Genome-wide Characterization of miR-34a Induced Changes in Protein and mRNA Expression by a Combined Pulsed SILAC and Microarray Analysis

Name: Work Video:
Duration: 3 min 30 s
Markus Kaller; Sven‐Thorsten Liffers; Silke Oeljeklaus; Katja Kuhlmann; Simone Röh; Reinhard Hoffmann; Bettina Warscheid; Heiko Hermeking
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'https://openalex.org/W2070765029', 'https://openalex.org/W2072451938', 'https://openalex.org/W2078830718', 'https://openalex.org/W2080752012', 'https://openalex.org/W2083158631', 'https://openalex.org/W2091436921', 'https://openalex.org/W2092627144', 'https://openalex.org/W2099013228', 'https://openalex.org/W2106382644', 'https://openalex.org/W2111655556', 'https://openalex.org/W2118827241', 'https://openalex.org/W2119239003', 'https://openalex.org/W2119337308', 'https://openalex.org/W2121085194', 'https://openalex.org/W2124826504', 'https://openalex.org/W2130419781', 'https://openalex.org/W2130638154', 'https://openalex.org/W2132089284', 'https://openalex.org/W2134104386', 'https://openalex.org/W2137713702', 'https://openalex.org/W2140694202', 'https://openalex.org/W2140946052', 'https://openalex.org/W2144038313', 'https://openalex.org/W2144154026', 'https://openalex.org/W2149563566', 'https://openalex.org/W2152658454', 'https://openalex.org/W2154294588', 'https://openalex.org/W2155631307', 'https://openalex.org/W2156843318', 'https://openalex.org/W2160998038', 'https://openalex.org/W2162674813', 'https://openalex.org/W2163106706', 'https://openalex.org/W2163471981', 'https://openalex.org/W2170685293', 'https://openalex.org/W2400431328', 'https://openalex.org/W4238448376', 'https://openalex.org/W4250555591'], 'related_works': ['https://openalex.org/W3143512440', 'https://openalex.org/W3081950544', 'https://openalex.org/W3081678557', 'https://openalex.org/W2796636403', 'https://openalex.org/W2605104905', 'https://openalex.org/W2389042962', 'https://openalex.org/W2133596287', 'https://openalex.org/W2079117034', 'https://openalex.org/W2015700328', 'https://openalex.org/W1990053051'], 'abstract_inverted_index': {'The': [0, 88, 132, 181, 251, 339, 383, 432, 502, 639, 676, 1058, 1080, 1235, 1847, 1995, 2015, 2034, 2229, 2772, 2847, 2914, 2937, 2958, 3072, 3116, 3290, 3707, 3962, 4070, 4088, 4115, 4239], 'gene': [1, 252, 511, 674, 681, 824, 1132, 2087, 2181], 'encoding': [2, 166, 253, 417, 610], 'the': [3, 11, 51, 74, 95, 100, 116, 148, 196, 245, 254, 262, 302, 325, 346, 351, 367, 399, 447, 496, 507, 527, 559, 616, 645, 729, 736, 880, 1035, 1064, 1297, 1336, 1348, 1351, 1411, 1416, 1422, 1427, 1433, 1461, 1466, 1471, 1513, 1516, 1527, 1542, 1593, 1630, 1648, 1733, 1741, 1787, 1821, 1836, 1840, 1871, 1976, 2023, 2042, 2049, 2128, 2132, 2207, 2211, 2226, 2233, 2253, 2282, 2375, 2435, 2502, 2569, 2689, 2830, 2907, 2987, 3015, 3040, 3057, 3063, 3066, 3070, 3077, 3134, 3144, 3202, 3322, 3376, 3379, 3498, 3577, 3659, 3693, 3717, 3727, 3778, 3788, 3839, 3857, 3862, 3882, 3901, 3915, 3933, 3945, 3956, 3968, 3974, 3994, 4091, 4109, 4158, 4204, 4243], 'miR-34a': [4, 64, 92, 130, 141, 175, 179, 186, 202, 217, 232, 255, 315, 343, 381, 392, 426, 430, 437, 453, 468, 483, 732, 819, 912, 958, 997, 1019, 1098, 1109, 1153, 1194, 1231, 1279, 1298, 1790, 1808, 1903, 1969, 2234, 3982, 4097, 4224], 'microRNA': [5, 256, 588, 617, 877, 1036, 1301, 1569, 1931, 4023], 'is': [6, 257, 512, 574, 683, 959, 1110, 1276, 1430, 1470, 1617, 1904, 2018, 3387, 3711, 3794], 'a': [7, 62, 67, 91, 104, 129, 258, 313, 318, 342, 355, 380, 960, 1129, 1332, 1344, 1477, 1551, 1605, 1705, 1783, 1798, 1824, 1905, 2009, 2110, 2158, 2357, 2421, 2560, 2766, 2780, 2806, 2868, 2921, 3028, 3036, 3085, 3097, 3388, 3554, 3563, 3701, 3987, 4130, 4217, 4231, 4252, 4264], 'transcriptional': [8, 259], 'target': [9, 260, 962, 1352, 1425, 1475, 1487, 