Constitutive patterns of gene expression regulated by RNA-binding proteins

Genome Biology

Volumn 15, Issue 1, 2014, Pages

  Cirillo, Davide ^a,b   Marchese, Domenica ^a,b   Agostini, Federico ^a,b   Livi, Carmen M ^a,b   Botta Orfila, Teresa ^a,b   Tartaglia, Gian G ^a,b  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEOPROTEIN; RNA BINDING PROTEIN; ELAV LIKE PROTEIN 1; ELAVL1 PROTEIN, HUMAN; LIN28B PROTEIN, HUMAN; MESSENGER RNA; TRANSCRIPTOME;

ARTICLE; CELL CYCLE REGULATION; CELL DIFFERENTIATION; CELL GROWTH; CELL PROLIFERATION; CELL SURVIVAL; COMPUTER MODEL; COMPUTER NETWORK; EX VIVO STUDY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMAN; HUMAN CELL; HUMAN TISSUE; INFORMATION PROCESSING; PROTEIN ANALYSIS; PROTEIN RNA BINDING; GENETICS; IMMUNOPRECIPITATION; METABOLISM; PROTEIN DOMAIN; SEQUENCE ANALYSIS;

ELAV-LIKE PROTEIN 1; GENE EXPRESSION REGULATION; HUMANS; IMMUNOPRECIPITATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; RNA, MESSENGER; RNA-BINDING PROTEINS; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84892149230     PISSN: None     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2014-15-1-r13     Document Type: Article

References (87)

1. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, Krijgsveld J, Hentze MW. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 2012, 149:1393-1406. 10.1016/j.cell.2012.04.031, 22658674.
2. Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, Wyler E, Bonneau R, Selbach M, Dieterich C, Landthaler M. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell 2012, 46:674-690. 10.1016/j.molcel.2012.05.021, 22681889.
3. Siomi H, Dreyfuss G. RNA-binding proteins as regulators of gene expression. Curr Opin Genet Dev 1997, 7:345-353. 10.1016/S0959-437X(97)80148-7, 9229110.
4. Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. RBPDB: a database of RNA-binding specificities. Nucleic Acids Res 2011, 39:D301-D308. 10.1093/nar/gkq1069, 3013675, 21036867.
5. Dassi E, Malossini A, Re A, Mazza T, Tebaldi T, Caputi L, Quattrone A. AURA: Atlas of UTR Regulatory Activity. Bioinforma Oxf Engl 2012, 28:142-144.
6. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 2012, 22:1760-1774. 10.1101/gr.135350.111, 3431492, 22955987.
7. Merkin J, Russell C, Chen P, Burge CB. Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science 2012, 338:1593-1599. 10.1126/science.1228186, 3568499, 23258891.
8. Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grützner F, Bergmann S, Nielsen R, Pääbo S, Kaessmann H. The evolution of gene expression levels in mammalian organs. Nature 2011, 478:343-348. 10.1038/nature10532, 22012392.
9. Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe MJH, Wilde A, Brudno M, Morris QD, Hughes TR. Conservation of core gene expression in vertebrate tissues. J Biol 2009, 8:33. 10.1186/jbiol130, 2689434, 19371447.
10. Wittkopp PJ, Haerum BK, Clark AG. Evolutionary changes in cis and trans gene regulation. Nature 2004, 430:85-88. 10.1038/nature02698, 15229602.
11. Masuda K, Kuwano Y, Nishida K, Rokutan K. General RBP expression in human tissues as a function of age. Ageing Res Rev 2012, 11:423-431. 10.1016/j.arr.2012.01.005, 22326651.
12. Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO. Diverse RNA-binding proteins interact with functionally related sets of RNAs. Suggesting an extensive regulatory system. PLoS Biol 2008, 6:e255. 10.1371/journal.pbio.0060255, 2573929, 18959479.
13. Vogel C, Marcotte EM. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet 2012, 13:227-232. 3654667, 22411467.
14. Maier T, Güell M, Serrano L. Correlation of mRNA and protein in complex biological samples. FEBS Lett 2009, 583:3966-3973. 10.1016/j.febslet.2009.10.036, 19850042.
15. Tartaglia GG, Pechmann S, Dobson CM, Vendruscolo M. Life on the edge: a link between gene expression levels and aggregation rates of human proteins. Trends Biochem Sci 2007, 32:204-206. 10.1016/j.tibs.2007.03.005, 17419062.
16. Greenbaum D, Colangelo C, Williams K, Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 2003, 4:117. 10.1186/gb-2003-4-9-117, 193646, 12952525.
