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Volumn 2016, Issue , 2016, Pages

Genic insights from integrated human proteomics in GeneCards

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; RNA;

EID: 85052189463     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/baw030     Document Type: Article
Times cited : (134)

References (53)
  • 1
    • 84874232489 scopus 로고    scopus 로고
    • The coming age of complete, accurate, and ubiquitous proteomes
    • Mann, M., Kulak, N. A., Nagaraj, N. et al. (2013) The coming age of complete, accurate, and ubiquitous proteomes. Mol. Cell, 49, 583-590.
    • (2013) Mol. Cell , vol.49 , pp. 583-590
    • Mann, M.1    Kulak, N.A.2    Nagaraj, N.3
  • 2
    • 79960179572 scopus 로고    scopus 로고
    • The human proteome project: Current state and future direction
    • Legrain, P., Aebersold, R., Archakov, A. et al. (2011) The human proteome project: current state and future direction. Mol. Cell Proteomics, 10, M111 009993.
    • (2011) Mol. Cell Proteomics , vol.10 , pp. M111009993
    • Legrain, P.1    Aebersold, R.2    Archakov, A.3
  • 3
    • 84863229647 scopus 로고    scopus 로고
    • The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome
    • Paik, Y. K., Jeong, S. K., Omenn, G. S. et al. (2012) The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat. Biotechnol., 30, 221-223.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 221-223
    • Paik, Y.K.1    Jeong, S.K.2    Omenn, G.S.3
  • 4
    • 84901599553 scopus 로고    scopus 로고
    • A draft map of the human proteome
    • Kim, M. S., Pinto, S. M., Getnet, D. et al. (2014) A draft map of the human proteome. Nature, 509, 575-581.
    • (2014) Nature , vol.509 , pp. 575-581
    • Kim, M.S.1    Pinto, S.M.2    Getnet, D.3
  • 5
    • 84901611036 scopus 로고    scopus 로고
    • Mass-spectrometry-based draft of the human proteome
    • Wilhelm, M., Schlegl, J., Hahne, H. et al. (2014) Mass-spectrometry-based draft of the human proteome. Nature, 509, 582-587.
    • (2014) Nature , vol.509 , pp. 582-587
    • Wilhelm, M.1    Schlegl, J.2    Hahne, H.3
  • 6
    • 84907958189 scopus 로고    scopus 로고
    • Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive resources for discovery and targeted proteomics
    • Kusebauch, U., Deutsch, E. W., Campbell, D. S. et al. (2014) Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Curr. Protoc. Bioinformatics, 46, 13 25 1-13 25 28.
    • (2014) Curr. Protoc. Bioinformatics , vol.46 , pp. 13251-132528
    • Kusebauch, U.1    Deutsch, E.W.2    Campbell, D.S.3
  • 7
    • 84874762979 scopus 로고    scopus 로고
    • The PRoteomics IDEntifications (PRIDE) database and associated tools: Status in 2013
    • Vizcaino, J. A., Cote, R. G., Csordas, A. et al. (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res., 41, D1063-D1069.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D1063-D1069
    • Vizcaino, J.A.1    Cote, R.G.2    Csordas, A.3
  • 8
    • 84941042092 scopus 로고    scopus 로고
    • Beyond protein expression, MOPED goes multi-omics
    • Montague, E., Janko, I., Stanberry, L. et al. (2015) Beyond protein expression, MOPED goes multi-omics. Nucleic Acids Res., 43, D1145-D1151.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D1145-D1151
    • Montague, E.1    Janko, I.2    Stanberry, L.3
  • 9
    • 84864817904 scopus 로고    scopus 로고
    • PaxDb, a database of protein abundance averages across all three domains of life
    • Wang, M., Weiss, M., Simonovic, M. et al. (2012) PaxDb, a database of protein abundance averages across all three domains of life. Mol. Cell Proteomics, 11, 492-500.
    • (2012) Mol. Cell Proteomics , vol.11 , pp. 492-500
    • Wang, M.1    Weiss, M.2    Simonovic, M.3
  • 10
    • 84857980282 scopus 로고    scopus 로고
    • Analysis of high accuracy, quantitative proteomics data in the MaxQB database
    • Schaab, C., Geiger, T., Stoehr, G. et al. (2012) Analysis of high accuracy, quantitative proteomics data in the MaxQB database. Mol. Cell Proteomics, 11, M111 014068.
