Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

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A.1 Differential Expression Appendix Gene symbol(s) Entrez gene ID(s) Ensembl 56 gene ID(s) Differential expression results Normalised tag counts log 2(F C) p-value FDR G144ED G144 G166 G179 CB541 CB660 NPTX2 4885 ENSG00000106236 -6.47 1.11E-08 1.78E-06 0.0 0.0 6.9 4.8 422.0 272.4 NR0B1 190 ENSG00000169297 Inf 6.79E-15 5.60E-12 0.0 0.0 0.0 1039.8 0.0 0.0 NR1D1 9572 ENSG00000126368 2.86 1.07E-03 3.15E-02 80.9 136.8 469.2 220.4 51.7 24.2 NR4A2 4929 ENSG00000153234 Inf 4.54E-04 1.64E-02 86.9 79.7 4.4 14.6 0.0 0.0 NRBF2 29982 ENSG00000148572 -Inf 2.85E-04 1.12E-02 0.0 0.0 0.0 0.0 12.9 59.5 NRG1 3084 ENSG00000157168 Inf 2.27E-04 9.29E-03 2.7 9.7 60.4 30.0 0.0 0.0 NRN1 51299 ENSG00000124785 Inf 6.59E-09 1.13E-06 317.7 235.8 49.5 48.5 0.0 0.0 NRP2 8828 ENSG00000118257 2.86 4.26E-04 1.58E-02 33.7 60.1 169.0 901.9 26.6 76.3 NTN1 9423 ENSG00000065320 -4.22 1.58E-06 1.48E-04 95.8 239.9 22.4 250.6 5458.0 966.2 NTRK2 4915 ENSG00000148053 3.61 4.89E-05 2.57E-03 90.7 163.9 174.8 219.5 0.0 30.3 NXPH1 30010 ENSG00000122584 4.57 4.70E-05 2.49E-03 325.0 414.1 0.0 26.6 8.4 4.0 OAS1 4938 ENSG00000089127 6.47 1.46E-04 6.41E-03 0.0 0.0 53.9 81.2 0.0 1.4 OAS2 4939 ENSG00000111335 Inf 2.18E-05 1.36E-03 0.0 0.0 73.4 65.7 0.0 0.0 OAS3 4940 ENSG00000111331 3.88 1.48E-03 4.03E-02 2.7 6.5 55.6 162.4 9.1 1.0 OASL 8638 ENSG00000135114 Inf 2.20E-08 3.30E-06 1.2 7.8 102.4 180.2 0.0 0.0 ODZ2 57451 ENSG00000145934 -3.68 1.49E-04 6.51E-03 27.0 25.0 2.5 36.0 212.8 329.5 OGN 4969 ENSG00000106809 -Inf 3.58E-04 1.36E-02 0.0 0.0 0.0 0.0 0.0 71.6 OLFM1 10439 ENSG00000130558 4.72 2.31E-04 9.44E-03 200.9 227.7 11.3 0.0 0.0 6.0 OTOR 56914 ENSG00000125879 9.92 3.31E-15 3.28E-12 1169.3 1474.1 0.0 0.0 0.0 1.0 OTX2 5015 ENSG00000165588 -Inf 6.59E-04 2.16E-02 0.0 0.0 0.0 0.0 40.1 14.8 OXTR 5021 ENSG00000180914 3.67 1.99E-03 5.00E-02 28.0 111.2 36.0 94.6 7.6 4.6 P2RX7 5027 ENSG00000089041 7.72 1.34E-11 4.42E-09 691.5 611.8 25.5 2.2 0.0 2.0 PARP12 64761 ENSG00000059378 2.92 1.36E-03 3.77E-02 18.2 21.9 196.2 300.2 24.5 21.2 PARP3 10039 ENSG00000041880 4.12 3.46E-05 1.93E-03 5.4 25.0 145.0 267.2 7.7 9.3 PAX8 7849 ENSG00000125618 -2.80 1.78E-03 4.66E-02 0.0 0.0 40.1 66.0 438.3 53.5 PCDH20 64881 ENSG00000197991 6.16 1.08E-05 7.67E-04 65.1 7.8 1.3 208.6 0.0 2.0 PCDHB12 56124 ENSG00000120328 -7.05 2.05E-03 5.09E-02 2.7 0.0 0.7 0.0 31.9 23.1 PCDHB3 56132 ENSG00000113205 5.39 1.08E-03 3.16E-02 90.5 107.6 0.0 35.2 2.3 0.0 PCDHB4 56131 ENSG00000081818 5.88 2.01E-06 1.85E-04 337.8 351.5 5.6 0.0 0.0 4.0 PCOLCE2 26577 ENSG00000163710 5.77 4.31E-03 9.05E-02 0.0 0.0 3.7 79.4 0.0 1.3 PDE1C 5137 ENSG00000154678 4.13 1.38E-06 1.32E-04 578.2 430.3 1117.8 981.4 45.7 50.8 PDE4B 5142 ENSG00000184588 -5.35 2.42E-03 5.74E-02 9.5 1.6 0.6 0.0 42.5 17.2 PDGFA 5154 ENSG00000197461 3.58 1.02E-04 4.80E-03 1540.7 1178.9 41.4 32.8 20.8 49.3 PDGFRA 5156 ENSG00000134853 7.42 1.03E-14 7.67E-12 2309.4 2706.9 66.4 355.6 0.0 12.1 PDGFRB 5159 ENSG00000113721 -3.44 1.87E-03 4.81E-02 