1492, 1907, 3989, 4024, 4093], 'of': [10, 56, 61, 73, 99, 139, 147, 157, 160, 184, 195, 247, 261, 307, 312, 324, 350, 390, 398, 408, 411, 435, 446, 498, 529, 545, 550, 571, 664, 673, 678, 692, 717, 770, 818, 879, 911, 949, 996, 1005, 1018, 1104, 1118, 1152, 1161, 1193, 1331, 1350, 1361, 1387, 1415, 1421, 1439, 1460, 1474, 1486, 1512, 1515, 1520, 1529, 1584, 1592, 1598, 1604, 1632, 1651, 1735, 1743, 1786, 1789, 1823, 1827, 1835, 1842, 1894, 1968, 1997, 2006, 2012, 2022, 2048, 2086, 2134, 2257, 2284, 2377, 2411, 2428, 2646, 2715, 2733, 2769, 2811, 2871, 3007, 3032, 3065, 3076, 3089, 3101, 3113, 3125, 3184, 3293, 3325, 3341, 3450, 3463, 3494, 3550, 3557, 3565, 3579, 3581, 3587, 3620, 3680, 3695, 3716, 3720, 3743, 3790, 3874, 3965, 3979, 4090, 4203, 4212, 4223, 4247], 'p53': [12, 220, 263, 471, 508, 534, 560, 572, 585, 614, 646, 741, 821, 881, 952, 961, 1033, 1065, 1897, 1906], 'tumor': [13, 27, 237, 264, 278, 488, 509, 540, 578, 647, 1066, 1130, 1845, 4132, 4266], 'suppressor': [14, 265, 510, 648, 883, 1067, 1131, 4133, 4267], 'protein': [15, 43, 54, 137, 266, 294, 305, 388, 694, 1646, 1663, 1746, 1767, 1795, 2139, 2655, 3165, 3179, 3308, 3411, 3501, 3523, 3583, 3606, 3611, 3642, 3703, 3705, 3728, 3784, 3812], 'and': [16, 24, 35, 44, 85, 119, 177, 211, 227, 242, 267, 275, 286, 295, 336, 370, 428, 462, 478, 493, 548, 826, 966, 1026, 1029, 1085, 1124, 1195, 1206, 1210, 1240, 1364, 1390, 1413, 1447, 1494, 1707, 1794, 1801, 1830, 1860, 1911, 2029, 2140, 2157, 2221, 2232, 2250, 2255, 2274, 2297, 2322, 2363, 2383, 2408, 2443, 2456, 2460, 2471, 2497, 2514, 2536, 2551, 2572, 2596, 2654, 2760, 2801, 2818, 2840, 2859, 2895, 2928, 3027, 3084, 3109, 3163, 3178, 3199, 3296, 3321, 3438, 3456, 3476, 3483, 3485, 3500, 3521, 3602, 3610, 3640, 3667, 3671, 3810, 3832, 3844, 3898, 3921, 3941, 3996, 4077, 4148, 4172, 4180, 4195, 4220, 4249], 'subject': [17, 268, 698, 1547], 'to': [18, 38, 49, 269, 289, 300, 685, 699, 734, 914, 1228, 1296, 1424, 1432, 1540, 1548, 1590, 1610, 1710, 1815, 1844, 2490, 2508, 2540, 2553, 2568, 2593, 2701, 3004, 3022, 3081, 3122, 3189, 3315, 3371, 3570, 3700, 3725, 3923, 3932, 3944, 4164], 'epigenetic': [19, 270], 'inactivation': [20, 271, 1192], 'in': [21, 42, 66, 94, 112, 134, 151, 235, 272, 293, 317, 345, 363, 385, 402, 486, 599, 644, 670, 1002, 1063, 1083, 1115, 1158, 1200, 1238, 1271, 1308, 1340, 1347, 1410, 1638, 1645, 1677, 1700, 1745, 1766, 1813, 1855, 2243, 2252, 2290, 2324, 2360, 2374, 2445, 2777, 2823, 2837, 2844, 2891, 2902, 3014, 3056, 3069, 3368, 3384, 3506, 3576, 3585, 3878, 4050, 4137, 4176, 4187, 4271], 'colorectal': [22, 68, 273, 319, 1122, 1848, 3297], 'cancer': [23, 69, 274, 320, 1084, 1239, 1849], 'numerous': [25, 276, 515, 536, 1116, 1810], 'other': [26, 277], 'types.': [28, 279], 'Here,': [29, 280], 'we': [30, 281, 1781, 3985], 'combined': [31, 282, 1799, 3988], 'pulsed': [32, 283], 'SILAC': [33, 284, 1670, 2492], '(pSILAC)': [34, 285], 'microarray': [36, 287, 1596, 1800], 'analyses': [37, 288], 'identify': [39, 290, 1541, 1611], 'miR-34a-induced': [40, 291], 'changes': [41, 292, 1765], 'mRNA': [45, 102, 150, 296, 353, 401, 1353, 1362, 1391, 1456, 1599, 1793], 'expression.': [46, 297, 675], 'pSILAC': [47, 171, 298, 422, 1736, 1802, 2547], 'allowed': [48, 299], 'quantify': [50, 301], 'de': [52, 135, 303, 386, 849], 'novo': [53, 136, 304, 387], 'synthesis': [55, 138, 306, 389, 1768], '1206': [57, 308], 'proteins': [58, 76, 82, 89, 127, 167, 197, 309, 327, 333, 340, 378, 418, 448, 1264, 1269, 1652, 1829, 3327, 3572, 3596], 'after': [59, 174, 310, 425, 1601, 2004, 2268, 2275, 2477, 4197, 4287], 'activation': [60, 311, 769, 910, 3105, 3111], 'conditional': [63, 314], 'allele': [65, 316], 'cell': [70, 120, 321, 371, 600, 1023, 1208, 1309, 1678, 1701, 1850, 1953, 1982, 3380, 3392], 'line.': [71, 322, 3393], '∼19%': [72, 323], 