References
- Venter JC, Adams MD Myers E et al. The sequence of the human genome. Science291, 1304–1351 (2001).
- Lander ES, Linton LM, Birren B et al. Initial sequencing and analysis of the human genome. Nature409, 860–921 (2001).
- Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science270, 467–470 (1995).
- Cloonan N, Forrest ARR, Kolle G et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Meth.5, 613–619 (2008).
- Nagalakshmi U, Wang Z, Waern K et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science320, 1344–1349 (2008).
- Linnarsson S. Recent advances in DNA sequencing methods – general principles of sample preparation. Exp. Cell Res.316, 1339–1343 (2010).
- Landgraf P, Rusu M, Sheridan R et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell129, 1401–1414 (2007).
- Trapnell C, Williams BA, Pertea G et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotech.28, 511–515 (2010).
- Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc. Natl Acad. Sci. USA104, 5860–5865 (2007).
- Denhardt DT. A membrane-filter technique for the detection of complementary DNA. Biochem. Biophys. Res. Commun.23, 641–646 (1966).
- Southern EM. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol.98, 503–517 (1975).
- Lehrach H, Diamond D, Wozney JM, Boedtker H. RNA molecular weight determinations by gel electrophoresis under denaturing conditions, a critical reexamination. Biochemistry16, 4743–4751 (1977).
- Alwine JC, Kemp DJ, Stark GR. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc. Natl Acad. Sci. USA74, 5350–5354 (1977).
- Stoeckle MY, Guan L. Improved resolution and sensitivity of northern blots using polyacrylamide-urea gels. Biotechniques15, 227, 230–231 (1993).
- Maniatis T, Fritsch EF, Sambrook J. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, NY, USA (1989).
- Chomczynski P. One-hour downward alkaline capillary transfer for blotting of DNA and RNA. Anal. Biochem.201, 134–139 (1992).
- Augenlicht LH, Kobrin D. Cloning and screening of sequences expressed in a mouse colon tumor. Cancer Res.42, 1088–1093 (1982).
- Kulesh DA, Clive DR, Zarlenga DS, Greene JJ. Identification of interferon-modulated proliferation-related cDNA sequences. Proc. Natl Acad. Sci. USA84, 8453–8457 (1987).
- Shalon D, Smith SJ, Brown PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res.6, 639–645 (1996).
- Velculescu VE, Zhang L, Zhou W et al. Characterization of the yeast transcriptome. Cell88, 243–251 (1997).
- Wepf A, Glatter T, Schmidt A, Aebersold R, Gstaiger M. Quantitative interaction proteomics using mass spectrometry. Nat. Methods6, 203–205 (2009).
- Breitkreutz A, Choi H, Sharom JR et al. A global protein kinase and phosphatase interaction network in yeast. Science328, 1043–1046 (2010).
- Kühner S, van Noort V, Betts MJ et al. Proteome organization in a genome-reduced bacterium. Science326, 1235–1240 (2009).
- de Godoy LMF, Olsen JV, Cox J et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature455, 1251–1254 (2008).
- Schrimpf SP, Weiss M, Reiter L et al. Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol.7, e1000048 (2009).
- Baerenfaller K, Grossmann J, Grobei MA et al. Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science320, 938–941 (2008).
- Beck M, Claassen M, Aebersold R. Comprehensive proteomics. Curr. Opin. Biotechnol.22, 3–8 (2011).
- Ghaemmaghami S, Huh W, Bower K et al. Global analysis of protein expression in yeast. Nature425, 737–741 (2003).
- O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem.250, 4007–4021 (1975).
- Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl Acad. Sci. USA97, 9390–9395 (2000).
- Delahunty C, Yates III JR. Protein identification using 2D-LC-MS/MS. Methods35, 248–255 (2005).
- Takahashi N, Ishioka N, Takahashi Y, Putnam FW. Automated tandem high-performance liquid chromatographic system for separation of extremely complex peptide mixtures. J. Chromatogr.326, 407–418 (1985).
