期刊论文详细信息
BMC Medical Genomics
A common gene expression signature in Huntington’s disease patient brain regions
Gillian P Bates1  Andreas Neueder1 
[1] Department of Medical and Molecular Genetics, King’s College London, London SE1 9RT, UK
关键词: Therapeutic targets;    Network analysis;    Transcriptional dysregulation;    Huntington’s disease;    Neurodegenerative diseases;   
Others  :  1090302
DOI  :  10.1186/s12920-014-0060-2
 received in 2014-07-03, accepted in 2014-10-06,  发布年份 2014
PDF
【 摘 要 】

Background

Gene expression data provide invaluable insights into disease mechanisms. In Huntington’s disease (HD), a neurodegenerative disease caused by a tri-nucleotide repeat expansion in the huntingtin gene, extensive transcriptional dysregulation has been reported. Conventional dysregulation analysis has shown that e.g. in the caudate nucleus of the post mortem HD brain the gene expression level of about a third of all genes was altered. Owing to this large number of dysregulated genes, the underlying relevance of expression changes is often lost in huge gene lists that are difficult to comprehend.

Methods

To alleviate this problem, we employed weighted correlation network analysis to archival gene expression datasets of HD post mortem brain regions.

Results

We were able to uncover previously unidentified transcription dysregulation in the HD cerebellum that contained a gene expression signature in common with the caudate nucleus and the BA4 region of the frontal cortex. Furthermore, we found that yet unassociated pathways, e.g. global mRNA processing, were dysregulated in HD. We provide evidence to show that, contrary to previous findings, mutant huntingtin is sufficient to induce a subset of stress response genes in the cerebellum and frontal cortex BA4 region. The comparison of HD with other neurodegenerative disorders showed that the immune system, in particular the complement system, is generally activated. We also demonstrate that HD mouse models mimic some aspects of the disease very well, while others, e.g. the activation of the immune system are inadequately reflected.

Conclusion

Our analysis provides novel insights into the molecular pathogenesis in HD and identifies genes and pathways as potential therapeutic targets.

【 授权许可】

   
2014 Neueder and Bates; licensee BioMed Central Ltd.

【 预 览 】
附件列表
Files Size Format View
20150128155842316.pdf 2223KB PDF download
Figure 2. 29KB Image download
Figure 7. 91KB Image download
Figure 6. 84KB Image download
Figure 4 . 72KB Image download
Figure 4. 55KB Image download
Figure 3. 97KB Image download
Figure 2. 75KB Image download
Figure 1. 55KB Image download
【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 4 .

Figure 6.

Figure 7.

Figure 2.