'detected': [75, 169, 326, 420, 1659], 'were': [77, 122, 172, 328, 373, 423, 1868, 1955, 1973, 1984, 2236, 2241, 2266, 2288, 2310, 2334, 2418, 2438, 2485, 2506, 2521, 2531, 2538, 2549, 2557, 2582, 2588, 2675, 2729, 2803, 2875, 2952, 2963, 3012, 3047, 3141, 3187, 3429, 3473, 3478, 3537, 3597, 3655, 3676, 3683, 3937, 3950, 4073, 4086, 4100, 4117, 4155, 4185, 4284], 'differentially': [78, 329, 3621], 'regulated,': [79, 330], 'with': [80, 90, 144, 331, 341, 395, 596, 688, 1305, 1343, 1419, 1444, 1653, 1870, 1959, 1975, 1988, 2105, 2143, 2184, 2200, 2217, 2336, 2365, 2420, 2451, 2480, 2533, 2574, 2753, 2779, 2829, 2855, 2861, 2881, 2887, 2898, 2911, 2920, 3062, 3103, 3201, 3431, 3553, 3850, 3885, 3914, 4108, 4157, 4200], '113': [81, 332], 'being': [83, 334, 697], 'down-': [84, 335], '115': [86, 337], 'up-regulated.': [87, 338], 'seed-matching-sequence': [93, 344], '3′-untranslated': [96, 347], 'region': [97, 348], '(UTR)': [98, 349], 'corresponding': [101, 149, 352, 400], 'showed': [103, 354], 'clear': [105, 356], 'bias': [106, 357], 'toward': [107, 358], 'translational': [108, 359, 1388, 1633], 'repression.': [109, 360, 1634], 'Proteins': [110, 361, 2556, 3536], 'involved': [111, 362, 669, 1270], 'DNA': [113, 364, 531, 2403], 'replication,': [114, 365], 'e.g.': [115, 366], 'MCM': [117, 368], 'proteins,': [118, 369, 3314], 'proliferation,': [121, 372], 'over-represented': [123, 374], 'among': [124, 375, 1120], 'indirectly': [125, 243, 376, 494], 'down-regulated': [126, 173, 377, 424], 'lacking': [128, 379], 'seed-match.': [131, 382], 'decrease': [133, 384], 'direct': [140, 182, 391, 433, 1230], 'targets': [142, 393, 716, 1232, 1328, 1624], 'correlated': [143, 394, 3200], 'reduced': [145, 396], 'levels': [146, 397, 1600, 1664], 'most': [152, 403, 737, 1639, 3042, 3192], 'cases,': [153, 404], 'indicating': [154, 405], 'an': [155, 406, 661, 1101, 1934, 2019, 2090, 2106, 2201, 2702, 3104, 3110, 3446], 'interdependence': [156, 407], 'both': [158, 409], 'types': [159, 410, 1004, 1117, 1160], 'regulation.': [161, 412], 'In': [162, 230, 413, 481, 2543, 3561], 'addition,': [163, 414], '43': [164, 415], 'mRNAs': [165, 201, 416, 452, 713, 1224, 1293, 1426, 1488, 1585, 3980, 4094], 'not': [168, 419, 1524, 1657, 3590], 'by': [170, 199, 221, 240, 421, 450, 472, 491, 506, 514, 701, 740, 820, 951, 954, 998, 1112, 1154, 1197, 1366, 1384, 1454, 1550, 1660, 1674, 1697, 1732, 1750, 1770, 1819, 1896, 1899, 1933, 1957, 1986, 2040, 2238, 2312, 2345, 2356, 2487, 2650, 2677, 2717, 3051, 3348, 3375, 3413, 3542, 3592, 3600, 3613, 3690, 3731, 3750, 3777, 3781, 3960, 3973, 3993, 4134, 4150, 4268], 'expression': [176, 246, 427, 497, 682, 825, 1017, 1603, 1711, 1791, 1796, 1822, 1873, 1932, 1979, 2036, 2187, 2413], 'contained': [178, 429, 3575], 'seed-matches.': [180, 431], 'regulation': [183, 434, 700, 948, 1549, 1650, 1893, 2182], 'selected': [185, 436, 3048, 3127], 'target-mRNAs': [187, 438], 'was': [188, 439, 1730, 1853, 2000, 2038, 2215, 2390, 2722, 2774, 2849, 2909, 2918, 2939, 2996, 3020, 3079, 3093, 3120, 3130, 3373, 3465, 3534, 3568, 3663, 3876, 3893, 3912, 3967], 'confirmed': [189, 440], 'using': [190, 441, 1554, 1665, 1797, 1949, 2089, 2688, 2805, 2942, 3143, 3396, 3417, 3658, 3861, 3900, 3955, 4080], 'reporter': [191, 442, 4208, 4214], 'assays.': [192, 443], 'Via': [193, 444], 'down-regulation': [194, 445], 'encoded': [198, 449, 505], 'these': [200, 451, 3595], 'presumably': [203, 233, 454, 484, 1480], 'inhibits': [204, 455, 1027], 'glycolysis': [205, 456], '(LDHA),': [206, 457], 'WNT-signaling': [207, 458], '(LEF1),': [208, 459], 'invasion/migration': [209, 460], '(AXL)': [210, 461], 'lipid': [212, 463], 'metabolism': [213, 464], '(ACSL1,': [214, 465], 'ACSL4).': [215, 466], 'Furthermore,': [216, 467], 'may': [218, 469, 1099, 1125, 1406, 1656, 3853], 'activate': [219, 470], 