{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["9606"],"full_dataset_link":["https://pax-db.org/dataset/9606/84271349"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["Global 'multi-omics' profiling of cancer cells harbours the potential for characterizing the signalling networks associated with specific oncogenes. Here we profile the transcriptome, proteome and phosphoproteome in a panel of non-small cell lung cancer (NSCLC) cell lines in order to reconstruct targetable networks associated with KRAS dependency. We develop a two-step bioinformatics strategy addressing the challenge of integrating these disparate data sets. We first define an 'abundance-score' combining transcript, protein and phospho-protein abundances to nominate differentially abundant proteins and then use the Prize Collecting Steiner Tree algorithm to identify functional sub-networks. We identify three modules centred on KRAS and MET, LCK and PAK1 and β-Catenin. We validate activation of these proteins in KRAS-dependent (KRAS-Dep) cells and perform functional studies defining LCK as a critical gene for cell proliferation in KRAS-Dep but not KRAS-independent NSCLCs. These results suggest that LCK is a potential druggable target protein in KRAS-Dep lung cancers."],"pubmed_title":["Reconstructing targetable pathways in lung cancer by integrating diverse omics data."],"pubmed_authors":["Balbin O Alejandro OA, Prensner John R JR, Sahu Anirban A, Yocum Anastasia A, Shankar Sunita S, Malik Rohit R, Fermin Damian D, Dhanasekaran Saravana M SM, Chandler Benjamin B, Thomas Dafydd D, Beer David G DG, Cao Xuhong X, Nesvizhskii Alexey I AI, Chinnaiyan Arul M AM"],"data_synonyms":["Add, 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, ratio"],"pubmed_title_synonyms":["Lung Cancer, Pulmonary Neoplasms, Lung cancer, Lung, Pulmonary Neoplasm, alveolar cell carcinoma, Neoplasms, lung cancer, LNCR, Cancer of Lung, Lung Cancers, Cancers, Lung Neoplasm, cancer of lung, data., cancer of the lung, Neoplasm, Nonsmall cell lung cancer, protection against, NOS, Pulmonary Cancers, lung neoplasm, Cancer of the Lung, Pulmonary Cancer, Pulmonary, Cancer"],"name_synonyms":["NAT, Nat, Fsrg1., D6S113E, 11alpha, D17H6S113E, alpha-L-Talopyranuronic acid, TalANAc, RNF3, Rnf3, Frg-1, Cell Lines, alpha-L-N-acetyltalosaminuronic acid, Ring3, 15S)-, 2-(acetylamino)-2-deoxy-, FSH, Cell, 13E, RING3, AW228947, (5Z, FSRG1, Line, mKIAA4005, Fsrg-1, alpha-L-2-N-acetylamino-2-desoxytaluronic acid, Lines"],"pubmed_abstract_synonyms":["Panomics, E 920, Materials, Hgfr, F730027O18Rik, Gene Expression Profile, Non-Small Cell Lung Cancer, 5730555F13Rik, Profiles, protein, Tumor, Cell Growth in Number, SUB, dmTAF[[II]]230, Lung Carcinomas, protein polypeptide chains, ras, DmelCG12298, HGFR, p56-lt-lck-gt-, GRP1, Grp1, Non-Small-Cell Lung Carcinoma, Cell Number Growth, SCRAMBLED, Transforming, 2-amino-3-mercaptopropanoic acid, Cystein, Non-Small Cell Lung Carcinoma, protein aggregate, C-K-RAS, k-ras, KIF20A, rask2, C, Lung Cancer, Growth, TFIID TAF250, cel, MUB3_18, cisteina, M, PTPSTEP, Non-Small Cell Lung, proteins, Lung Cancers, MUB3.18, CG10295, Non Small Cell Lung Carcinoma, PaK, Signatures, Transforming Genes, malignant neoplasm, Expression Signature, signaling process, l(2)k08110, Transcriptomes, Hck-3, Malignancies, RG7MT1, Racemethionine, PAK, single organism signaling, GPH, Tumors, Carcinoma, p65[PAK], dTAF[[II]]230, proto-oncogene c-Met, Ki-ras, PRO, dpak1, pp58lck, Expression Profiles, STRUBBELIG, 2-Amino-4-(methylthio)butyric acid, TAF200, Cancer of Lung, PRKCL1, TAFII-250, TAF250/230, 