【 参考文献 】
  • [1]Riley BE, Orr HT: Polyglutamine neurodegenerative diseases and regulation of transcription: assembling the puzzle. Genes Dev 2006, 20:2183-2192.
  • [2]Renner M, Melki R: Protein aggregation and prionopathies. Pathol Biol (Paris) 2014, 62:162-168.
  • [3]Irwin DJ, Lee VM, Trojanowski JQ: Parkinson’s disease dementia: convergence of alpha-synuclein, tau and amyloid-beta pathologies. Nat Rev Neurosci 2013, 14:626-636.
  • [4]Rotunno MS, Bosco DA: An emerging role for misfolded wild-type SOD1 in sporadic ALS pathogenesis. Front Cell Neurosci 2013, 7:253.
  • [5]Guo W, Chen Y, Zhou X, Kar A, Ray P, Chen X, Rao EJ, Yang M, Ye H, Zhu L, Liu J, Xu M, Yang Y, Wang C, Zhang D, Bigio EH, Mesulam M, Shen Y, Xu Q, Fushimi K, Wu JY: An ALS-associated mutation affecting TDP-43 enhances protein aggregation, fibril formation and neurotoxicity. Nat Struct Mol Biol 2011, 18:822-830.
  • [6]Nomura T, Watanabe S, Kaneko K, Yamanaka K, Nukina N, Furukawa Y: Intranuclear aggregation of mutant FUS/TLS as a molecular pathomechanism of amyotrophic lateral sclerosis. J Biol Chem 2014, 289:1192-1202.
  • [7]Allende DS, Prayson RA: The expanding family of glioneuronal tumors. Adv Anat Pathol 2009, 16:33-39.
  • [8]Ellwardt E, Zipp F: Molecular mechanisms linking neuroinflammation and neurodegeneration in MS.Exp Neurol 2014.
  • [9]Gupta S, Kulhara P: What is schizophrenia: A neurodevelopmental or neurodegenerative disorder or a combination of both? A critical analysis. Indian J Psychiatry 2010, 52:21-27.
  • [10]DeJesus-Hernandez M, Mackenzie IR, Boeve BF, Boxer AL, Baker M, Rutherford NJ, Nicholson AM, Finch NA, Flynn H, Adamson J, Kouri N, Wojtas A, Sengdy P, Hsiung GY, Karydas A, Seeley WW, Josephs KA, Coppola G, Geschwind DH, Wszolek ZK, Feldman H, Knopman DS, Petersen RC, Miller BL, Dickson DW, Boylan KB, Graff-Radford NR, Rademakers R: Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 2011, 72:245-256.
  • [11]Renton AE, Majounie E, Waite A, Simon-Sanchez J, Rollinson S, Gibbs JR, Schymick JC, Laaksovirta H, van Swieten JC, Myllykangas L, Kalimo H, Paetau A, Abramzon Y, Remes AM, Kaganovich A, Scholz SW, Duckworth J, Ding J, Harmer DW, Hernandez DG, Johnson JO, Mok K, Ryten M, Trabzuni D, Guerreiro RJ, Orrell RW, Neal J, Murray A, Pearson J, Jansen IE, et al.: A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron 2011, 72:257-268.
  • [12]Ling SC, Polymenidou M, Cleveland DW: Converging mechanisms in ALS and FTD: disrupted RNA and protein homeostasis. Neuron 2013, 79:416-438.
  • [13]Fardaei M, Rogers MT, Thorpe HM, Larkin K, Hamshere MG, Harper PS, Brook JD: Three proteins, MBNL, MBLL and MBXL, co-localize in vivo with nuclear foci of expanded-repeat transcripts in DM1 and DM2 cells. Hum Mol Genet 2002, 11:805-814.
  • [14]Brook JD, Mccurrach ME, Harley HG, Buckler AJ, Church D, Aburatani H, Hunter K, Stanton VP, Thirion JP, Hudson T, Sohn R, Zemelman B, Snell RG, Rundle SA, Crow S, Davies J, Shelbourne P, Buxton J, Jones C, Juvonen V, Johnson K, Harper PS, Shaw DJ, Housman DE: Molecular basis of myotonic dystrophy: expansion of a trinucleotide (CTG) repeat at the 3′ end of a transcript encoding a protein kinase family member. Cell 1992, 68:799-808.
  • [15]Mahadevan M, Tsilfidis C, Sabourin L, Shutler G, Amemiya C, Jansen G, Neville C, Narang M, Barcelo J, O’Hoy K, Ohoy K, Leblond S, Earlemacdonald J, Dejong PJ, Wieringa B, Korneluk RG: Myotonic dystrophy mutation: an unstable CTG repeat in the 3′ untranslated region of the gene. Science 1992, 255:1253-1255.
  • [16]Fu YH, Pizzuti A, Fenwick RG, King J, Rajnarayan S, Dunne PW, Dubel J, Nasser GA, Ashizawa T, Dejong P, Wieringa B, Korneluk R, Perryman MB, Epstein HF, Caskey CT: An unstable triplet repeat in a gene related to myotonic muscular dystrophy. Science 1992, 255:1256-1258.
