Identification of transcriptional regulatory networks specific to pilocytic astrocytoma

BMC Medical Genomics

Volumn 4, Issue , 2011, Pages

  Deshmukh, Hrishikesh ^a   Yu, Jinsheng ^a   Shaik, Jahangheer ^a   MacDonald, Tobey J ^b   Perry, Arie ^a   Payton, Jacqueline E ^a   Gutmann, David H ^a   Watson, Mark A ^a   Nagarajan, Rakesh ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER CLASSIFICATION; CELL LINEAGE; CONTROLLED STUDY; ELK3 GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENE IDENTIFICATION; GENE INTERACTION; GENE REGULATORY NETWORK; GENE TARGETING; GLIOBLASTOMA; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; LMO2 GENE; MICROARRAY ANALYSIS; OLIGODENDROGLIOMA; ONCOGENE; ONECUT2 GENE; PHENOTYPE; PILOCYTIC ASTROCYTOMA; PRIORITY JOURNAL; RUNX1 GENE; STAT4 GENE; THRB GENE; TRANSCRIPTION REGULATION; ASTROCYTOMA; GENETICS; META ANALYSIS; METABOLISM; PATHOLOGY;

RNA;

ASTROCYTOMA; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; GLIOBLASTOMA; HUMANS; OLIGODENDROGLIOMA; RNA, NEOPLASM;

EID: 79960057046     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-4-57     Document Type: Article

References (30)