34.3 18.8 29.9 3.3 58.0 316.0 PDPN 10630 ENSG00000162493 4.68 4.08E-08 5.72E-06 1470.9 1283.2 107.6 2041.3 12.9 75.3 PDZRN3 23024 ENSG00000121440 -4.40 1.38E-05 9.38E-04 18.4 22.1 12.6 3.0 278.2 251.3 PEA15 8682 ENSG00000162734 -2.44 2.01E-03 5.04E-02 1189.8 1377.8 590.8 1060.2 9727.1 1297.6 PERP 64065 ENSG00000112378 3.83 4.28E-04 1.58E-02 1.4 0.0 200.3 108.2 11.4 3.3 PHACTR3 116154 ENSG00000087495 Inf 2.70E-04 1.07E-02 44.0 117.1 0.0 0.0 0.0 0.0 PHLPP1 23239 ENSG00000081913 -2.64 8.54E-04 2.61E-02 469.3 331.2 166.3 100.8 1557.1 924.7 PI15 51050 ENSG00000137558 -6.45 4.25E-10 9.29E-08 20.2 3.3 2.5 5.5 397.8 262.2 PIGA 5277 ENSG00000165195 3.43 1.79E-03 4.67E-02 13.9 10.3 182.7 97.2 16.1 2.0 PION 54103 ENSG00000186088 Inf 7.59E-05 3.75E-03 7.3 18.7 13.2 87.4 0.0 0.0 PITPNC1 26207 ENSG00000154217 3.72 5.25E-04 1.80E-02 293.0 215.2 39.5 54.9 1.7 13.7 PITX1 5307 ENSG00000069011 6.80 7.33E-13 2.94E-10 1.4 3.1 480.6 531.7 6.2 0.0 PKNOX2 63876 ENSG00000165495 -2.77 3.36E-03 7.40E-02 62.9 32.3 1.5 1.9 109.0 53.4 PLA2G2A 5320 ENSG00000188257 Inf 3.34E-18 1.24E-14 1227.8 4419.1 0.6 6.3 0.0 0.0 PLA2G4A 5321 ENSG00000116711 7.34 1.68E-15 1.92E-12 909.7 1226.5 483.7 755.9 0.0 10.1 PLAC9 219348 ENSG00000189129 2.81 2.96E-03 6.69E-02 182.5 578.2 0.6 18.7 0.0 56.6 PLCB1 23236 ENSG00000182621 -2.27 2.87E-03 6.55E-02 103.0 73.1 8.4 53.8 366.7 70.9 PLCH1 23007 ENSG00000114805 -3.41 4.41E-05 2.38E-03 152.0 134.0 83.3 118.9 2002.9 384.3 244
A.1 Differential Expression Appendix Gene symbol(s) Entrez gene ID(s) Ensembl 56 gene ID(s) Differential expression results Normalised tag counts log 2(F C) p-value FDR G144ED G144 G166 G179 CB541 CB660 PLD3 23646 ENSG00000105223 -3.31 2.42E-04 9.76E-03 228.5 33.1 87.5 9.8 700.5 162.0 PLEKHA6 22874 ENSG00000143850 -5.40 3.21E-03 7.18E-02 6.8 0.0 0.6 1.6 39.9 24.7 PLS1 5357 ENSG00000120756 2.94 9.39E-04 2.82E-02 67.5 149.4 218.6 344.8 36.5 25.3 PLS3 5358 ENSG00000102024 3.83 3.67E-06 3.06E-04 360.2 776.6 476.6 367.2 0.0 75.6 PLSCR1 5359 ENSG00000188313 2.45 4.58E-03 9.47E-02 37.0 137.7 307.6 533.6 81.2 38.1 PMEPA1 56937 ENSG00000124225 4.36 4.99E-07 5.41E-05 240.8 123.3 621.8 297.2 11.7 22.1 PMP2 5375 ENSG00000147588 Inf 9.08E-15 7.10E-12 948.1 1312.7 0.0 0.0 0.0 0.0 PNMA2 10687 ENSG00000240694 -2.28 1.93E-03 4.90E-02 155.7 183.7 8.8 368.1 1517.6 305.5 PNP 4860 ENSG00000198805 3.92 3.87E-03 8.32E-02 36.5 20.7 115.6 8.3 2.4 3.7 PPAP2C 8612 ENSG00000141934 7.37 4.02E-07 4.52E-05 21.6 6.3 242.9 3.1 0.0 1.2 PPCS 79717 ENSG00000127125 2.94 3.03E-04 1.18E-02 57.1 106.2 771.9 214.9 32.7 61.6 PPEF1 5475 ENSG00000086717 4.44 6.87E-04 2.21E-02 12.2 165.1 9.6 23.0 0.0 6.4 PPHLN1 51535 ENSG00000134283 3.56 7.59E-04 2.37E-02 98.5 165.8 119.1 6.6 2.6 14.1 PPL 5493 ENSG00000118898 2.45 4.84E-03 9.82E-02 2.7 1.6 90.7 358.0 11.2 43.8 PPM1K 152926 ENSG00000163644 5.15 1.93E-03 4.90E-02 16.2 28.1 56.3 23.6 0.0 2.4 PPP4R1 9989 ENSG00000154845 -2.16 2.30E-03 5.54E-02 168.6 215.1 42.9 218.4 1239.4 180.3 PRIMA1 145270 ENSG00000175785 6.84 2.97E-09 5.51E-07 865.4 465.5 0.0 54.9 0.0 3.0 PROCR 10544 