  • [17]Liquori CL, Ricker K, Moseley ML, Jacobsen JF, Kress W, Naylor SL, Day JW, Ranum LP: Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. Science 2001, 293:864-867.
  • [18]Kanadia RN, Johnstone KA, Mankodi A, Lungu C, Thornton CA, Esson D, Timmers AM, Hauswirth WW, Swanson MS: A muscleblind knockout model for myotonic dystrophy. Science 2003, 302:1978-1980.
  • [19]Sathasivam K, Neueder A, Gipson TA, Landles C, Benjamin AC, Bondulich MK, Smith DL, Faull RLM, Roos RAC, Howland D, Detloff PJ, Housman DE, Bates GP: Aberrant splicing of HTT generates the pathogenic exon 1 protein in Huntington disease. Proc Natl Acad Sci U S A 2013, 110:2366-2370.
  • [20]Cooper-Knock J, Kirby J, Ferraiuolo L, Heath PR, Rattray M, Shaw PJ: Gene expression profiling in human neurodegenerative disease. Nat Rev Neurol 2012, 8:518-530.
  • [21]Chandra A, Johri A, Beal MF: Prospects for neuroprotective therapies in prodromal Huntington’s disease. Mov Disord 2014, 29(Suppl 3):285-293.
  • [22]Ross CA, Shoulson I: Huntington disease: pathogenesis, biomarkers, and approaches to experimental therapeutics. Parkinsonism Relat Disord 2009, 15(Suppl 3):S135-138.
  • [23]Bjorkqvist M, Wild EJ, Thiele J, Silvestroni A, Andre R, Lahiri N, Raibon E, Lee RV, Benn CL, Soulet D, Magnusson A, Woodman B, Landles C, Pouladi MA, Hayden MR, Khalili-Shirazi A, Lowdell MW, Brundin P, Bates GP, Leavitt BR, Moller T, Tabrizi SJ: A novel pathogenic pathway of immune activation detectable before clinical onset in Huntington’s disease. J Exp Med 2008, 205:1869-1877.
  • [24]Becanovic K, Pouladi MA, Lim RS, Kuhn A, Pavlidis P, Luthi-Carter R, Hayden MR, Leavitt BR: Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis. Hum Mol Genet 2010, 19:1438-1452.
  • [25]Zabel C, Mao L, Woodman B, Rohe M, Wacker MA, Klare Y, Koppelstatter A, Nebrich G, Klein O, Grams S, Strand A, Luthi-Carter R, Hartl D, Klose J, Bates GP: A large number of protein expression changes occur early in life and precede phenotype onset in a mouse model for huntington disease. Mol Cell Proteomics 2009, 8:720-734.
  • [26]Benn CL, Sun T, Sadri-Vakili G, McFarland KN, DiRocco DP, Yohrling GJ, Clark TW, Bouzou B, Cha JH: Huntingtin modulates transcription, occupies gene promoters in vivo, and binds directly to DNA in a polyglutamine-dependent manner. J Neurosci 2008, 28:10720-10733.
  • [27]Hodges A, Strand AD, Aragaki AK, Kuhn A, Sengstag T, Hughes G, Elliston LA, Hartog C, Goldstein DR, Thu D, Hollingsworth ZR, Collin F, Synek B, Holmans PA, Young AB, Wexler NS, Delorenzi M, Kooperberg C, Augood SJ, Faull RLM, Olson JM, Jones L, Luthi-Carter R: Regional and cellular gene expression changes in human Huntington’s disease brain. Hum Mol Genet 2006, 15:965-977.
  • [28]Kuhn A, Goldstein DR, Hodges A, Strand AD, Sengstag T, Kooperberg C, Becanovic K, Pouladi MA, Sathasivam K, Cha JH, Cha JHJ, Hannan AJ, Hayden MR, Leavitt BR, Dunnett SB, Ferrante RJ, Albin R, Shelbourne P, Delorenzi M, Augood SJ, Faull RLM, Olson JM, Bates GP, Jones L, Luthi-Carter R: Mutant huntingtin’s effects on striatal gene expression in mice recapitulate changes observed in human Huntington’s disease brain and do not differ with mutant huntingtin length or wild-type huntingtin dosage. Hum Mol Genet 2007, 16:1845-1861.
  • [29]Langfelder P, Horvath S: WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008, 9:559. BioMed Central Full Text
  • [30]Oldham MC, Konopka G, Iwamoto K, Langfelder P, Kato T, Horvath S, Geschwind DH: Functional organization of the transcriptome in human brain. Nat Neurosci 2008, 11:1271-1282.