1. High-resolution, dual-platform aCGH analysis reveals frequent HIPK2 amplification and increased expression in pilocytic astrocytomas. Deshmukh H, Yeh TH, Yu J, Sharma MK, Perry A, Leonard JR, Watson MA, Gutmann DH, Nagarajan R, Oncogene 2008 27 34 4745 4751 10.1038/onc.2008.110 18408760
2. Genomic changes in progression of low-grade gliomas. Idbaih A, Carvalho Silva R, Crinière E, Marie Y, Carpentier C, Boisselier B, Taillibert S, Rousseau A, Mokhtari K, Ducray F, Thillet J, Sanson M, Hoang-Xuan K, Delattre JY, J Neurooncol 2008 90 2 133 140 10.1007/s11060-008-9644-z 18618226
3. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Cancer Genome Atlas Research Network, Nature 2008 455 7216 1061 1068 10.1038/nature07385 18772890
4. Distinct genetic signatures among pilocytic astrocytomas relate to their brain region origin. Sharma MK, Mansur DB, Reifenberger G, Perry A, Leonard JR, Aldape KD, Albin MG, Emnett RJ, Loeser S, Watson MA, Nagarajan R, Gutmann DH, Cancer Research 2007 67 3 890 900 10.1158/0008-5472.CAN-06-0973 17283119
5. Gene expression profiling of gliomas strongly predicts survival. Freije WA, Castro-Vargas FE, Fang Z, Horvath S, Cloughesy T, Liau LM, Mischel PS, Nelson SF, Cancer Research 2004 64 18 6503 6510 10.1158/0008-5472.CAN-04-0452 15374961 (Pubitemid 39297907)
6. Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays. French PJ, Peeters J, Horsman S, Duijm E, Siccama I, van den Bent MJ, Luider TM, Kros JM, van der Spek P, Sillevis Smitt PA, Cancer Research 2007 67 12 5635 5642 10.1158/0008-5472. CAN-06-2869 17575129 (Pubitemid 46984994)
7. Molecularly targeted therapies for glioma. Yamanaka R, Saya H, Ann Neurol 2009 66 6 717 729 10.1002/ana.21793 20035507
8. Transcriptional pathway signatures predict MEK addiction and response to selumetinib (AZD6244). Dry JR, Pavey S, Pratilas CA, Harbron C, Runswick S, Hodgson D, Chresta C, McCormack R, Byrne N, Cockerill M, Graham A, Beran G, Cassidy A, Haggerty C, Brown H, Ellison G, Dering J, Taylor BS, Stark M, Bonazzi V, Ravishankar S, Packer L, Xing F, Solit DB, Finn RS, Rosen N, Hayward NK, French T, Smith PD, Cancer Research 2010 70 6 2264 2273 10.1158/0008-5472.CAN- 09-1577 20215513
9. Duplication of 7q34 is specific to juvenile pilocytic astrocytomas and a hallmark of cerebellar and optic pathway tumors. Jacob K, Albrecht S, Sollier C, Faury D, Sader E, Montpetit A, Serre D, Hauser P, Garami M, Bognar L, Hanzely Z, Montes JL, Atkinson J, Farmer JP, Bouffet E, Hawkins C, Tabori U, Jabado N, Br J Cancer 2009 101 4 722 733 10.1038/sj.bjc.6605179 19603027
10. Duplication of 7q34 in pediatric low-grade astrocytomas detected by high-density single-nucleotide polymorphism-based genotype arrays results in a novel BRAF fusion gene. Sievert AJ, Jackson EM, Gai X, Hakonarson H, Judkins AR, Resnick AC, Sutton LN, Storm PB, Shaikh TH, Biegel JA, Brain Pathol 2009 19 3 449 458 10.1111/j.1750-3639.2008.00225.x 19016743
11. Systematic analysis of gene expression in human brains before and after death. Franz H, Ullmann C, Becker A, Ryan M, Bahn S, Arendt T, Simon M, Paabo S, Khaitovich P, Genome biology 2005 6 13 112 10.1186/gb-2005-6-13-r112 16420671 (Pubitemid 43871840)
12. Positive selection on gene expression in the human brain. Khaitovich P, Tang K, Franz H, Kelso J, Hellmann I, Enard W, Lachmann M, Paabo S, Curr Biol 2006 16 10 356 358 10.1016/j.cub.2006.03.082 16618540 (Pubitemid 43728218)
13. Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Phillips HS, Kharbanda S, Chen R, Forrest WF, Soriano RH, Wu TD, Misra A, Nigro JM, Colman H, Soroceanu L, Williams PM, Modrusan Z, Feuerstein BG, Aldape K, Cancer cell 2006 9 3 157 173 10.1016/j.ccr.2006.02.019 16530701 (Pubitemid 43357943)
14. Significance analysis of microarrays applied to the ionizing radiation response. Tusher VG, Tibshirani R, Chu G, Proc Natl Acad Sci USA 2001 98 5116 5121 10.1073/pnas.091062498 11309499 (Pubitemid 32397092)
15. PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. Chang LW, Fontaine BR, Stormo GD, Nagarajan R, Nucleic acids research 2007 35 Web Server 238 244 10.1093/nar/gkm308 17517777
16. Bioinformatics applications for pathway analysis of microarray data. Werner T, Current opinion in biotechnology 2008 19 1 50 54 10.1016/j.copbio. 2007.11.005 18207385
17. Reducing multiclass cancer classification to binary by output coding and SVM. Shen L, Tan EC, Computational biology and chemistry 2006 30 1 63 71 10.1016/j.compbiolchem.2005.10.008 16321568 (Pubitemid 43144433)
18. Network-based support vector machine for classification of microarray samples. Zhu Y, Shen X, Pan W, BMC bioinformatics 2009 10 Suppl 1 21 10.1186/1471-2105-10-S1-S21 19534747
19. GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data. Wu CC, Huang HC, Juan HF, Chen ST, Bioinformatics (Oxford, England) 2004 20 18 3691 3693 10.1093/bioinformatics/bth428 (Pubitemid 40136818)
20. PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Demir E, Babur O, Dogrusoz U, Gursoy A, Nisanci G, Cetin-Atalay R, Ozturk M, Bioinformatics (Oxford, England) 2002 18 7 996 1003 10.1093/bioinformatics/18.7.996 (Pubitemid 34846483)
21. Bioinformatics applications for pathway analysis of microarray data. Werner T, Current opinion in biotechnology 2008 19 1 50 54 10.1016/j.copbio. 2007.11.005 18207385
22. Reverse engineering of regulatory networks in human B cells. Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A, Nat Genet 2005 37 4 382 90 10.1038/ng1532 15778709
23. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A, BMC Bioinformatics 2006 7 Suppl 1 7 10.1186/1471-2105-7-S1-S7 17254312 (Pubitemid 46437495)
24. The transcriptional network for mesenchymal transformation of brain tumours. Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao X, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A, Nature 2010 463 7279 318 25 10.1038/nature08712 20032975
25. PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. Chang LW, Fontaine BR, Stormo GD, Nagarajan R, Nucleic acids research 2007 35 Web Server 238 244 10.1093/nar/gkm308 17517777
26. A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles. Chang LW, Nagarajan R, Magee JA, Milbrandt J, Stormo GD, Genome research 2006 16 3 405 413 10.1101/gr.4303406 16449500 (Pubitemid 43328875)
27. Complex regulation of acetylcholinesterase gene expression in human brain tumors. Perry C, Sklan EH, Birikh K, Shapira M, Trejo L, Eldor A, Soreq H, Oncogene 2002 21 55 8428 8441 10.1038/sj.onc.1205945 12466963 (Pubitemid 36054884)
28. Identification of astrocytoma associated genes including cell surface markers. Boon K, Edwards JB, Eberhart CG, Riggins GJ, BMC cancer 2004 4 39 10.1186/1471-2407-4-39 15265232 (Pubitemid 40180247)
29. WHO Classification of Tumors of the Nervous System. Louis DN, Ohgaki H, Wiestler OD, Cavenee WK, IARC: Lyon 2007
30. Oligodendroglial-specific transcriptional factor SOX10 is ubiquitously expressed in human gliomas. Bannykh SI, Stolt CC, Kim J, Perry A, Wegner M, J Neurooncol 2006 76 2 115 127 10.1007/s11060-005-5533-x 16205963 (Pubitemid 43135844)