9130215G10Rik, pak, INSDC_feature:misc_RNA, CYS, Cys, results, non-small cell lung cancer, Gene Expression, D-Pak, TAFII250, Benign, YT16, Expression Signatures, Algorithm, p21, 3.1.3.48, Genetic Materials, Cellular, Methionin, Hmet, (2R)-2-amino-3-sulfanylpropanoic acid, Expression Profile, non-small cell lung carcinoma (disease), and GLY protein 2, activation, Genetic Material, Transcriptome Profiles, Carcinomas, HGF receptor, HGF/SF receptor, Multi Omics, and GLY protein 1, Step, CG11628, Integrative, PAK1, Pak1, Benign Neoplasms, Striatum-enriched protein-tyrosine phosphatase, INSDC_feature:gene, hCMT1c, Lck1, CG17603, c-Met, TAF[[II]], PAK2, Non Small Cell Lung, L-Cystein, Malignant Neoplasms, non-small cell carcinoma of lung, pak1, pakalpha, Oncogene, Taf250, RASK2, Dpak1, STEP, Material, SR3-5, Proliferation, PRK1, Lsk-t, Cell Number, Cistron, Cancer of the Lung, Proteomes, TAF230, dPAK1, KI-RAS, p56lck, AT1G11140, Paka, biological signaling, d230, Lung, 2-amino-4-(methylsulfanyl)butanoic acid, orb2, GRP1/cytohesin 1, Transcriptome Profile, non-small cell lung carcinoma, Neoplasms, DmPAK1, Kras2, NS3, Benign Neoplasm, L-Zystein, Gene, dTAFII250, Non-Small-Cell Lung, non-small cell carcinoma of the lung, PAK-1, protein-containing complex, Malignant, EfW1, CG12298, p56Lck, Multi-Omics, CG11633, non-small cell cancer of the lung, cytohesin/GRP1, HGF, polypeptide chain, Lung., dmTAF1, Taf230, Gene Products, Kras-2, F15E12.6, AW045634, NSCLC - non-small cell lung cancer, RCCP2, Number Growth, Pulmonary Cancer, KRAS2, Pulmonary, TAF250, KRAS1, p21B, Prkcl1, Taf200, F15E12_6, dTAF[[II]]250, Transforming Gene, 1-(2-(dodecyloxy)ethyl)pyrrolidine.HCl, Genetic, Malignancy, cell, scatter factor receptor, Profile, mei-1794, E-920, Stk3, K-RAS4B, K-RAS4A, l(2)SH2 0323, Taf1p, Omics, Hcys, Lung Carcinoma, AUTS9, Neoplasias, dTAF250, NSCLC, cell proliferation, p56<lck>, Neural-specific protein-tyrosine phosphatase, 2-amino-4-(methylthio)butanoic acid, Lung Neoplasm, CYSTEINE, DmelCG10295, Nonsmall Cell Lung Cancer, FREE CYSTEINE, Pan-Omics, SRF9, Lskt, AI838057, (2R)-2-amino-3-mercaptopropanoic acid, TAF, metionina, Non-Small-Cell Lung Carcinomas, PAKalpha, Cancer, Multiplication, data, TAF[[II]]250, X-PAK1, Pulmonary Neoplasms, Integrative-Omics, Transcriptome, Cellular Proliferation, Malignant Neoplasm, DL-Methionine, protein complex, DBK, K-RAS2B, K-RAS2A, Proteins, total expressed protein, l(3)84Ab, K-ras, stepk, DPAK, DPak, BG:DS00004.13, c-Ki-ras, Tree, dpak, Integrative Omics, Cistrons, Cell, dTAF230, whole transcriptome, STRUBBELIG-RECEPTOR FAMILY 9, LSK, Lsk, PKN-ALPHA, MT, native protein, natural protein, p230, Gene Expression Signatures, Protein, Multi-Omic, Neoplasm, Pan Omics, TAF[[II]]250/230, TFIID, PKN, Pkn, XPak1, Gene Expression Signature, Non-small cell lung cancer, AI929937, dPak, dPAK, l(2)SH0323, Zystein, Met, MET, ATCMPG1, ATCMPG2, CYH1, Taf[[II]]250, primary cancer, NS, Genes, TAF[[II]]230, IMD22, 2-amino-3-sulfanylpropanoic acid, Pulmonary Neoplasm, tyrosine-protein kinase Met, Dub, L-2-Amino-3-mercaptopropionic acid, TAF[II]250, (R)-2-amino-3-mercaptopropanoic acid, Cancers, malignant tumor, 2-Amino-3-mercaptopropionic acid, signalling, DmelCG11628, Protein Gene Products, Gene Proteins, DmelCG17603, signalling process, pak-1, Gene Expression Profiles, kras, CFC2, DEP, Cell Multiplication, alpha-amino-gamma-methylmercaptobutyric acid, E920, Lcktkr, Pulmonary Cancers, Par4, Dpak, Signature, non-small cell cancer of lung, T19D16.8, 5730455C01Rik, Neoplasia, SCM, SF receptor, Non-Small-Cell, 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