'inhibiting': [222, 473], 'its': [223, 474], 'acetylation': [224, 475], '(MTA2,': [225, 476], 'HDAC1)': [226, 477], 'degradation': [228, 479, 1457, 1591], '(YY1).': [229, 480], 'summary,': [231, 482], 'participates': [234, 485], 'multiple': [236, 487, 1003, 1159, 3588], 'suppressive': [238, 489, 541], 'pathways': [239, 490, 1812], 'directly': [241, 492], 'suppressing': [244, 495], 'numerous,': [248, 499], 'critical': [249, 500], 'proteins.': [250, 501], 'transcription': [503], 'factor': [504], 'activated': [513], 'cellular': [516, 1811], 'insults': [517], 'such': [518, 3770, 3786], 'as': [519, 543, 1282, 1619, 1669, 1704, 2601, 2725, 2877, 2964, 3443, 3445, 3467, 3480, 3487, 3504, 3604, 3713, 3771, 4129, 4216, 4251, 4263], 'γ-irradiation': [520], 'or': [521, 1483, 1557, 3573, 3704, 3867, 4230], 'deregulated': [522], 'oncogene': [523], 'expression,': [524, 2286], 'which': [525, 538, 1252, 1739, 2587, 3316], 'have': [526, 1225, 1537, 1839], 'commonality': [528], 'inducing': [530, 4135, 4269], 'damage.': [532], 'Activated': [533], 'regulates': [535, 1280, 1481, 1809], 'genes,': [537], 'mediate': [539], 'processes': [542], 'inhibition': [544, 1438], 'cell-cycle': [546, 2279, 2331], 'progression': [547], 'induction': [549, 739, 2479], 'apoptosis': [551, 965, 1910, 4136, 4270], '(1Vogelstein': [552], 'B.': [553, 936, 1181, 1683, 1755, 1881, 2643, 3289], 'Lane': [554], 'D.': [555, 863, 938, 978, 1134, 1883, 3219, 3251, 4002], 'Levine': [556], 'A.J.': [557, 749], 'Surfing': [558], 'network.Nature.': [561, 884], '2000;': [562, 3005], '408:': [563], '307-310Crossref': [564], 'PubMed': [565, 628, 654, 723, 784, 838, 888, 926, 972, 1011, 1047, 1073, 1092, 1167, 1218, 1247, 1373, 1398, 1505, 1577, 1723, 1775, 1917, 1944, 2099, 2152, 2194, 2668, 3171, 3302, 3361, 3424, 3529, 3648, 3763, 3818, 4030, 4065, 4143, 4277], 'Scopus': [566, 629, 655, 724, 785, 839, 889, 927, 973, 1012, 1048, 1074, 1093, 1168, 1219, 1248, 1374, 1399, 1506, 1578, 1724, 1776, 1918, 1945, 2100, 2153, 2195, 2669, 3172, 3303, 3362, 3425, 3530, 3649, 3764, 3819, 4031, 4066, 4144, 4278], '(5799)': [567], 'Google': [568, 631, 657, 726, 787, 841, 891, 929, 975, 1014, 1050, 1076, 1095, 1170, 1221, 1250, 1376, 1401, 1508, 1580, 1726, 1778, 1920, 1947, 2102, 2155, 2197, 2671, 3174, 3305, 3364, 3427, 3532, 3651, 3766, 3821, 4033, 4068, 4146, 4280], 'Scholar).': [569, 658, 727, 1015, 1096, 1222, 1402, 1509, 1581, 1727, 1779, 2672, 3175, 3365, 3767, 3822, 4069, 4281], 'Loss': [570], 'function': [573], 'commonly': [575, 3318], 'observed': [576, 3319], 'during': [577], 'development.': [579], 'Apart': [580], 'from': [581, 2219, 2523, 3685, 3856, 3895, 3952, 4075, 4102, 4105], 'regulating': [582], 'protein-coding': [583], 'genes': [584, 611, 696], 'also': [586, 1268], 'controls': [587], '(miRNA)': [589], '1The': [590], 'abbreviations': [591], 'used': [592, 1609, 2954, 3383, 3724, 3986, 4169], 'are:miRNAmicroRNASILACstable': [593], 'isotope': [594, 1303, 1672, 1695], 'labeling': [595, 1304, 1673, 1696, 3919], 'amino': [597, 1306, 1675, 1698, 2519, 3441, 3559, 3674], 'acids': [598, 1307, 1676, 1699, 2520, 3442], 'cultureRIPAradioimmunoprecipitation': [601], 'assayHPLChigh': [602], 'performance': [603, 1314, 2680], 'liquid': [604, 1315, 2681], 'chromatographyESIelectrospray': [605], 'ionizationMS/MStandem': [606], 'MSTFAtrifluoroacetic': [607], 'acidUTRuntranslated': [608], 'regions.': [609, 1324], '(2Hermeking': [612, 1031], 'H.': [613, 946, 988, 994, 1032, 1079, 1144, 1150, 1189, 1234, 1689, 1891, 1929, 2080, 2621, 3336, 3738], 'enters': [615, 1034], 'world.Cancer': [618, 1037], 'Cell.': [619, 829, 917, 1038, 4056], '2007;': [620, 651, 776, 830, 885, 918, 969, 1039, 1070, 1914, 2660, 3299, 4057, 4140, 4274], '12:': [621, 1040, 1396], '414-418Abstract': [622, 1041], 'Full': [623, 625, 779, 781, 833, 835, 