ENSG00000101000 4.09 1.87E-03 4.81E-02 5.5 0.0 181.8 0.0 6.3 1.5 PRSS12 8492 ENSG00000164099 3.66 1.95E-03 4.92E-02 128.0 49.8 55.6 87.1 0.0 10.1 PSORS1C1 170679 ENSG00000204540 Inf 1.11E-07 1.43E-05 0.0 0.0 212.3 29.0 0.0 0.0 PSPH 5723 ENSG00000146733 3.45 1.87E-03 4.81E-02 40.0 60.0 168.5 1.9 4.0 10.2 PTEN 5728 ENSG00000171862 -5.00 5.70E-05 2.94E-03 2.7 0.0 14.8 0.0 191.7 126.9 PTGS1 5742 ENSG00000095303 -3.91 4.31E-03 9.05E-02 12.2 6.8 1.6 0.0 61.9 20.2 PTPRD 5789 ENSG00000153707 -3.18 2.97E-03 6.69E-02 2.8 20.1 7.0 0.0 101.0 63.7 PTPRH 5794 ENSG00000080031 2.67 3.36E-03 7.40E-02 13.5 2.0 162.7 371.3 35.8 19.7 PTPRR 5801 ENSG00000153233 5.05 2.78E-03 6.42E-02 0.0 0.0 12.8 88.6 0.0 2.0 PXDN 7837 ENSG00000130508 3.01 6.69E-04 2.18E-02 1025.9 1801.8 163.8 146.9 41.9 132.8 PYGL 5836 ENSG00000100504 3.71 6.76E-05 3.41E-03 569.0 837.9 179.4 74.3 36.2 19.4 RAB11FIP1 80223 ENSG00000156675 -3.57 4.79E-03 9.75E-02 19.1 6.9 19.0 0.0 56.8 140.1 RAB38 23682 ENSG00000123892 3.17 2.79E-04 1.10E-02 137.3 221.7 53.7 963.8 58.6 33.4 RAB6B 51560 ENSG00000154917 -3.75 8.86E-05 4.27E-03 36.5 22.8 10.7 8.2 303.4 76.3 RAB7L1 8934 ENSG00000117280 6.23 5.37E-04 1.83E-02 82.1 62.9 52.1 0.0 0.0 1.0 RAD50 10111 ENSG00000113522 3.49 3.57E-03 7.77E-02 25.7 49.4 70.3 84.2 6.3 5.7 RADIL 55698 ENSG00000157927 3.00 4.70E-03 9.64E-02 113.9 92.3 13.5 137.8 0.0 20.3 RARRES1 5918 ENSG00000118849 6.00 5.06E-11 1.42E-08 5.6 0.0 16.6 1153.4 6.1 6.3 RARRES3 5920 ENSG00000133321 3.53 2.08E-04 8.65E-03 64.8 26.5 64.7 471.8 24.3 8.1 RASGEF1C 255426 ENSG00000146090 4.10 3.55E-03 7.75E-02 471.5 143.6 2.8 9.8 0.0 6.0 RASGRP3 25780 ENSG00000152689 Inf 2.81E-03 6.45E-02 0.0 5.2 26.1 38.5 0.0 0.0 REC8 9985 ENSG00000100918 -2.64 1.11E-03 3.22E-02 99.8 91.8 23.9 125.9 633.6 373.3 RGAG4 340526 ENSG00000242732 -3.26 7.97E-04 2.45E-02 21.3 18.6 28.2 19.8 267.2 157.6 RGL3 57139 ENSG00000205517 Inf 3.90E-04 1.47E-02 10.2 4.7 61.0 30.3 0.0 0.0 RGS17 26575 ENSG00000091844 4.76 7.40E-04 2.33E-02 84.3 107.6 5.6 50.7 0.0 4.2 RGS20 8601 ENSG00000147509 -3.16 4.95E-03 9.97E-02 0.0 0.0 7.1 25.6 136.0 56.5 RGS5 8490 ENSG00000143248 -4.82 3.40E-06 2.87E-04 4.1 13.5 6.9 3.0 343.5 112.5 RHBDF2 79651 ENSG00000129667 3.41 3.12E-05 1.78E-03 9.5 18.8 214.9 956.3 10.7 63.6 RHOBTB3 22836 ENSG00000164292 2.77 2.60E-03 6.09E-02 3292.5 2727.3 146.6 130.6 90.0 203.9 RHPN1 114822 ENSG00000158106 -4.18 2.88E-03 6.56E-02 21.7 5.9 0.0 0.0 40.3 35.3 RIPK4 54101 ENSG00000183421 6.16 6.76E-04 2.19E-02 2.4 0.0 50.8 58.0 0.0 1.0 RNASEH1 246243 ENSG00000171865 2.43 4.37E-03 9.14E-02 68.9 165.9 213.0 440.5 48.5 52.6 RNF175 285533 ENSG00000145428 6.81 5.25E-05 2.74E-03 225.4 165.0 5.1 0.0 0.0 1.1 RP11-473I1.1 ENSG00000220793 2.89 5.13E-04 1.78E-02 73.0 177.2 882.0 3.2 48.9 46.0 RP11-93B14.2,hCG_2018279 100127888 ENSG00000232803 Inf 3.11E-03 6.99E-02 41.3 72.1 1.3 0.0 0.0 0.0 245
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Transcriptional Characterization of
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This dissertation is my own work an
