthias M"],"name_synonyms":["Histiocytic Lymphoma, DLBCL, Taxonomy, taxonomy, Histiocytic, Machine, Large-Cell Lymphomas, Learning, Systematics, LYMPHOMA LARGE DIFFUSE, DIFFUSE LARGE LYMPHOMA, LARGE LYMPHOMA DIFFUSE, Client, Diffuse, Diffuse Large-Cell, Classifications, polypeptide, Taxonomies, Large-Cell, Large Cell Lymphoma, Diffuse Histiocytic Lymphomas, proteins., Diffuse Large Cell Lymphoma, hierarchies, hierarchy, Large Lymphoid Lymphoma, Histiocytic Lymphomas, Patient, Large B-Cell, systematics, LARGE LYMPHOMA, LYMPHOMA LARGE, Clients, Lymphoma, Diffuse Histiocytic Lymphoma, Diffuse Large-Cell Lymphomas, large B-cell lymphoma, Large Cell, Diffuse Large Cell, Lymphomas, LYMPHOMA DIFFUSE LARGE, Diffuse Large-Cell Lymphoma, Large Lymphoid, Diffuse Histiocytic, Large-Cell Lymphoma"],"description_synonyms":["[H]C([H])=O, data, Formol, InChIKey=WSFSSNUMVMOOMR-UHFFFAOYAT, mol, Arts, Large-Cell Lymphomas, number, FBN, DIFFUSE LARGE LYMPHOMA, 9930121L06Rik, LARGE LYMPHOMA DIFFUSE, presence, Client, Cell, CH2O, ACMICD, polypeptide, count in organism, Experiment, count, Large Lymphoid Lymphoma, ECTOL1, Large B-Cell, LARGE LYMPHOMA, LYMPHOMA LARGE, Methanal, Parafilm, MFS1, FORMALIN, large B-cell lymphoma, Large Cell, Diffuse Large Cell, fixed, Lymphomas, WMS, Diffuse Large-Cell Lymphoma, WMS2, Large-Cell Lymphoma, AI661365, Art, Histiocytic Lymphoma, DLBCL, absence, Histiocytic, cell, absent from organism, Formaldehyd, Tissue, Oxomethane, LYMPHOMA LARGE DIFFUSE, proteins, present in organism, MASS, free, Methylene oxide, OCTD, InChI=1/CH2O/c1-2/h1H2, Diffuse, patient., Diffuse Large-Cell, Large-Cell, Large Cell Lymphoma, Diffuse Histiocytic Lymphomas, Diffuse Large Cell Lymphoma, Snm1l, Formalin, Oxomethylene, Patient, Histiocytic Lymphomas, Clients, Lymphoma, Diffuse Histiocytic Lymphoma, SSKS, Diffuse Large-Cell Lymphomas, quantitative, GPHYSD2, LYMPHOMA DIFFUSE LARGE, Large Lymphoid, Diffuse Histiocytic, SGS, presence or absence in organism"],"pubmed_title_synonyms":["Histiocytic Lymphoma, DLBCL, Taxonomy, taxonomy, Histiocytic, Machine, Large-Cell Lymphomas, Learning, Systematics, LYMPHOMA LARGE DIFFUSE, DIFFUSE LARGE LYMPHOMA, LARGE LYMPHOMA DIFFUSE, Client, Diffuse, Diffuse Large-Cell, Classifications, polypeptide, Taxonomies, Large-Cell, Large Cell Lymphoma, Diffuse Histiocytic Lymphomas, proteins., Diffuse Large Cell Lymphoma, hierarchies, hierarchy, Large Lymphoid Lymphoma, Histiocytic Lymphomas, Patient, Large B-Cell, systematics, LARGE LYMPHOMA, LYMPHOMA LARGE, Clients, Lymphoma, Diffuse Histiocytic Lymphoma, Diffuse Large-Cell Lymphomas, large B-cell lymphoma, Large Cell, Diffuse Large Cell, Lymphomas, LYMPHOMA DIFFUSE LARGE, Diffuse Large-Cell Lymphoma, Large Lymphoid, Diffuse Histiocytic, Large-Cell Lymphoma"],"pubmed_abstract_synonyms":["[H]C([H])=O, Formol, 2abeta, determination, neutral endopeptidase, C85356, Tumor, extracted material, Readability, Methanal, Parafilm, Line, 1, 2, 3, 4, 5, 6, 7, 8, 9, Lymphomas, WMS, AI661365, Art, Histiocytic Lymphoma, me75, A930035N22, COXIV, Machine, 7aalpha)-, Formaldehyd, Tissue, Oxomethane, SFE, cell