921, 923, 1042, 1044, 1500, 1502, 1718, 1720, 2663, 2665, 2998, 3356, 3358, 3758, 3760, 4060, 4062], 'Text': [624, 626, 780, 782, 834, 836, 922, 924, 1043, 1045, 1501, 1503, 1719, 1721, 2664, 2666, 3357, 3359, 3759, 3761, 4061, 4063], 'PDF': [627, 783, 837, 925, 1046, 1504, 1722, 2667, 3360, 3762, 4064], '(420)': [630, 1049], 'Scholar,': [632, 788, 842, 892, 930, 976, 1051, 1077, 1171, 1377, 1921, 4034], '3He': [633, 1052], 'X.': [634, 846, 1053], 'He': [635, 845, 1054], 'L.': [636, 844, 859, 1055, 1185, 2623, 4008], 'Hannon': [637, 874, 1056], 'G.J.': [638, 875, 1057], "guardian's": [640, 1059], 'little': [641, 1060], 'helper:': [642, 1061], 'microRNAs': [643, 950, 1062, 1895], 'network.Cancer': [649, 1068], 'Res.': [650, 719, 1069, 1940, 2095], '67:': [652, 1071], '11099-11101Crossref': [653, 1072], '(274)': [656, 1075], 'miRNAs': [659, 679, 702, 731, 1587, 1637, 1751], 'represent': [660, 1128], 'abundant': [662], 'class': [663], 'small': [665, 1449], '∼21-nucleotide-long,': [666], 'noncoding': [667], 'RNAs': [668, 1544], 'post-transcriptional': [671], 'control': [672, 2085, 2504, 3019, 3075, 4233, 4237, 4254], 'influence': [677], 'on': [680, 1792, 2306, 2559, 3344, 3497, 3616, 3665, 3746, 3871], 'predicted': [684], 'be': [686, 1100, 1229, 1608, 1658, 3854, 3869], 'widespread,': [687], 'more': [689], 'than': [690], '60%': [691], 'human': [693, 3294, 3307, 3372, 3389], 'coding': [695], '(4Friedman': [703], 'R.C.': [704], 'Farh': [705, 4037], 'K.K.': [706, 4038], 'Burge': [707], 'C.B.': [708], 'Bartel': [709, 4045], 'D.P.': [710, 1490, 2116, 4046], 'Most': [711], 'mammalian': [712], 'are': [714, 1523, 1546, 1626, 3692, 3774, 3836, 4174], 'conserved': [715, 4084], 'microRNAs.Genome': [718], '2009;': [720, 1497, 3353, 3755], '19:': [721], '92-105Crossref': [722], '(6361)': [725], 'Among': [728], 'p53-regulated': [730], 'seems': [733], 'display': [735], 'pronounced': [738], '(5Bommer': [742], 'G.T.': [743], 'Gerin': [744], 'I.': [745, 1685, 4015], 'Feng': [746], 'Y.': [747, 755, 855, 900, 3237, 4124, 4258], 'Kaczorowski': [748], 'Kuick': [750], 'R.': [751, 1761, 2609, 2631, 3239, 3247, 4006], 'Love': [752], 'R.E.': [753], 'Zhai': [754], 'Giordano': [756], 'T.J.': [757], 'Qin': [758], 'Z.S.': [759], 'Moore': [760], 'B.B.': [761], 'MacDougald': [762], 'O.A.': [763, 794], 'Cho': [764], 'K.R.': [765], 'Fearon': [766], 'E.R.': [767], 'p53-mediated': [768, 915], 'miRNA34': [771], 'candidate': [772], 'tumor-suppressor': [773], 'genes.Curr.': [774], 'Biol.': [775, 1573], '17:': [777, 1090, 1245, 1575], '1298-1307Abstract': [778], '(970)': [786], '6Chang': [789], 'T.C.': [790], 'Wentzel': [791], 'E.A.': [792], 'Kent': [793], 'Ramachandran': [795], 'K.': [796, 2167, 3259], 'Mullendore': [797], 'M.': [798, 804, 806, 908, 1173, 1177, 1562, 1693, 1753, 2064, 2066, 2068, 2611, 2617, 3152, 3253, 3338, 3510, 3629, 3740, 3799, 4019], 'Lee': [799], 'K.H.': [800, 2120], 'Feldmann': [801], 'G.': [802, 944, 1889, 2060, 3283], 'Yamakuchi': [803], 'Ferlito': [805], 'Lowenstein': [807], 'C.J.': [808], 'Arking': [809], 'D.E.': [810], 'Beer': [811], 'M.A.': [812, 873], 'Maitra': [813], 'A.': [814, 940, 942, 982, 1138, 1187, 1566, 1691, 1885, 1887, 1923, 1927, 2070, 4000, 4036], 'Mendell': [815], 'J.T.': [816], 'Transactivation': [817], 'broadly': [822], 'influences': [823], 'promotes': [827], 'apoptosis.Mol.': [828, 916], '26:': [831, 919, 3169, 3527, 3646, 3816, 4141, 4275], '745-752Abstract': [832], '(1711)': [840], '7He': [843], 'Lim': [847, 4043], 'L.P.': [848, 4044], 'Stanchina': [850], 'E.': [851, 896, 898, 1379, 1381, 3275], 'Xuan': [852], 'Z.': [853, 906, 1759, 3231, 3245], 'Liang': [854], 'Xue': [856], 'W.': [857, 1359, 2027, 2078, 2169, 2177, 2629, 2637], 'Zender': [858], 'Magnus': [860], 'J.': [861, 992, 1148, 1175, 1183, 1564, 2062, 2076, 2082, 2633, 3150, 3213, 