17. Cox B, Kislinger T, Emili A. Integrating gene and protein expression data: pattern analysis and profile mining. Methods San Diego Calif 2005, 35:303-314.
18. Greenbaum D, Jansen R, Gerstein M. Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinforma Oxf Engl 2002, 18:585-596.
19. Bellucci M, Agostini F, Masin M, Tartaglia GG. Predicting protein associations with long noncoding RNAs. Nat Methods 2011, 8:444-445. 10.1038/nmeth.1611, 21623348.
20. Cirillo D, Agostini F, Tartaglia GG. Predictions of protein-RNA interactions. Wiley Interdiscip Rev Comput Mol Sci 2013, 3:161-175.
21. Agostini F, Cirillo D, Bolognesi B, Tartaglia GG. X-inactivation: quantitative predictions of protein interactions in the Xist network. Nucleic Acids Res 2013, 41:e31. 10.1093/nar/gks968, 3592426, 23093590.
22. Iglesias-Platas I, Martin-Trujillo A, Cirillo D, Court F, Guillaumet-Adkins A, Camprubi C, Bourc'his D, Hata K, Feil R, Tartaglia G, Arnaud P, Monk D. Characterization of novel paternal ncRNAs at the Plagl1 locus, including Hymai, predicted to interact with regulators of active chromatin. PLoS One 2012, 7:e38907. 10.1371/journal.pone.0038907, 3378578, 22723905.
23. Cirillo D, Agostini F, Klus P, Marchese D, Rodriguez S, Bolognesi B, Tartaglia GG. Neurodegenerative diseases: quantitative predictions of protein-RNA interactions. RNA 2013, 19:129-140. 10.1261/rna.034777.112, 3543085, 23264567.
24. Johnson R, Noble W, Tartaglia GG, Buckley NJ. Neurodegeneration as an RNA disorder. Prog Neurobiol 2012, 99:293-315. 10.1016/j.pneurobio.2012.09.006, 23063563.
25. Zanzoni A, Marchese D, Agostini F, Bolognesi B, Cirillo D, Botta-Orfila M, Livi CM, Rodriguez-Mulero S, Tartaglia GG. Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein. Nucleic Acids Res 2013, 41:9987-9998. 10.1093/nar/gkt794, 24003031.
26. Agostini F, Zanzoni A, Klus P, Marchese D, Cirillo D, Tartaglia GG. catRAPID omics: a web server for large-scale prediction of protein-RNA interactions. Bioinformatics 2013, 29:2928-2930. 10.1093/bioinformatics/btt495, 3810848, 23975767.
27. catRAPID express. [http://service.tartaglialab.com/page/catrapid_express_group].
28. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
29. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets - update. Nucleic Acids Res 2012, 41:D991-D995. 3531084, 23193258.
30. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone S-A, et al. ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 2009, 37:D868-D872. 10.1093/nar/gkn889, 2686529, 19015125.
31. Lebedeva S, Jens M, Theil K, Schwanhäusser B, Selbach M, Landthaler M, Rajewsky N. Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. Mol Cell 2011, 43:340-352. 10.1016/j.molcel.2011.06.008, 21723171.
32. Graf R, Munschauer M, Mastrobuoni G, Mayr F, Heinemann U, Kempa S, Rajewsky N, Landthaler M. Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation. RNA Biol 2013, 10:1146-1159. 10.4161/rna.25194, 3849162, 23770886.
33. Hafner M, Max KEA, Bandaru P, Morozov P, Gerstberger S, Brown M, Molina H, Tuschl T. Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition. RNA 2013, 19:613-626. 10.1261/rna.036491.112, 23481595.
34. Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, Wernerus H, Björling L, Ponten F. Towards a knowledge-based human protein atlas. Nat Biotechnol 2010, 28:1248-1250. 10.1038/nbt1210-1248, 21139605.
35. Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 2007, 25:117-124. 10.1038/nbt1270, 17187058.
36. Dosztányi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinforma Oxf Engl 2005, 21:3433-3434.
37. Gsponer J, Babu MM. Cellular strategies for regulating functional and nonfunctional protein aggregation. Cell Rep 2012, 2:1425-1437. 10.1016/j.celrep.2012.09.036, 3607227, 23168257.
38. Babu MM, van der Lee R, de Groot NS, Gsponer J. Intrinsically disordered proteins: regulation and disease. Curr Opin Struct Biol 2011, 21:432-440. 10.1016/j.sbi.2011.03.011, 21514144.