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Acknowledgements I would like to th
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5.9 External Dataset Expression Cor
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Introduction 1
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1.1 Glial Cells in the Central Nerv
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1.2 Glioblastoma Multiforme Introdu
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1.3 Primary and Secondary Glioblast
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1.4 Pathways Involved in Glioblasto
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1.5 Pathway Crosstalk Introduction
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Chapter 2 Neurogenesis Contents 2.1
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2.1 Radial Glia Introduction VZ adj
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2.2 Neural Stem Cells Introduction
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Chapter 3 Brain Cancer Stem Cells C
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3.1 The Cancer Stem Cell Hypothesis
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3.1 The Cancer Stem Cell Hypothesis
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3.2 Brain Cancer Stem Cells Introdu
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3.3 Glioma Culture Systems Introduc
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Chapter 4 The Non-Coding RNA World
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4.1 MicroRNA regulation Introductio
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4.1 MicroRNA regulation Introductio
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4.2 Target Prediction and Validatio
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Methods 93
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5.1 Tag-sequencing Data Processing
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5.1 Tag-sequencing Data Processing
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5.2 Array Comparative Genomic Hybri
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5.4 Quantitative Real Time-PCR Vali
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5.5 Literature Mining Methods Figur
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5.5 Literature Mining Methods How m
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5.6 Differential Isoform Expression
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5.9 External Dataset Expression Cor
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5.10 Glioblastoma Pathway Construct
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5.11 MicroRNA Target Prediction Ana
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Results 119
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6.2 Tag mapping Results Table 6.1:
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6.2 Tag mapping Results 123 Figure
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6.3 Copy Number Aberrations Results
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6.3 Copy Number Aberrations Results