- Lundell N, Markides K. Two-dimensional liquid chromatography of peptides: an optimization strategy. Chromatographia34, 369–375 (1992).
- Gatlin CL, Kleemann GR, Hays LG, Link AJ, Yates JR. Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. Anal. Biochem.263, 93–101 (1998).
- Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol.17, 994–999 (1999).
- Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics3, 1154–1169 (2004).
- Ong S, Blagoev B, Kratchmarova I et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics1, 376–386 (2002).
- Oda Y, Huang K, Cross FR, Cowburn D, Chait BT. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl Acad. Sci. USA96, 6591-6596 (1999).
- Zhang Y, Wolf-Yadlin A, Ross PL et al. Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell. Proteomics4, 1240–1250 (2005).
- Julka S, Regnier F. Quantification in proteomics through stable isotope coding: a review. J. Proteome Res.3, 350–363 (2004).
- Ow SY, Salim M, Noirel J, Evans C, Rehman I, Wright PC. iTRAQ Underestimation in simple and complex mixtures: ‘the good, the bad and the ugly’. J. Proteome Res.8, 5347–5355 (2009).
- Hynes NE, Lane HA. ERBB receptors and cancer: the complexity of targeted inhibitors. Nat. Rev. Cancer5, 341–354 (2005).
- Yarden Y, Sliwkowski MX. Untangling the ErbB signalling network. Nat. Rev. Mol. Cell. Biol.2, 127–137 (2001).
- Citri A, Yarden Y. EGF–ERBB signalling: towards the systems level. Nat. Rev. Mol. Cell. Biol.7, 505–516 (2006).
- Lemmon MA, Schlessinger J. Cell signaling by receptor tyrosine kinases. Cell141, 1117–1134 (2010).
- Jorissen RN, Walker F, Pouliot N, Garrett TPJ, Ward CW, Burgess AW. Epidermal growth factor receptor: mechanisms of activation and signalling. Exp. Cell. Res.284, 31–53 (2003).
- Hynes NE, MacDonald G. ErbB receptors and signaling pathways in cancer. Curr. Opin. Cell Biol.21, 177–184 (2009).
- MacBeath G. Protein microarrays and proteomics. Nat. Genet.32(Suppl.), 526–532 (2002).
- Liotta LA, Espina V, Mehta AI et al. Protein microarrays: meeting analytical challenges for clinical applications. Cancer Cell3, 317–325 (2003).
- Krutzik PO, Irish JM, Nolan GP, Perez OD. Analysis of protein phosphorylation and cellular signaling events by flow cytometry: techniques and clinical applications. Clin. Immunol.110, 206–221 (2004).
- Krutzik PO, Nolan GP. Intracellular phospho-protein staining techniques for flow cytometry: monitoring single cell signaling events. Cytometry55A, 61–70 (2003).
- Perez OD, Nolan GP. Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry. Nat. Biotechnol.20, 155–162 (2002).
- Haab BB, Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol.2, RESEARCH0004 (2001).
- Nielsen UB, Cardone MH, Sinskey AJ, MacBeath G, Sorger PK. Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc. Natl Acad. Sci. USA100, 9330–9335 (2003).
- Poetz O, Henzler T, Hartmann M et al. Sequential multiplex analyte capturing for phosphoprotein profiling. Mol. Cell. Proteomics9, 2474–2481 (2010).
- Paweletz CP, Charboneau L, Bichsel VE et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene20, 1981–1989 (2001).
- Liotta LA, Paweletz CP, Charboneau L et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene20, 1981–1989 (2001).
- Paweletz CP, Liotta LA, Petricoin EF. New technologies for biomarker analysis of prostate cancer progression: laser capture microdissection and tissue proteomics. Urology57, 160–163 (2001).