  • [31]Oldham MC, Horvath S, Geschwind DH: Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A 2006, 103:17973-17978.
  • [32]Saris CGJ, Horvath S, van Vught PWJ, van Es MA, Blauw HM, Fuller TF, Langfelder P, DeYoung J, Wokke JHJ, Veldink JH, van den Berg LH, Ophoff RA: Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients. BMC Genomics 2009, 10:405. BioMed Central Full Text
  • [33]Miller JA, Oldham MC, Geschwind DH: A systems level analysis of transcriptional changes in Alzheimer’s disease and normal aging. J Neurosci 2008, 28:1410-1420.
  • [34]Miller JA, Horvath S, Geschwind DH: Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc Natl Acad Sci U S A 2010, 107:12698-12703.
  • [35]Durrenberger PF, Fernando FS, Magliozzi R, Kashefi SN, Bonnert TP, Ferrer I, Seilhean D, Nait-Oumesmar B, Schmitt A, Gebicke-Haerter PJ, Falkai P, Grunblatt E, Palkovits M, Parchi P, Capellari S, Arzberger T, Kretzschmar H, Roncaroli F, Dexter DT, Reynolds R: Selection of novel reference genes for use in the human central nervous system: a BrainNet Europe Study. Acta Neuropathol 2012, 124:893-903.
  • [36]Pouladi MA, Morton AJ, Hayden MR: Choosing an animal model for the study of Huntington’s disease. Nat Rev Neurosci 2013, 14:708-721.
  • [37]Bates GP, Landles C: Preclinical Experimental Therapeutics. In Huntington’s Disease. Volume Fourth edition. Edited by Bates GP, Tabrizi SJ, Jones L. Oxford Monographs on Medical Genetics, OUP USA; 2014:410-461.
  • [38]Oldham MC, Langfelder P, Horvath S: Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease. BMC Syst Biol 2012, 6:63. BioMed Central Full Text
  • [39]Vonsattel JP, Myers RH, Stevens TJ, Ferrante RJ, Bird ED, Richardson EP Jr: Neuropathological classification of Huntington’s disease. J Neuropathol Exp Neurol 1985, 44:559-577.
  • [40]Bayram-Weston Z, Torres EM, Jones L, Dunnett SB, Brooks SP: Light and electron microscopic characterization of the evolution of cellular pathology in the Hdh(CAG)150 Huntington’s disease knock-in mouse. Brain Res Bull 2012, 88:189-198.
  • [41]Dodds L, Chen J, Berggren K, Fox J: Characterization of Striatal Neuronal Loss and Atrophy in the R6/2 Mouse Model of Huntington’s Disease.PLoS Curr 2014, 6
  • [42]Rattray I, Smith E, Gale R, Matsumoto K, Bates GP, Modo M: Correlations of behavioral deficits with brain pathology assessed through longitudinal MRI and histopathology in the R6/2 mouse model of HD. PLoS One 2013, 8:e60012.
  • [43]Zuccato C, Valenza M, Cattaneo E: Molecular mechanisms and potential therapeutical targets in Huntington’s disease. Physiol Rev 2010, 90:905-981.
  • [44]Chen CM: Mitochondrial dysfunction, metabolic deficits, and increased oxidative stress in Huntington’s disease. Chang Gung Med J 2011, 34:135-152.
  • [45]Fossale E, Seong IS, Coser KR, Shioda T, Kohane IS, Wheeler VC, Gusella JF, MacDonald ME, Lee JM: Differential effects of the Huntington’s disease CAG mutation in striatum and cerebellum are quantitative not qualitative. Hum Mol Genet 2011, 20:4258-4267.
  • [46]Khatri P, Draghici S: Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005, 21:3587-3595.
  • [47]Langfelder P, Mischel PS, Horvath S: When is hub gene selection better than standard meta-analysis? PLoS One 2013, 8:e61505.
  • [48]Soulet D, Cicchetti F: The role of immunity in Huntington’s disease. Mol Psychiatry 2011, 16:889-902.
  • [49]Zhang B, Gaiteri C, Bodea LG, Wang Z, McElwee J, Podtelezhnikov AA, Zhang CS, Xie T, Tran L, Dobrin R, Fluder E, Clurman B, Melquist S, Narayanan M, Suver C, Shah H, Mahajan M, Gillis T, Mysore J, MacDonald ME, Lamb JR, Bennett DA, Molony C, Stone DJ, Gudnason V, Myers AJ, Schadt EE, Neumann H, Zhu J, Emilsson V: Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer’s disease. Cell 2013, 153:707-720.