    • (2012) Mol. Cell Proteomics , vol.11 , pp. M111014068
    • Schaab, C.1    Geiger, T.2    Stoehr, G.3
  • 11
    • 78049480691 scopus 로고    scopus 로고
    • GeneCards Version 3: The human gene integrator
    • Safran, M., Dalah, I., Alexander, J. et al. (2010) GeneCards Version 3: the human gene integrator. Database (Oxford), 2010, baq020.
    • (2010) Database (Oxford) , vol.2010 , pp. baq020
    • Safran, M.1    Dalah, I.2    Alexander, J.3
  • 12
    • 84985000589 scopus 로고    scopus 로고
    • PathCards: Multisource consolidation of human biological pathways
    • 2015
    • Belinky, F., Nativ, N., Stelzer, G. et al. (2015) PathCards: multisource consolidation of human biological pathways. Database (Oxford), 2015
    • (2015) Database (Oxford)
    • Belinky, F.1    Nativ, N.2    Stelzer, G.3
  • 13
    • 84876569934 scopus 로고    scopus 로고
    • The TissueNet database of human tissue protein-protein interactions
    • Barshir, R., Basha, O., Eluk, A. et al. (2013) The TissueNet database of human tissue protein-protein interactions. Nucleic Acids Res., 41, D841-D844.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D841-D844
    • Barshir, R.1    Basha, O.2    Eluk, A.3
  • 14
    • 84941028211 scopus 로고    scopus 로고
    • COXPRESdb in 2015: Coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems
    • Okamura, Y., Aoki, Y., Obayashi, T. et al. (2015) COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems. Nucleic Acids Res., 43, D82-D86.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D82-D86
    • Okamura, Y.1    Aoki, Y.2    Obayashi, T.3
  • 15
    • 84920269464 scopus 로고    scopus 로고
    • Proteomics. Tissue-based map of the human proteome
    • Uhlen, M., Fagerberg, L., Hallstrom, B. M. et al. (2015) Proteomics. Tissue-based map of the human proteome. Science, 347, 1260419.
    • (2015) Science , vol.347 , pp. 1260419
    • Uhlen, M.1    Fagerberg, L.2    Hallstrom, B.M.3
  • 16
    • 84884416048 scopus 로고    scopus 로고
    • Human housekeeping genes, revisited
    • Eisenberg, E. and Levanon, E. Y. (2013) Human housekeeping genes, revisited. Trends Genet., 29, 569-574.
    • (2013) Trends Genet. , vol.29 , pp. 569-574
    • Eisenberg, E.1    Levanon, E.Y.2
  • 17
    • 79960819723 scopus 로고    scopus 로고
    • Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis
    • Chang, C. W., Cheng, W. C., Chen, C. R. et al. (2011) Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis. PLoS One, 6, e22859.
    • (2011) PLoS One , vol.6 , pp. e22859
    • Chang, C.W.1    Cheng, W.C.2    Chen, C.R.3
  • 18
    • 84941051170 scopus 로고    scopus 로고
    • STRING v10: Protein-protein interaction networks, integrated over the tree of life
    • Szklarczyk, D., Franceschini, A., Wyder, S. et al. (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res., 43, D447-D452.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D447-D452
    • Szklarczyk, D.1    Franceschini, A.2    Wyder, S.3
  • 19
    • 72949089708 scopus 로고    scopus 로고
    • Global signatures of protein and mRNA expression levels
    • de Sousa Abreu, R., Penalva, L. O., Marcotte, E. M. et al. (2009) Global signatures of protein and mRNA expression levels. Mol. Biosyst., 5, 1512-1526.
    • (2009) Mol. Biosyst. , vol.5 , pp. 1512-1526
    • De Sousa Abreu, R.1    Penalva, L.O.2    Marcotte, E.M.3
  • 20
    • 84858439862 scopus 로고    scopus 로고
    • Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
    • Vogel, C. and Marcotte, E. M. (2012) Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet., 13, 227-232.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 227-232
    • Vogel, C.1    Marcotte, E.M.2
  • 21
    • 84941799987 scopus 로고    scopus 로고
    • Next-generation analysis of gene expression regulation - Comparing the roles of synthesis and degradation
    • McManus, J., Cheng, Z. and Vogel, C. (2015) Next-generation analysis of gene expression regulation - comparing the roles of synthesis and degradation. Mol. Biosyst., 11, 2680-2689.