3225, 3249, 3271, 3508, 3627, 3797], 'Ridzon': [862], 'Jackson': [864], 'A.L.': [865], 'Linsley': [866], 'P.S.': [867], 'Chen': [868, 4123, 4257], 'C.': [869, 984, 1140, 2054, 2056, 2163, 2165, 2179, 2619, 3332, 3734, 4122, 4256], 'Lowe': [870], 'S.W.': [871], 'Cleary': [872], 'A': [876, 2180, 3490], 'component': [878], 'tumour': [882], '447:': [886], '1130-1134Crossref': [887], '(2302)': [890], '8Raver-Shapira': [893], 'N.': [894, 902, 904, 1357, 1757, 1763, 3227, 3277, 4021], 'Marciano': [895], 'Meiri': [897], 'Spector': [899], 'Rosenfeld': [901], 'Moskovits': [903], 'Bentwich': [905], 'Oren': [907], 'Transcriptional': [909], 'contributes': [913], '731-743Abstract': [920], '(1119)': [928], '9Tarasov': [931], 'V.': [932, 980, 1136, 1877, 2982, 3233], 'Jung': [933, 1878, 1924], 'P.': [934, 990, 1146, 1879, 1925, 2175, 3279, 4012, 4042], 'Verdoodt': [935, 1180, 1880], 'Lodygin': [937, 1882], 'Epanchintsev': [939, 981, 1137, 1884], 'Menssen': [941, 1886, 1926], 'Meister': [943, 1888], 'Hermeking': [945, 993, 1149, 1188, 1890, 1928], 'Differential': [947, 1892], 'revealed': [953, 1898, 3347, 3749], 'massively': [955, 1900], 'parallel': [956, 1901], 'sequencing:': [957, 1902], 'that': [963, 1278, 1290, 1545, 1625, 1636, 1807, 1908, 3378, 3787], 'induces': [964, 1020, 1909], 'G1-arrest.Cell': [967, 1912], 'Cycle.': [968, 1007, 1163, 1913], '6:': [970, 1915, 2661], '1586-1593Crossref': [971, 1916], '(804)': [974, 1919], '10Lodygin': [977], 'Tarasov': [979, 1135], 'Berking': [983, 1139], 'Knyazeva': [985, 1141], 'T.': [986, 1142, 2607, 2625, 3215, 3223, 3235], 'Körner': [987, 1143], 'Knyazev': [989, 1145], 'Diebold': [991, 1147], 'Inactivation': [995, 1151], 'aberrant': [999, 1155], 'CpG': [1000, 1113, 1156, 1198], 'methylation': [1001, 1114, 1157, 1199], 'cancer.Cell': [1006, 1162], '2008;': [1008, 1164, 1772, 3168, 3526, 3645, 3815], '7:': [1009, 1165], '2591-2600Crossref': [1010, 1166], '(689)': [1013, 1169], 'Ectopic': [1016], 'apoptosis,': [1021], 'senescence,': [1022], 'cycle': [1024], 'arrest': [1025], 'migration': [1028], 'invasion': [1030, 1272], '11Hermeking': [1078], 'miR-34': [1081, 1236], 'family': [1082, 1237], 'apoptosis.Cell': [1086, 1241], 'Death': [1087, 1242], 'Differ.': [1088, 1243], '2010;': [1089, 1244, 1370, 1574], '193-199Crossref': [1091, 1246], '(1011)': [1094, 1249], 'Therefore,': [1097, 1534], 'important': [1102], 'mediator': [1103], "p53's": [1105], 'tumor-suppressive': [1106], 'activities.': [1107], 'Interestingly,': [1108, 1832], 'silenced': [1111], 'tumors,': [1119], 'them': [1121, 2489, 3551], 'cancer,': [1123], 'therefore': [1126], 'itself': [1127], '(10Lodygin': [1133], '12Vogt': [1172], 'Munding': [1174], 'Grüner': [1176], 'Liffers': [1178], 'S.T.': [1179], 'Hauk': [1182], 'Steinstraesser': [1184], 'Tannapfel': [1186], 'Frequent': [1190], 'concomitant': [1191], 'miR-34b/c': [1196], 'colorectal,': [1201], 'pancreatic,': [1202], 'mammary,': [1203], 'ovarian,': [1204], 'urothelial,': [1205], 'renal': [1207], 'carcinomas': [1209], 'soft': [1211], 'tissue': [1212], 'sarcomas.Virchows': [1213], 'Arch.': [1214], '2011;': [1215, 1395], '458:': [1216], '313-322Crossref': [1217], '(281)': [1220], 'Several': [1223], 'been': [1226, 1538, 3329], 'shown': [1227], '(11Hermeking': [1233], 'Scholar),': [1251, 2156, 2198], 'encode': [1253], 'factors': [1254], 'required': [1255], 'for': [1256, 1526, 1963, 1992, 2271, 2278, 2303, 2327, 2399, 2409, 2598, 2762, 2852, 2955, 3049, 3133, 3453, 3459, 3653, 3776, 3889, 4170], 'G1/S': [1257], 'transition': [1258], '(c-MYC,': [1259], 'E2F,': [1260], 'CDK4,': [1261], 'CDK6),': [1262], 'anti-apoptotic': [1263], '(Bcl2,': [1265], 'SIRT1),': [1266], 'but': [1267], '(c-MET).': [1273], 'However,': [1274, 1510, 1614], 'it': [1275, 1620], 'likely': [1277], 'additional,': [1281], 'yet': [1283], 'unconfirmed': [1284], 