  • [50]Venkova-Hristova K, Christov A, Kamaluddin Z, Kobalka P, Hensley K: Progress in therapy development for amyotrophic lateral sclerosis. Neurol Res Int 2012, 2012:187234.
  • [51]Kantarci OH, Pirko I, Rodriguez M: Novel immunomodulatory approaches for the management of multiple sclerosis. Clin Pharmacol Ther 2014, 95:32-44.
  • [52]Deleidi M, Gasser T: The role of inflammation in sporadic and familial Parkinson’s disease. Cell Mol Life Sci 2013, 70:4259-4273.
  • [53]Crotti A, Benner C, Kerman BE, Gosselin D, Lagier-Tourenne C, Zuccato C, Cattaneo E, Gage FH, Cleveland DW, Glass CK: Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors. Nat Neurosci 2014, 17:513-521.
  • [54]Tong X, Ao Y, Faas GC, Nwaobi SE, Xu J, Haustein MD, Anderson MA, Mody I, Olsen ML, Sofroniew MV, Khakh BS: Astrocyte Kir4.1 ion channel deficits contribute to neuronal dysfunction in Huntington’s disease model mice. Nat Neurosci 2014, 17:694-703.
  • [55]Singhrao SK, Neal JW, Morgan BP, Gasque P: Increased complement biosynthesis by microglia and complement activation on neurons in Huntington’s disease. Exp Neurol 1999, 159:362-376.
  • [56]Rus H, Cudrici C, David S, Niculescu F: The complement system in central nervous system diseases. Autoimmunity 2006, 39:395-402.
  • [57]Labbadia J, Morimoto RI: Huntington’s disease: underlying molecular mechanisms and emerging concepts. Trends Biochem Sci 2013, 38:378-385.
  • [58]Carnemolla A, Labbadia JP, Lazell H, Neueder A, Moussaoui S, Bates GP: Contesting the dogma of an age-related heat shock response impairment: implications for cardiac-specific age-related disorders. Hum Mol Genet 2014, 23:3641-3656.
  • [59]Fernandez-Nogales M, Cabrera JR, Santos-Galindo M, Hoozemans JJ, Ferrer I, Rozemuller AJ, Hernandez F, Avila J, Lucas JJ: Huntington’s disease is a four-repeat tauopathy with tau nuclear rods. Nat Med 2014, 20:881-885.
  • [60]Scarffe LA, Stevens DA, Dawson VL, Dawson TM: Parkin and PINK1: much more than mitophagy. Trends Neurosci 2014, 37:315-324.
  • [61]Jin K, LaFevre-Bernt M, Sun Y, Chen S, Gafni J, Crippen D, Logvinova A, Ross CA, Greenberg DA, Ellerby LM: FGF-2 promotes neurogenesis and neuroprotection and prolongs survival in a transgenic mouse model of Huntington’s disease. Proc Natl Acad Sci U S A 2005, 102:18189-18194.
  • [62]Hands SL, Mason R, Sajjad MU, Giorgini F, Wyttenbach A: Metallothioneins and copper metabolism are candidate therapeutic targets in Huntington’s disease. Biochem Soc Trans 2010, 38:552-558.
  • [63]Labbadia J, Cunliffe H, Weiss A, Katsyuba E, Sathasivam K, Seredenina T, Woodman B, Moussaoui S, Frentzel S, Luthi-Carter R, Paganetti P, Bates GP: Altered chromatin architecture underlies progressive impairment of the heat shock response in mouse models of Huntington disease. J Clin Invest 2011, 121:3306-3319.
  • [64]Hayashida N, Fujimoto M, Tan K, Prakasam R, Shinkawa T, Li L, Ichikawa H, Takii R, Nakai A: Heat shock factor 1 ameliorates proteotoxicity in cooperation with the transcription factor NFAT. EMBO J 2010, 29:3459-3469.
  • [65]Vidal RL, Figueroa A, Court FA, Thielen P, Molina C, Wirth C, Caballero B, Kiffin R, Segura-Aguilar J, Cuervo AM, Glimcher LH, Hetz C: Targeting the UPR transcription factor XBP1 protects against Huntington’s disease through the regulation of FoxO1 and autophagy. Hum Mol Genet 2012, 21:2245-2262.
  • [66]Anglada-Huguet M, Giralt A, Perez-Navarro E, Alberch J, Xifro X: Activation of Elk-1 participates as a neuroprotective compensatory mechanism in models of Huntington’s disease. J Neurochem 2012, 121:639-648.