    • (2015) Mol. Biosyst. , vol.11 , pp. 2680-2689
    • McManus, J.1    Cheng, Z.2    Vogel, C.3
  • 22
    • 79956322553 scopus 로고    scopus 로고
    • Global quantification of mammalian gene expression control
    • Schwanhausser, B., Busse, D., Li, N. et al. (2011) Global quantification of mammalian gene expression control. Nature, 473, 337-342.
    • (2011) Nature , vol.473 , pp. 337-342
    • Schwanhausser, B.1    Busse, D.2    Li, N.3
  • 23
    • 84874541273 scopus 로고    scopus 로고
    • In silico estimation of translation efficiency in human cell lines: Potential evidence for widespread translational control
    • Stevens, S. G. and Brown, C. M. (2013) In silico estimation of translation efficiency in human cell lines: potential evidence for widespread translational control. PLoS One, 8, e57625.
    • (2013) PLoS One , vol.8 , pp. e57625
    • Stevens, S.G.1    Brown, C.M.2
  • 25
    • 84891783174 scopus 로고    scopus 로고
    • Activities at the universal protein resource (UniProt)
    • UniProt, C. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-D198.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D191-D198
    • UniProt, C.1
  • 26
    • 84878682420 scopus 로고    scopus 로고
    • The genotype-tissue expression (GTEx) project
    • GTEx Consortium. (2013) The Genotype-Tissue Expression (GTEx) project. Nat. Genet., 45, 580-585.
    • (2013) Nat. Genet. , vol.45 , pp. 580-585
    • GTEx Consortium1
  • 27
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love, M. I., Huber, W. and Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 550.
    • (2014) Genome Biol. , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 28
    • 84929015296 scopus 로고    scopus 로고
    • Human genomics. The human transcriptome across tissues and individuals
    • Mele, M., Ferreira, P. G., Reverter, F. et al. (2015) Human genomics. The human transcriptome across tissues and individuals. Science, 348, 660-665.
    • (2015) Science , vol.348 , pp. 660-665
    • Mele, M.1    Ferreira, P.G.2    Reverter, F.3
  • 29
    • 84887620404 scopus 로고    scopus 로고
    • What is the total number of protein molecules per cell volume? A call to rethink some published values
    • Milo, R. (2013) What is the total number of protein molecules per cell volume? A call to rethink some published values. Bioessays, 35, 1050-1055.
    • (2013) Bioessays , vol.35 , pp. 1050-1055
    • Milo, R.1
  • 30
    • 84899633396 scopus 로고    scopus 로고
    • Defining functional DNA elements in the human genome
    • Kellis, M., Wold, B., Snyder, M. P. et al. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. U S A., 111, 6131-6138.
    • (2014) Proc. Natl. Acad. Sci. U S A. , vol.111 , pp. 6131-6138
    • Kellis, M.1    Wold, B.2    Snyder, M.P.3
  • 31
    • 84901788541 scopus 로고    scopus 로고
    • COMPARTMENTS: Unification and visualization of protein subcellular localization evidence
    • Binder, J. X., Pletscher-Frankild, S., Tsafou, K. et al. (2014) COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database (Oxford), 2014, bau012.
    • (2014) Database (Oxford) , vol.2014 , pp. bau012
    • Binder, J.X.1    Pletscher-Frankild, S.2    Tsafou, K.3
  • 32
    • 84937919422 scopus 로고    scopus 로고
    • MalaCards: A comprehensive automatically-mined database of human diseases
    • Rappaport, N., Twik, M., Nativ, N. et al. (2014) MalaCards: a comprehensive automatically-mined database of human diseases. Curr. Protoc. Bioinformatics, 47, 1 24 1-1 24 19.
    • (2014) Curr. Protoc. Bioinformatics , vol.47 , pp. 1241-12419
    • Rappaport, N.1    Twik, M.2    Nativ, N.3
  • 33
    • 71849119227 scopus 로고    scopus 로고
    • GeneDecks: Paralog hunting and gene-set distillation with GeneCards annotation
    • Stelzer, G., Inger, A., Olender, T. et al. (2009) GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation. Omics, 13, 477-487.