'targets,': [1285, 1970], 'because': [1286, 1511], 'bioinformatic': [1287, 1518, 3977], 'predictions': [1288, 1519, 4085], 'suggest': [1289], 'several': [1291, 1535, 3571], 'hundred': [1292], 'contain': [1294, 3190], 'matches': [1295], 'seed': [1299, 3983, 4054], 'sequence.': [1300], 'stable': [1302], 'culture': [1310], 'radioimmunoprecipitation': [1311], 'assay': [1312], 'high': [1313, 2679, 2947, 3155, 3513, 3632, 3802], 'chromatography': [1316, 2682], 'electrospray': [1317], 'ionization': [1318, 2684], 'tandem': [1319, 2651], 'MS': [1320, 2686, 3000, 3067], 'trifluoroacetic': [1321, 2756], 'acid': [1322, 2757, 2815, 2822], 'untranslated': [1323], 'MiRNAs': [1325], 'regulate': [1326], 'their': [1327, 1341], 'via': [1329, 1408, 2225], 'association': [1330], '∼7': [1333], 'nucleotide': [1334], 'stretch,': [1335], 'so-called': [1337], 'seed-sequence,': [1338], 'located': [1339], '5′-portion': [1342], 'complementary': [1345, 4245], 'sequence': [1346, 2130, 2214, 3415, 4246], '3′-UTR': [1349], '(13Fabian': [1354], 'M.R.': [1355], 'Sonenberg': [1356], 'Filipowicz': [1358], 'Regulation': [1360], 'translation': [1363, 1440, 1747], 'stability': [1365], 'microRNAs.Annu.': [1367], 'Rev.': [1368, 1393], 'Biochem.': [1369], '79:': [1371], '351-379Crossref': [1372], '(2304)': [1375], '14Huntzinger': [1378], 'Izaurralde': [1380], 'Gene': [1382, 2189], 'silencing': [1383], 'microRNAs:': [1385], 'contributions': [1386], 'repression': [1389, 2113], 'decay.Nat.': [1392], 'Genet.': [1394, 4026], '99-110Crossref': [1397], '(1724)': [1400], 'Additional': [1403], 'base': [1404], 'pairing': [1405], 'occur': [1407], 'nucleotides': [1409], 'middle': [1412], '3′-portion': [1414], 'miRNA.': [1417], 'Along': [1418], 'binding': [1420, 2145, 4098], 'miRNA': [1423, 1479, 1532, 1553, 1606, 1612, 1623], 'RISC/Ago2': [1428], 'complex': [1429, 1436], 'recruited': [1431], 'mRNA.': [1434], 'This': [1435, 1728], 'mediates': [1437], 'initiation': [1441], 'through': [1442, 1458, 1586], 'interfering': [1443], 'eIF4F-cap': [1445], 'recognition': [1446, 1493], '40S': [1448], 'ribosomal': [1450], 'subunit': [1451], 'recruitment': [1452, 1459], 'and/or': [1453], 'enhancing': [1455], 'CCR4-NOT1': [1462], 'deadenylase': [1463], 'complex.': [1464], 'Because': [1465, 1582], 'relatively': [1467], 'short': [1468], 'seed-region': [1469], 'primary': [1472], 'determinant': [1473], 'recognition,': [1476], 'single': [1478, 3605], 'dozens': [1482], 'even': [1484], 'hundreds': [1485], '(15Bartel': [1489], 'MicroRNAs:': [1491], 'regulatory': [1495], 'functions.Cell.': [1496], '136:': [1498], '215-233Abstract': [1499], '(15855)': [1507], 'shortness': [1514], 'seed-regions': [1517], 'miRNA/mRNA': [1521], 'interactions': [1522], 'reliable': [1525], 'identification': [1528, 3157, 3412, 3515, 3634, 3804, 3978], 'biologically': [1530], 'relevant': [1531], 'targets.': [1533, 1613], 'attempts': [1536], 'made': [1539], 'messenger': [1543], 'specific': [1552], 'unbiased': [1555], 'genome-': [1556], 'proteome-wide': [1558, 3164, 3522, 3641, 3811], 'experimental': [1559], 'approaches': [1560], '(16Thomas': [1561], 'Lieberman': [1563], 'Lal': [1565], 'Desperately': [1567], 'seeking': [1568], 'targets.Nat.': [1570], 'Struct.': [1571], 'Mol.': [1572], '1169-1174Crossref': [1576], '(419)': [1579], 'targeting': [1583, 4048], 'often': [1588], 'leads': [1589], 'respective': [1594], 'mRNA,': [1595], 'analysis': [1597, 1785, 2273, 2283, 2332, 2395, 2405, 2600], 'ectopic': [1602], 'can': [1607], 'this': [1615, 3385, 3851], 'approach': [1616, 1709], 'limited': [1618], 'cannot': [1621], 'detect': [1622], 'solely': [1627], 'regulated': [1628], 'at': [1629, 2008, 2319, 2341, 2352, 2396, 2765, 2867, 3009, 3096, 3191, 3543, 3547, 3838, 4190], 'level': [1631], 'Assuming': [1635], 'cases': [1640], 'only': [1641, 4082], 