- Wulfkuhle JD, McLean KC, Paweletz CP et al. New approaches to proteomic analysis of breast cancer. Proteomics1, 1205–1215 (2001).
- Charboneau L, Tory H, Chen T et al. Utility of reverse phase protein arrays: applications to signalling pathways and human body arrays. Brief. Funct. Genomic Proteomic1, 305–315 (2002).
- Espina V, Munson PJ, Petricoin E et al. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc. Natl Acad. Sci. USA100, 14229–14234 (2003).
- Grubb RL, Calvert VS, Wulkuhle JD et al. Signal pathway profiling of prostate cancer using reverse phase protein arrays. Proteomics3, 2142–2146 (2003).
- Sheehan KM, Calvert VS, Kay EW et al. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol. Cell. Proteomics4, 346–355 (2005).
- Mills GB, Liotta LA, Petricoin EF et al. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol. Cell. Proteomics4, 346–355 (2005).
- Tibes R, Qiu Y, Lu Y et al. Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol. Cancer Ther.5, 2512–2521 (2006).
- Sevecka M, MacBeath G. State-based discovery: a multidimensional screen for small-molecule modulators of EGF signaling. Nat. Methods3, 825–831 (2006).
- Sevecka M, Wolf-Yadlin A, Macbeath G. Lysate microarrays enable high-throughput, quantitative investigations of cellular signaling. Mol. Cell. Proteomics10(4), M110.005363 (2011).
- Ciaccio MF, Wagner JP, Chuu C, Lauffenburger DA, Jones RB. Systems analysis of EGF receptor signaling dynamics with microwestern arrays. Nat. Methods7, 148–155 (2010).
- Janes KA, Yaffe MB. Data-driven modelling of signal-transduction networks. Nat. Rev. Mol. Cell. Biol.7, 820–828 (2006).
- Woolf PJ, Prudhomme W, Daheron L, Daley GQ, Lauffenburger DA. Bayesian analysis of signaling networks governing embryonic stem cell fate decisions. Bioinformatics21, 741–753 (2005).
- Prudhomme W, Daley GQ, Zandstra P, Lauffenburger DA. Multivariate proteomic analysis of murine embryonic stem cell self-renewal versus differentiation signaling. Proc. Natl Acad. Sci. USA101, 2900–2905 (2004).
- Alexopoulos LG, Saez-Rodriguez J, Cosgrove BD, Lauffenburger DA, Sorger PK. Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. Mol. Cell. Proteomics9, 1849–1865 (2010).
- Janes KA, Gaudet S, Albeck JG, Nielsen UB, Lauffenburger DA, Sorger PK. The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell124, 1225–1239 (2006).
- Janes KA, Reinhardt HC, Yaffe MB. Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell135, 343–354 (2008).
- Miller-Jensen K, Janes KA, Brugge JS, Lauffenburger DA. Common effector processing mediates cell-specific responses to stimuli. Nature448, 604–608 (2007).
- Cosgrove BD, Alexopoulos LG, Hang T et al. Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation. Mol. BioSyst.6, 1195 (2010).
- Nakakuki T, Birtwistle MR, Saeki Y et al. Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell141, 884–896 (2010).
- Melzer D, Perry JRB, Hernandez D et al. A genome-wide association study identifies protein quantitative trait loci (pQTLs). PLoS Genet.4, e1000072 (2008).
- Garge N, Pan H, Rowland MD et al. Identification of quantitative trait loci underlying proteome variation in human lymphoblastoid cells. Mol. Cell. Proteomics9, 1383–1399 (2010).
- Foss EJ, Radulovic D, Shaffer SA et al. Genetic basis of proteomevariation in yeast. Nat. Genet.39, 1369–1375 (2007).
- Ghazalpour A, Bennett B, Petyuk VA et al. Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genet.7, e1001393 (2011).
- Mann M. Can proteomics retire the western blot? J. Proteome Res.7, 3065 (2008).