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6.4 Core Differentially Expressed G
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6.5 Large-scale qRT-PCR Validation
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6.6 Literature Mining for Different
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6.7 Isoform Differential Expression
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6.8 Long ncRNA Differential Express
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6.8 Long ncRNA Differential Express
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Chapter 7 Dataset Correlation Analy
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7.1 Enrichment Analysis Results Tab
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7.1 Enrichment Analysis Results Fig
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7.1 Enrichment Analysis Results Tab
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7.2 Glioblastoma Expression Signatu
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7.3 Tumour Expression Correlation R
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7.4 Survival Analysis Results Table
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7.4 Survival Analysis Results 867 g
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7.5 Glioblastoma Pathway Analysis R
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E. Exon Array Data Appendix Average
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F. MicroRNA Array Data Appendix Tab
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F. MicroRNA Array Data Appendix GNS
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F. MicroRNA Array Data Appendix GNS
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Ln Natural logarithm LOH Loss of He
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3.3 Schematisation of cell cycle ph
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8.3 Workflows at the core of the pr
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7.1 Selected Gene Ontology terms an
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Bibliography [1] Cell signaling tec
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[38] G. Bain, D. Kitchens, M. Yao,
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[78] S. Bustin, V. Benes, J. Garson
Page 329 and 330:
[112] M. Czystowska, J. Han, M. Szc
Page 331 and 332:
[153] T. Fujiwara, M. Bandi, M. Nit
Page 333 and 334:
[192] M. Hernandez, M. Nieto, and M
Page 335 and 336:
[231] T.-M. Kim, W. Huang, R. Park,
Page 337 and 338:
[268] H. Lemjabbar-Alaoui, A. van Z
Page 339 and 340:
[305] K. MAEDA, S. MATSUHASHI, K. T
Page 341 and 342:
[342] H. Moon, M. Ahn, J. Park, K.
Page 343 and 344:
[379] D. Park and J. Rich. Biology
Page 345 and 346:
[417] P. Rakic. Guidance of neurons
Page 347 and 348:
[456] T. Shima, N. Okumura, T. Taka
Page 349 and 350:
[490] P. A. C. t’Hoen, Y. Ariyure
Page 351 and 352:
[523] T. Watanabe, A. Takeda, T. Ts
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