39. Vavouri T, Semple JI, Garcia-Verdugo R, Lehner B. Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity. Cell 2009, 138:198-208. 10.1016/j.cell.2009.04.029, 19596244.
40. Strausberg RL, Buetow KH, Emmert-Buck MR, Klausner RD. The cancer genome anatomy project: building an annotated gene index. Trends Genet TIG 2000, 16:103-106.
41. Cai S, Everitt JI, Kugo H, Cook J, Kleymenova E, Walker CL. Polycystic kidney disease as a result of loss of the tuberous sclerosis 2 tumor suppressor gene during development. Am J Pathol 2003, 162:457-468. 10.1016/S0002-9440(10)63840-0, 1851170, 12547704.
42. Simonnet H, Demont J, Pfeiffer K, Guenaneche L, Bouvier R, Brandt U, Schagger H, Godinot C. Mitochondrial complex I is deficient in renal oncocytomas. Carcinogenesis 2003, 24:1461-1466. 10.1093/carcin/bgg109, 12844484.
43. Wahl MC, Will CL, Lührmann R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009, 136:701-718. 10.1016/j.cell.2009.02.009, 19239890.
44. Crabtree JS, Jelinsky SA, Harris HA, Choe SE, Cotreau MM, Kimberland ML, Wilson E, Saraf KA, Liu W, McCampbell AS, Dave B, Broaddus RR, Brown EL, Kao W, Skotnicki JS, Abou-Gharbia M, Winneker RC, Walker CL. Comparison of human and rat uterine leiomyomata: identification of a dysregulated mammalian target of rapamycin pathway. Cancer Res 2009, 69:6171-6178. 10.1158/0008-5472.CAN-08-4471, 19622772.
45. Francia G, Man S, Teicher B, Grasso L, Kerbel RS. Gene expression analysis of tumor spheroids reveals a role for suppressed DNA mismatch repair in multicellular resistance to alkylating agents. Mol Cell Biol 2004, 24:6837-6849. 10.1128/MCB.24.15.6837-6849.2004, 444854, 15254249.
46. Manalo DJ, Rowan A, Lavoie T, Natarajan L, Kelly BD, Ye SQ, Garcia JGN, Semenza GL. Transcriptional regulation of vascular endothelial cell responses to hypoxia by HIF-1. Blood 2005, 105:659-669. 10.1182/blood-2004-07-2958, 15374877.
47. Beyer S, Kristensen MM, Jensen KS, Johansen JV, Staller P. The histone demethylases JMJD1A and JMJD2B are transcriptional targets of hypoxia-inducible factor HIF. J Biol Chem 2008, 283:36542-36552. 10.1074/jbc.M804578200, 2662309, 18984585.
48. Rohan S, Tu JJ, Kao J, Mukherjee P, Campagne F, Zhou XK, Hyjek E, Alonso MA, Chen Y-T. Gene expression profiling separates chromophobe renal cell carcinoma from oncocytoma and identifies vesicular transport and cell junction proteins as differentially expressed genes. Clin Cancer Res Off J Am Assoc Cancer Res 2006, 12:6937-6945.
49. Tan M-H, Wong CF, Tan HL, Yang XJ, Ditlev J, Matsuda D, Khoo SK, Sugimura J, Fujioka T, Furge KA, Kort E, Giraud S, Ferlicot S, Vielh P, Amsellem-Ouazana D, Debré B, Flam T, Thiounn N, Zerbib M, Benoît G, Droupy S, Molinié V, Vieillefond A, Tan PH, Richard S, Teh BT. Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma. BMC Cancer 2010, 10:196. 10.1186/1471-2407-10-196, 2883967, 20462447.
50. Martin P, Parkhurst SM. Parallels between tissue repair and embryo morphogenesis. Dev Camb Engl 2004, 131:3021-3034.
51. Lu H, Ouyang W, Huang C. Inflammation, a key event in cancer development. Mol Cancer Res MCR 2006, 4:221-233.
52. Rider CC, Mulloy B. Bone morphogenetic protein and growth differentiation factor cytokine families and their protein antagonists. Biochem J 2010, 429:1-12. 10.1042/BJ20100305, 20545624.
53. Standart N, Jackson RJ. Regulation of translation by specific protein/mRNA interactions. Biochimie 1994, 76:867-879. 10.1016/0300-9084(94)90189-9, 7880904.