    • (2009) Omics , vol.13 , pp. 477-487
    • Stelzer, G.1    Inger, A.2    Olender, T.3
  • 34
    • 84964907479 scopus 로고    scopus 로고
    • GeneAnalytics: An integrative gene set analysis tool
    • in press
    • Ben-Ari, Fuchs S, Lieder, I, Stelzer, G. et al. (2016) GeneAnalytics: An integrative gene set analysis tool, OMICS, in press.
    • (2016) OMICS
    • Ben-Ari, F.S.1    Lieder, I.2    Stelzer, G.3
  • 35
    • 0037255084 scopus 로고    scopus 로고
    • Human gene-centric databases at the weizmann institute of science: GeneCards, UDB, CroW 21 and HORDE
    • Safran, M., Chalifa-Caspi, V., Shmueli, O. et al. (2003) Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. Nucleic Acids Res., 31, 142-146.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 142-146
    • Safran, M.1    Chalifa-Caspi, V.2    Shmueli, O.3
  • 36
    • 71849092560 scopus 로고    scopus 로고
    • GIFtS: Annotation landscape analysis with GeneCards
    • Harel, A., Inger, A., Stelzer, G. et al. (2009) GIFtS: annotation landscape analysis with GeneCards. BMC Bioinformatics, 10, 348.
    • (2009) BMC Bioinformatics , vol.10 , pp. 348
    • Harel, A.1    Inger, A.2    Stelzer, G.3
  • 37
    • 78651317908 scopus 로고    scopus 로고
    • Entrez Gene: Gene-centered information at NCBI
    • Maglott, D., Ostell, J., Pruitt, K. D. et al. (2011) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res., 39, D52-D57.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D52-D57
    • Maglott, D.1    Ostell, J.2    Pruitt, K.D.3
  • 38
    • 84930603726 scopus 로고    scopus 로고
    • Can "normal" protein expression ranges be estimated with high-throughput proteomics?
    • Higdon, R. and Kolker, E. (2015) Can "normal" protein expression ranges be estimated with high-throughput proteomics? J. Proteome Res., 14, 2398-407.
    • (2015) J. Proteome Res. , vol.14 , pp. 2398-2407
    • Higdon, R.1    Kolker, E.2
  • 39
    • 84905372152 scopus 로고    scopus 로고
    • Analyzing the first drafts of the human proteome
    • Ezkurdia, I., Vazquez, J., Valencia, A. et al. (2014) Analyzing the first drafts of the human proteome. J. Proteome Res., 13, 3854-3855.
    • (2014) J. Proteome Res. , vol.13 , pp. 3854-3855
    • Ezkurdia, I.1    Vazquez, J.2    Valencia, A.3
  • 40
    • 33746092533 scopus 로고    scopus 로고
    • Widespread ectopic expression of olfactory receptor genes
    • Feldmesser, E., Olender, T., Khen, M. et al. (2006) Widespread ectopic expression of olfactory receptor genes. BMC Genomics, 7, 121.
    • (2006) BMC Genomics , vol.7 , pp. 121
    • Feldmesser, E.1    Olender, T.2    Khen, M.3
  • 41
    • 84920070787 scopus 로고    scopus 로고
    • Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
    • Perez-Riverol, Y., Alpi, E., Wang, R. et al. (2015) Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics, 15, 930-949.
    • (2015) Proteomics , vol.15 , pp. 930-949
    • Perez-Riverol, Y.1    Alpi, E.2    Wang, R.3
  • 42
    • 84941089280 scopus 로고    scopus 로고
    • Recent advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light
    • Paik, Y. K., Omenn, G. S., Overall, C. M. et al. (2015) Recent advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light. J. Proteome Res., 14, 3409-3414.
    • (2015) J. Proteome Res. , vol.14 , pp. 3409-3414
    • Paik, Y.K.1    Omenn, G.S.2    Overall, C.M.3
  • 43
    • 84940547273 scopus 로고    scopus 로고
    • A scalable approach for protein false discovery rate estimation in large proteomic data sets
    • Savitski, M. M., Wilhelm, M., Hahne, H. et al. (2015) A scalable approach for protein false discovery rate estimation in large proteomic data sets. Mol. Cell Proteomics, 14, 2394-2404.
