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(Sigma-Aldrich, St. Louis, MO). High-quality genomic DNA (500ng) from each sample werehybridized on Agilent Human 4x44K CGH Microarrays (Agilent Technologies, Santa Clara,CA) using a standard direct method as described in the Agilent Oligonucleotide Array-BasedCGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells or Tissues(www.chem.agilent.com) using a male commercial genomic DNA (Promega, USA) asreference. After slides scanning (Agilent scanner at 5 µm resolution), the array data wasextracted using the default CGH settings of the Feature Extraction v.10.1.1.1 (AgilentTechnologies, Santa Clara, CA).Identification of significant CNAs by using JISTIC. Copy number analysis wasperformed using segmented genomic dataset (DNAcopy,http://www.bioconductor.org/packages/2.3/bioc/html/DNAcopy.html) and JISTIC algorithm[22]. JISTIC gives G DEL and G AMP scores for each altered region (loss and gains,respectively), multiplied by the increase average in the ratio in log 2 amplified sample. Scoring(G score) is based on the amplitude mean (a) of the aberration type (G DEL or G AMP ) andfrequency (f) on the data set. The meaning of each score is determined by comparison withsimilar results obtained after permutation within each sample. All regions with a q-valuebelow a threshold (0.25) are deemed significant. For large aberrations, the sub-region with aminimal q-value is identified as a peak driver region.Transcriptional profiling. Total RNA was extracted from frozen tissues using theRNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions.Microarray experiments were performed using Two-Color Human GE 4x44K Microarrays.Isolated RNA (500-1000ng) was converted to cDNA with reverse transcriptase and anoligo(dT) primer bearing a T7 promotor followed by in vitro transcription with T7 RNApolymerase to create amplified antisense RNA. RNA reference [23] was amplified as above.Microarray image analysis was done using Feature Extraction v.10.1.1.1 (Agilent5
Technologies, Santa Clara, CA). Statistical analysis was performed using backgroundcorrectedmean signal intensities from each dye channel. Microarray data were normalizedusing intensity-dependent global normalization (LOWESS) using Feature Extractionv.10.1.1.1 software (Agilent Technologies, Santa Clara, CA).Significant genes based on expression analysis. The raw data from array scans werenormalized by median-centering genes for each array, and log 2 transformed. Additionally,genes with 30 or more ‘absent’ scores were filtered out. A total of 16354 sequences wereanalyzed. In order to identify significant genes, the Significance Analysis of Microarrays(SAM) method was applied [24]. The False Discovery Ratio (FDR)
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Universidade Estadual Paulista “J
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AGRADECIMENTOSÀ minha orientadora
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LISTA DE FIGURASFigura 1 A - Freqü
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sonda A_14_P131252 que mapeia o gen
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esultante da análise do SAM (Tushe
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Figura 33 Agrupamento hierárquico
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LISTA DE TABELASQuadro 1Relação d
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LISTA DE SIGLAS E ABREVIATURASANG A
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SUMÁRIO1 Introdução ............
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Cirilo, PDRINTRODUÇÃO11. Introdu
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Cirilo, PDRINTRODUÇÃO3dados em li
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Cirilo, PDRINTRODUÇÃO5infertilida
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Cirilo, PDRINTRODUÇÃO7foram despe
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Cirilo, PDRINTRODUÇÃO9(10q24.33),
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Cirilo, PDRINTRODUÇÃO11somente fo
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Cirilo, PDRINTRODUÇÃO13Segundo a
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Cirilo, PDRINTRODUÇÃO15(Sargent e
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Cirilo, PDRINTRODUÇÃO171 geralmen
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Cirilo, PDRINTRODUÇÃO19transcrita
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Cirilo, PDRINTRODUÇÃO21amostras.
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Cirilo, PDRINTRODUÇÃO23evento que
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Cirilo, PDRINTRODUÇÃO25também os
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Cirilo, PDRINTRODUÇÃO27tratamento
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Cirilo, PDRINTRODUÇÃO29Hodge et a
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Cirilo, PDRMATERIAL E MÉTODOS313.