54. De Moor CH, Richter JD. Translational control in vertebrate development. Int Rev Cytol 2001, 203:567-608.
55. Quenneville S, Turelli P, Bojkowska K, Raclot C, Offner S, Kapopoulou A, Trono D. The KRAB-ZFP/KAP1 system contributes to the early embryonic establishment of site-specific DNA methylation patterns maintained during development. Cell Rep 2012, 2:766-773. 10.1016/j.celrep.2012.08.043, 3677399, 23041315.
56. Zhang Z, Theler D, Kaminska KH, Hiller M, de la Grange P, Pudimat R, Rafalska I, Heinrich B, Bujnicki JM, Allain FH-T, Stamm S. The YTH domain is a novel RNA binding domain. J Biol Chem 2010, 285:14701-14710. 10.1074/jbc.M110.104711, 2863249, 20167602.
57. Harigaya Y, Tanaka H, Yamanaka S, Tanaka K, Watanabe Y, Tsutsumi C, Chikashige Y, Hiraoka Y, Yamashita A, Yamamoto M. Selective elimination of messenger RNA prevents an incidence of untimely meiosis. Nature 2006, 442:45-50. 10.1038/nature04881, 16823445.
58. Rafalska I, Zhang Z, Benderska N, Wolff H, Hartmann AM, Brack-Werner R, Stamm S. The intranuclear localization and function of YT521-B is regulated by tyrosine phosphorylation. Hum Mol Genet 2004, 13:1535-1549. 10.1093/hmg/ddh167, 15175272.
59. Zhang B, Zur Hausen A, Orlowska-Volk M, Jäger M, Bettendorf H, Stamm S, Hirschfeld M, Yiqin O, Tong X, Gitsch G, Stickeler E. Alternative splicing-related factor YT521: an independent prognostic factor in endometrial cancer. Int J Gynecol Cancer Off J Int Gynecol Cancer Soc 2010, 20:492-499.
60. Baldwin RM, Morettin A, Paris G, Goulet I, Côté J. Alternatively spliced protein arginine methyltransferase 1 isoform PRMT1v2 promotes the survival and invasiveness of breast cancer cells. Cell Cycle 2012, 11:4597-4612. 10.4161/cc.22871, 3562305, 23187807.
61. Zhong J, Cao R-X, Zu X-Y, Hong T, Yang J, Liu L, Xiao X-H, Ding W-J, Zhao Q, Liu J-H, Wen G-B. Identification and characterization of novel spliced variants of PRMT2 in breast carcinoma. FEBS J 2012, 279:316-335. 10.1111/j.1742-4658.2011.08426.x, 22093364.
62. Yan T-D, Wu H, Zhang H-P, Lu N, Ye P, Yu F-H, Zhou H, Li W-G, Cao X, Lin Y-Y, He J-Y, Gao W-W, Zhao Y, Xie L, Chen J-B, Zhang X-K, Zeng J-Z. Oncogenic potential of retinoic acid receptor-gamma in hepatocellular carcinoma. Cancer Res 2010, 70:2285-2295. 10.1158/0008-5472.CAN-09-2968, 20197465.
63. Li D-P, Li Z-Y, Sang W, Cheng H, Pan X-Y, Xu K-L. HOXA9 gene expression in acute myeloid leukemia. Cell Biochem Biophys 2013, 67:935-938. 10.1007/s12013-013-9586-8, 23575938.
64. Hirschfeld M, Zhang B, Jaeger M, Stamm S, Erbes T, Mayer S, Tong X, Stickeler E. Hypoxia-dependent mRNA expression pattern of splicing factor YT521 and its impact on oncological important target gene expression. Mol Carcinog 2013, in press.
65. Harris AL. Hypoxia - a key regulatory factor in tumour growth. Nat Rev Cancer 2002, 2:38-47. 10.1038/nrc704, 11902584.
66. Piecyk M, Wax S, Beck AR, Kedersha N, Gupta M, Maritim B, Chen S, Gueydan C, Kruys V, Streuli M, Anderson P. TIA-1 is a translational silencer that selectively regulates the expression of TNF-alpha. EMBO J 2000, 19:4154-4163. 10.1093/emboj/19.15.4154, 306595, 10921895.
67. Dixon DA, Balch GC, Kedersha N, Anderson P, Zimmerman GA, Beauchamp RD, Prescott SM. Regulation of cyclooxygenase-2 expression by the translational silencer TIA-1. J Exp Med 2003, 198:475-481. 10.1084/jem.20030616, 2194089, 12885872.