    • (2015) Mol. Cell Proteomics , vol.14 , pp. 2394-2404
    • Savitski, M.M.1    Wilhelm, M.2    Hahne, H.3
  • 44
    • 84941749221 scopus 로고    scopus 로고
    • Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines
    • Wang, M., Herrmann, C. J., Simonovic, M. et al. (2015) Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics, 15, 3163-3168.
    • (2015) Proteomics , vol.15 , pp. 3163-3168
    • Wang, M.1    Herrmann, C.J.2    Simonovic, M.3
  • 45
    • 84941717906 scopus 로고    scopus 로고
    • Comprehensive comparison of large-scale tissue expression datasets
    • Santos, A., Tsafou, K., Stolte, C. et al. (2015) Comprehensive comparison of large-scale tissue expression datasets. PeerJ, 3, e1054.
    • (2015) PeerJ , vol.3 , pp. e1054
    • Santos, A.1    Tsafou, K.2    Stolte, C.3
  • 46
    • 76249090489 scopus 로고    scopus 로고
    • BioGPS: An extensible and customizable portal for querying and organizing gene annotation resources
    • Wu, C., Orozco, C., Boyer, J. et al. (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol., 10, R130.
    • (2009) Genome Biol. , vol.10 , pp. R130
    • Wu, C.1    Orozco, C.2    Boyer, J.3
  • 47
    • 84930607351 scopus 로고    scopus 로고
    • Sharing and Specificity of Co-expression Networks across 35 Human Tissues
    • Pierson, E., Consortium, G. T., Koller, D. et al. (2015) Sharing and Specificity of Co-expression Networks across 35 Human Tissues. PLoS Comput. Biol., 11, e1004220.
    • (2015) PLoS Comput. Biol. , vol.11 , pp. e1004220
    • Pierson, E.1    Consortium, G.T.2    Koller, D.3
  • 48
    • 84901269108 scopus 로고    scopus 로고
    • High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation
    • Levy, E. D., Kowarzyk, J. and Michnick, S. W. (2014) High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation. Cell Rep., 7, 1333-1340.
    • (2014) Cell Rep. , vol.7 , pp. 1333-1340
    • Levy, E.D.1    Kowarzyk, J.2    Michnick, S.W.3
  • 49
    • 84884518215 scopus 로고    scopus 로고
    • Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data
    • Lopez-Kleine, L., Leal, L. and Lopez, C. (2013) Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data. Brief Funct. Genomics, 12, 457-467.
    • (2013) Brief Funct. Genomics , vol.12 , pp. 457-467
    • Lopez-Kleine, L.1    Leal, L.2    Lopez, C.3
  • 50
    • 20144376345 scopus 로고    scopus 로고
    • Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
    • Yanai, I., Benjamin, H., Shmoish, M. et al. (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics, 21, 650-659.
    • (2005) Bioinformatics , vol.21 , pp. 650-659
    • Yanai, I.1    Benjamin, H.2    Shmoish, M.3
  • 51
    • 80855128254 scopus 로고    scopus 로고
    • Deep proteome and transcriptome mapping of a human cancer cell line
    • Nagaraj, N., Wisniewski, J. R., Geiger, T. et al. (2011) Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol., 7, 548.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 548
    • Nagaraj, N.1    Wisniewski, J.R.2    Geiger, T.3
  • 52
    • 13844254513 scopus 로고    scopus 로고
    • LIP index for peptide classification using MS/MS and SEQUEST search via logistic regression
    • Higdon, R., Kolker, N., Picone, A. et al. (2004) LIP index for peptide classification using MS/MS and SEQUEST search via logistic regression. OMICS: JIB, 8, 357-369.
    • (2004) OMICS: JIB , vol.8 , pp. 357-369
    • Higdon, R.1    Kolker, N.2    Picone, A.3
  • 53
    • 84902265781 scopus 로고    scopus 로고
    • MOPED 2.5-An integrated multi-omics resource: Multi-omics profiling expression database now includes transcriptomics data
    • Montague, E., Stenberry, L., Higdon, R. et al. (2014) MOPED 2.5-An integrated multi-omics resource: Multi-omics profiling expression database now includes transcriptomics data. OMICS: JIB., 18, 335-343.
    • (2014) OMICS: JIB. , vol.18 , pp. 335-343
    • Montague, E.1    Stenberry, L.2    Higdon, R.3


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