  • [67]Perrin V, Dufour N, Raoul C, Hassig R, Brouillet E, Aebischer P, Luthi-Carter R, Deglon N: Implication of the JNK pathway in a rat model of Huntington’s disease. Exp Neurol 2009, 215:191-200.
  • [68]Rigamonti D, Mutti C, Zuccato C, Cattaneo E, Contini A: Turning REST/NRSF dysfunction in Huntington’s disease into a pharmaceutical target. Curr Pharm Des 2009, 15:3958-3967.
  • [69]Steffan JS, Kazantsev A, Spasic-Boskovic O, Greenwald M, Zhu YZ, Gohler H, Wanker EE, Bates GP, Housman DE, Thompson LM: The Huntington’s disease protein interacts with p53 and CREB-binding protein and represses transcription. Proc Natl Acad Sci U S A 2000, 97:6763-6768.
  • [70]Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U: ArrayExpress update–trends in database growth and links to data analysis tools. Nucleic Acids Res 2013, 41:D987-990.
  • [71]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 2013, 41:D991-995.
  • [72]Lim WK, Wang K, Lefebvre C, Califano A: Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics 2007, 23:i282-288.
  • [73]Miller JA, Cai C, Langfelder P, Geschwind DH, Kurian SM, Salomon DR, Horvath S: Strategies for aggregating gene expression data: the collapseRows R function. BMC Bioinformatics 2011, 12:322. BioMed Central Full Text
  • [74]Langfelder P, Zhang B, Horvath S: Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 2008, 24:719-720.
  • [75]Chen BE, Sakoda LC, Hsing AW, Rosenberg PS: Resampling-based multiple hypothesis testing procedures for genetic case–control association studies. Genet Epidemiol 2006, 30:495-507.
  • [76]Langfelder P, Luo R, Oldham MC, Horvath S: Is my network module preserved and reproducible? PLoS Comput Biol 2011, 7:e1001057.
  • [77]Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
  • [78]Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N: GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics 2012, 28:2209-2210.
  • [79]Zhang B, Kirov S, Snoddy J: WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res 2005, 33:W741-748.
  • [80]da Huang W, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
  • [81]Vihola A, Bachinski LL, Sirito M, Olufemi SE, Hajibashi S, Baggerly KA, Raheem O, Haapasalo H, Suominen T, Holmlund-Hampf J, Paetau A, Cardani R, Meola G, Kalimo H, Edstrom L, Krahe R, Udd B: Differences in aberrant expression and splicing of sarcomeric proteins in the myotonic dystrophies DM1 and DM2. Acta Neuropathol 2010, 119:465-479.
  • [82]Pescatori M, Broccolini A, Minetti C, Bertini E, Bruno C, D'Amico A, Bernardini C, Mirabella M, Silvestri G, Giglio V, Modoni A, Pedemonte M, Tasca G, Galluzzi G, Mercuri E, Tonali PA, Ricci E: Gene expression profiling in the early phases of DMD: a constant molecular signature characterizes DMD muscle from early postnatal life throughout disease progression. FASEB J 2007, 21:1210-1226.
  • [83]Barth AS, Kuner R, Buness A, Ruschhaupt M, Merk S, Zwermann L, Kaab S, Kreuzer E, Steinbeck G, Mansmann U, Poustka A, Nabauer M, Sultmann H: Identification of a common gene expression signature in dilated cardiomyopathy across independent microarray studies. J Am Coll Cardiol 2006, 48:1610-1617.
  • [84]Lenburg ME, Liou LS, Gerry NP, Frampton GM, Cohen HT, Christman MF: Previously unidentified changes in renal cell carcinoma gene expression identified by parametric analysis of microarray data. BMC Cancer 2003, 3:31. BioMed Central Full Text
  • [85]Fassunke J, Majores M, Tresch A, Niehusmann P, Grote A, Schoch S, Becker AJ: Array analysis of epilepsy-associated gangliogliomas reveals expression patterns related to aberrant development of neuronal precursors. Brain 2008, 131:3034-3050.
  文献评价指标  
  下载次数:41次 浏览次数:10次