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Cirilo, PDRMATERIAL E MÉTODOS33Tam
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Cirilo, PDRMATERIAL E MÉTODOS35for
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Cirilo, PDRMATERIAL E MÉTODOS370,1
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Cirilo, PDRMATERIAL E MÉTODOS39alt
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Cirilo, PDRMATERIAL E MÉTODOS413)
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Cirilo, PDRRESULTADOS43Tabela 1. Da
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Cirilo, PDRRESULTADOS45ABFigura 1.
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Cirilo, PDRRESULTADOS47Este estudo
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Cirilo, PDRRESULTADOS494.2.1 Caract
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Cirilo, PDRRESULTADOS51Entre as 45
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Cirilo, PDRRESULTADOS53(10%)Cromoss
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Cirilo, PDRRESULTADOS55Cromossomo 1
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Cirilo, PDRRESULTADOS574.2.2 Tumore
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Cirilo, PDRRESULTADOS59Tabela 4. De
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Cirilo, PDRRESULTADOS61629T 629T_A,
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Cirilo, PDRRESULTADOS63279,263-1,48
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Cirilo, PDRRESULTADOS65ABFigura 7.
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Cirilo, PDRRESULTADOS67ABFigura 8 -
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ABCirilo, PDRRESULTADOS69Figura 10.
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Cirilo, PDRRESULTADOS71Figura 11. A
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Cirilo, PDRRESULTADOS73Grupo 1tumor
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Cirilo, PDRRESULTADOS77631T_C 99,55
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Cirilo, PDRRESULTADOS794.3 Análise
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Cirilo, PDRRESULTADOS81Tabela 7. Re
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ABCirilo, PDRRESULTADOS83Figura 16.
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Cirilo, PDRRESULTADOS85Figura 17. V
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Cirilo, PDRRESULTADOS87Figura 19. R
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Cirilo, PDRRESULTADOS894.3.1 Análi
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Cirilo, PDRRESULTADOS93Entre os cas
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Cirilo, PDRRESULTADOS97Tabela 8. Ge
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Cirilo, PDRRESULTADOS99HAPLN1 HAPLN
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Cirilo, PDRRESULTADOS101beta 4MYO10
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Cirilo, PDRRESULTADOS103DIO1 DIO1 d
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Cirilo, PDRRESULTADOS105inhibits CD
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Cirilo, PDRRESULTADOS107CENPK CENPK
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Cirilo, PDRRESULTADOS109pareamento
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Cirilo, PDRRESULTADOS111JUB, ↓MAG
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Cirilo, PDRRESULTADOS113Figura 25.
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Cirilo, PDRRESULTADOS1194.5.1 CGH a
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Cirilo, PDRRESULTADOS123Tabela 10.
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Cirilo, PDRRESULTADOS125
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Cirilo, PDRRESULTADOS1274.5.3.1 Pre
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Cirilo, PDRRESULTADOS129PKP3 - -PRE
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Cirilo, PDRRESULTADOS133Perda (1) N
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ABCirilo, PDRRESULTADOS135Figura 33
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Cirilo, PDRRESULTADOS1374.5.3.4 Fre
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Cirilo, PDRRESULTADOS1414.5.3.6 An
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Cirilo, PDRRESULTADOS145ativação
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ACirilo, PDRRESULTADOS147BFigura 36
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Cirilo, PDRDISCUSSÃO1515. Discuss