line cell, proteins, present in organism, free, D17Mit170, cell line, T1, CD10, InChI=1/CH2O/c1-2/h1H2, 7-epoxy-1, Large Cell Lymphoma, forecasting, Cox4, atriopeptidase, signaling process, CALLA, 2a, neutral endopeptidase 24.11, 1.3.3.3, GPHYSD2, COX-VA, single organism signaling, SGS, Tumors, GG2-1, AS160, KIAA1274, AV295684, Arts, Learning, Tl3, Tl2, tumours, predicted, ACMICD, MME, count, VA, LARGE LYMPHOMA, LYMPHOMA LARGE, AL024441, 4a, Diffuse Large Cell, fixed, MMPAL, Large-Cell Lymphoma, Lines, Epistemology, absence, Coprogen oxidase, COX IV-1, As160, MASS, Diffuse Large-Cell, 8a-hexahydro-6- methyl-6, Matrix Proteins, Patient, 6a, Lymphoma, 6abeta, NDED, 6-Methanonaphth(2, Diffuse Histiocytic, Cox4a, EPN, biological signaling, InChIKey=WSFSSNUMVMOOMR-UHFFFAOYAT, 6030454K05Rik, mol, PALD, enkephalinase, Neoplasms, nucleocapsid, number, FBN, Gene, DIFFUSE LARGE LYMPHOMA, 9930121L06Rik, LARGE LYMPHOMA DIFFUSE, presence, NEOPL, Large Lymphoid Lymphoma, SCC-S2, ECTOL1, Gene Products, 8-hexachloro-1a, Low, malignant tumour, DLBCL, Coproporphyrinogenase, 6alpha, cell, absent from organism, malignant neoplasia, tumour, OCTD, Diffuse, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), Large-Cell, Diffuse Large Cell Lymphoma, 9-hexachloro-1, Formalin, Histiocytic Lymphomas, Clients, Pald, COX, Extracellular, mKIAA1274, Diffuse Large-Cell Lymphomas, NEP, Nep, LYMPHOMA DIFFUSE LARGE, Neoplastic Growth, NIDDM5, single organism signaling., Cancer, Malignant Neoplasm, cou, 5930406J04Rik, Large-Cell Lymphomas, Proteins, Cell Lines, cell_line, MDC-3.13, 3-b)oxirene, 3alpha, Client, CH2O, Cell, futurology, polypeptide, count in organism, Lr, Large B-Cell, Protein, chemical analysis, proteomic analysis, core, MFS1, FORMALIN, IV-1, large B-cell lymphoma, (1aalpha, Large Cell, Diffuse Large-Cell Lymphoma, WMS2, SCCS2, Histiocytic, 4-methanonaphthalene, LYMPHOMA LARGE DIFFUSE, patient, Cancers, Understanding, malignant tumor, Methylene oxide, signalling, Protein Gene Products, Gene Proteins, Diffuse Histiocytic Lymphomas, 7a-octahydro-1a-methyl-, Extracellular Matrix, signalling process, Snm1l, Oxomethylene, Diffuse Histiocytic Lymphoma, SSKS, Bra, common acute lymphocytic leukemia antigen, assay, quantitative, NEOPLASMS BENIGN, Neoplasia, Large Lymphoid, presence or absence in 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Experiment: TRR37, file: folder summary. Published as part of Mol Cell Proteomics. 2015 Aug 26  . From the Abstract: {{i}} ... Here, we develop a state of the art quantitative mass spectrometric pipeline to characterize formalin-fixed paraffin-embedded (FFPE) tissues of patients with closely related subtypes of diffuse large B-cell lymphoma (DLBCL). We combined a super-SILAC approach with label-free quantification (hybrid LFQ), to address situations where the protein is absent in the super-SILAC standard yet present in the patient samples ... {{/i}}","dates":{"submission":"2015-09-11"},"accession":"GPM32320017943","cross_references":{"pubmed":["26311899"],"Pride":["PXD002052"],"pride":[],"Pride Archive":["PXD002052"]}}