68. Yamasaki S, Stoecklin G, Kedersha N, Simarro M, Anderson P. T-cell intracellular antigen-1 (TIA-1)-induced translational silencing promotes the decay of selected mRNAs. J Biol Chem 2007, 282:30070-30077. 10.1074/jbc.M706273200, 17711853.
69. Wang Z, Kayikci M, Briese M, Zarnack K, Luscombe NM, Rot G, Zupan B, Curk T, Ule J. iCLIP predicts the dual splicing effects of TIA-RNA interactions. PLoS Biol 2010, 8:e1000530. 10.1371/journal.pbio.1000530, 2964331, 21048981.
70. Kidd M, Modlin IM, Mane SM, Camp RL, Eick G, Latich I. The role of genetic markers - NAP1L1, MAGE-D2, and MTA1 - in defining small-intestinal carcinoid neoplasia. Ann Surg Oncol 2006, 13:253-262. 10.1245/ASO.2006.12.011, 16424981.
71. Drozdov I, Kidd M, Nadler B, Camp RL, Mane SM, Hauso O, Gustafsson BI, Modlin IM. Predicting neuroendocrine tumor (carcinoid) neoplasia using gene expression profiling and supervised machine learning. Cancer 2009, 115:1638-1650. 10.1002/cncr.24180, 2743551, 19197975.
72. Guidi F, Puglia M, Gabbiani C, Landini I, Gamberi T, Fregona D, Cinellu MA, Nobili S, Mini E, Bini L, Modesti PA, Modesti A, Messori L. 2D-DIGE analysis of ovarian cancer cell responses to cytotoxic gold compounds. Mol Biosyst 2012, 8:985-993. 10.1039/c1mb05386h, 22134777.
73. Nagata T, Takahashi Y, Ishii Y, Asai S, Nishida Y, Murata A, Koshinaga T, Fukuzawa M, Hamazaki M, Asami K, Ito E, Ikeda H, Takamatsu H, Koike K, Kikuta A, Kuroiwa M, Watanabe A, Kosaka Y, Fujita H, Miyake M, Mugishima H. Transcriptional profiling in hepatoblastomas using high-density oligonucleotide DNA array. Cancer Genet Cytogenet 2003, 145:152-160. 10.1016/S0165-4608(03)00065-7, 12935928.
74. Lawrence MG, Margaryan NV, Loessner D, Collins A, Kerr KM, Turner M, Seftor EA, Stephens CR, Lai J, Postovit L-M, Clements JA, Hendrix MJC, APC BioResource Reactivation of embryonic nodal signaling is associated with tumor progression and promotes the growth of prostate cancer cells. Prostate 2011, 71:1198-1209. 10.1002/pros.21335, 3234312, 21656830, APC BioResource.
75. Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest ARR, Gough J, Grimmond S, Han J-H, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 2010, 140:744-752. 10.1016/j.cell.2010.01.044, 2836267, 20211142.
76. Wu L, Candille SI, Choi Y, Xie D, Jiang L, Li-Pook-Than J, Tang H, Snyder M. Variation and genetic control of protein abundance in humans. Nature 2013, 499:79-82. 10.1038/nature12223, 3789121, 23676674.
77. Tartaglia GG, Vendruscolo M. Correlation between mRNA expression levels and protein aggregation propensities in subcellular localisations. Mol Biosyst 2009, 5:1873-1876. 10.1039/b913099n, 19763336.
78. Tartaglia GG, Pechmann S, Dobson CM, Vendruscolo M. A relationship between mRNA expression levels and protein solubility in E. coli. J Mol Biol 2009, 388:381-389. 10.1016/j.jmb.2009.03.002, 19281824.
79. Olzscha H, Schermann SM, Woerner AC, Pinkert S, Hecht MH, Tartaglia GG, Vendruscolo M, Hayer-Hartl M, Hartl FU, Vabulas RM. Amyloid-like aggregates sequester numerous metastable proteins with essential cellular functions. Cell 2011, 144:67-78. 10.1016/j.cell.2010.11.050, 21215370.
80. ArrayExpress. [http://www.ebi.ac.uk/arrayexpress].
81. ArrayExpress. [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-513].
82. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659. 10.1093/bioinformatics/btl158, 16731699.
83. Li X, Kazan H, Lipshitz HD, Morris QD. Finding the target sites of RNA-binding proteins. Wiley Interdiscip Rev RNA 2014, 5:111-130. 10.1002/wrna.1201, 24217996.
84. Tartaglia's group web servers. [http://service.tartaglialab.com].
85. Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinforma Oxf Engl 2007, 23:257-258.
86. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
87. Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet TIG 2000, 16:276-277.