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Cirilo, PDRDISCUSSÃO154informaçõ
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Cirilo, PDRDISCUSSÃO156descritos g
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Cirilo, PDRDISCUSSÃO158uma proteí
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Cirilo, PDRDISCUSSÃO160celulares e
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Cirilo, PDRDISCUSSÃO162apresentado
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Cirilo, PDRDISCUSSÃO164q14). Porta
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Cirilo, PDRDISCUSSÃO166Desde 1991,
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Cirilo, PDRDISCUSSÃO168núcleo das
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Cirilo, PDRDISCUSSÃO170sobre LHFPL
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Cirilo, PDRDISCUSSÃO172outras cate
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Cirilo, PDRDISCUSSÃO174Entre as ou
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Cirilo, PDRDISCUSSÃO176regiões de
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Cirilo, PDRDISCUSSÃO178da RNA Pol
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Cirilo, PDRDISCUSSÃO180proliferati
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Cirilo, PDRDISCUSSÃO182Entre os 20
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Cirilo, PDRDISCUSSÃO184propôs um
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Cirilo, PDRDISCUSSÃO186analisados
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Cirilo, PDRDISCUSSÃO188observados
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Cirilo, PDRDISCUSSÃO190moduladores
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Cirilo, PDRDISCUSSÃO192genômica/d
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Cirilo, PDRDISCUSSÃO194identificar
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Cirilo, PDRDISCUSSÃO196e também d
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Cirilo, PDRDISCUSSÃO198O gene COL3
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Cirilo, PDRDISCUSSÃO200resistênci
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Cirilo, PDRDISCUSSÃO202bioquímica
Page 227 and 228: Cirilo, PDRDISCUSSÃO204carcinoma c
Page 229 and 230: Cirilo, PDRCONCLUSÕES DISCUSSÃO20
Page 231 and 232: Cirilo, PDRREFERÊNCIAS2087. Refer
Page 233 and 234: Cirilo, PDRREFERÊNCIAS210Brazelle
Page 235 and 236: Cirilo, PDRREFERÊNCIAS212Churikov
Page 237 and 238: Cirilo, PDRREFERÊNCIAS214Gannon BR
Page 239 and 240: Cirilo, PDRREFERÊNCIAS216Holthause
Page 241 and 242: Cirilo, PDRREFERÊNCIAS218Kazmiercz
Page 243 and 244: Cirilo, PDRREFERÊNCIAS220Lloret M,
Page 245 and 246: Cirilo, PDRREFERÊNCIAS222Mitra R,
Page 247 and 248: Cirilo, PDRREFERÊNCIAS224Ozisik YY
Page 249 and 250: Cirilo, PDRREFERÊNCIAS226Redon R,
Page 251 and 252: Cirilo, PDRREFERÊNCIAS228Solyom S,
Page 253 and 254: Cirilo, PDRREFERÊNCIAS230Ueki K, R
Page 255 and 256: Cirilo, PDRREFERÊNCIAS232and poly(
Page 257 and 258: Skubitz KM e Skubitz APJ Lab Clin M
Page 259 and 260: Dimitrova IK et al. Fertil Steril,9
Page 261 and 262: 317T_B317T_C13 614T 44 LU prolifera
Page 263 and 264: 46 867T 46 LUM outros B 14 33,5 17
Page 265 and 266: 1015T 6q13-q14.1 75,806,978-76,314,
Page 267 and 268: MRPS31, SLC25A15, SUGT1L1 320d-1630
Page 269 and 270: 8q22.3-q23.1 105,831,966 107,742,33
Page 271 and 272: Anexo 5. Genes identificados na an
Page 273 and 274: + + CCDC8 0 51 37 14+ - CALM3 51 0
Page 275 and 276: ABSTRACTBackground: Uterine leiomyo
Page 277: Thus, these findings prompt us to i
Page 281 and 282: mapped at 1p36.13, 1q41, 2q32.1, 2q
Page 283 and 284: genetic disorder showed the higher
Page 285 and 286: The modulators were mainly associat
Page 287 and 288: egulation of cell cycle. Chegini an
Page 289 and 290: REFERENCES[1] Baird DD, Dunson DB (
Page 291 and 292: [37] Luo X, Ding L, Xu J et al. (20
Page 293 and 294: AArray CGHExpression arrayBtumoral
Page 295 and 296: ABDiseases and Disorders P value Mo
Page 298 and 299: Tabel 2. Genes identified on module
Page 300 and 301: Table S1. Clinical parameters and h
Page 302 and 303: 32 954T 45 M secretory W 12 33,7 18
Page 304 and 305: 16 28184420-30915100 2730680 p11.2
Page 306 and 307: MYPN hsa-miR-214 -NFKBIL2 - -PKP3 -
Page 308: Table S5. Ingenuity Pathways Analys
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