'cause': [1642], 'modest': [1643], 'decreases': [1644], 'translation,': [1647], 'miRNA-mediated': [1649], 'long': [1654], 'half-lives': [1655], 'measuring': [1661], 'steady-state': [1662], 'standard': [1666, 2943, 3714], 'proteomic': [1667], 'quantification': [1668, 1742, 3612, 3662], '(stable': [1671], 'culture)': [1679], '(17Ong': [1680], 'S.E.': [1681], 'Blagoev': [1682], 'Kratchmarova': [1684], 'Kristensen': [1686], 'D.B.': [1687], 'Steen': [1688], 'Pandey': [1690], 'Mann': [1692, 3151, 3337, 3509, 3628, 3739, 3798], 'Stable': [1694], 'culture,': [1702], 'SILAC,': [1703], 'simple': [1706], 'accurate': [1708], 'proteomics.Mol.': [1712], 'Cell': [1713, 2658, 3351, 3753], 'Proteomics.': [1714, 2659, 3352, 3754], '2002;': [1715], '1:': [1716], '376-386Abstract': [1717], '(4569)': [1725], 'problem': [1729], 'solved': [1731], 'introduction': [1734], '(pulsed': [1737], 'SILAC),': [1738], 'facilitated': [1740], 'differences': [1744], 'rates': [1748], 'caused': [1749], '(18Selbach': [1752], 'Schwanhäusser': [1754], 'Thierfelder': [1756], 'Fang': [1758], 'Khanin': [1760], 'Rajewsky': [1762, 4020], 'Widespread': [1764], 'induced': [1769, 3877], 'microRNAs.Nature.': [1771], '455:': [1773], '58-63Crossref': [1774], '(2783)': [1777], 'Here': [1780], 'describe': [1782], 'global': [1784], 'effect': [1788], 'analysis.': [1803, 2280, 2329, 2555], 'Our': [1804], 'results': [1805, 3829], 'indicate': [1806], 'addition': [1814, 2005], 'those': [1816], 'described': [1817, 2602, 3505], 'previously': [1818, 2603, 3126], 'modulating': [1820], 'large': [1825], 'number': [1826], 'diverse': [1828], 'mRNAs.': [1831], 'almost': [1833], 'all': [1834, 3326, 3696, 3721, 3783, 3791], 'miR-34a-mediated': [1837], 'regulations': [1838], 'potential': [1841, 4131, 4265], 'contributing': [1843], 'suppression.': [1846], 'line': [1851, 2778, 3381], 'SW480': [1852, 1866, 1971, 2432, 3382, 3879, 4106], 'kept': [1854], "Dulbecco's": [1856], 'modified': [1857], "Eagle's": [1858], 'medium': [1859, 2493, 3481], '10%': [1861, 2462], 'fetal': [1862], 'calf': [1863], 'serum': [1864], '(Invitrogen).': [1865, 1951], 'cells': [1867, 1972, 1999, 2265, 2287, 2309, 2333, 2407, 2415, 2484, 2505, 2530, 3880, 4107, 4184], 'transfected': [1869, 1974, 4196], 'episomal': [1872, 1936, 1977, 2091, 2208], 'vector': [1874, 1937, 2017, 2025, 2037, 2104, 3884, 4241], 'pRTS-miR-34a': [1875, 2220, 2436, 3883], '(9Tarasov': [1876], '19Epanchintsev': [1922], 'Inducible': [1930], 'all-in-one': [1935], 'system.Nucleic': [1938, 2093], 'Acids': [1939, 2094], '2006;': [1941, 2191], '34:': [1942], 'e119Crossref': [1943], '(22)': [1946], 'Scholar)': [1948, 2103, 3306, 3533, 3652, 4147], 'Lipofectamine2000': [1950], 'Polyclonal': [1952, 1981], 'pools': [1954, 1983], 'generated': [1956, 1985, 2039, 3181, 3894, 3992], 'selection': [1958, 1987, 3118], 'hygromycin': [1960], '(450': [1961], 'μg/ml)': [1962, 1991], '10': [1964, 1993, 2896], 'days.': [1965, 1994], 'For': [1966, 2262, 2281, 2330, 2402, 2983, 3176, 3976], 'characterization': [1967, 2645], 'pRTR-miR-34a': [1978, 2209], 'vector.': [1980], 'puromycin': [1989], '(2': [1990, 2246], 'percentage': [1996], 'RFP/GFP-positive': [1998], 'determined': [2001, 3712], '48': [2002, 4198], 'h': [2003, 2270, 2277, 4199], 'doxycycline': [2007, 2483, 3888], 'final': [2010], 'concentration': [2011], '100': [2013, 2258, 2468, 2481, 2981, 3196, 3732, 3886, 4201], 'ng/ml.': [2014], 'pRTR': [2016, 2035, 2224], 'improved': [2020], 'version': [2021], 'pRTS': [2024, 2050], '(Georg': [2026], 'Bornkamm': [2028], 'Christian': [2030], 'Berens,': [2031], 'unpublished': [2032], 'results).': [2033], 'replacing': [2041], 'KRAB': [2043], 'repressor': [2044], 'domain': [2045], 'containing': [2046, 2109, 2293, 2461, 3312, 3981, 4095], 'Tet-trans-silencer': [2047], '(20Bornkamm': [2051], 'G.W.': [2052], 'Berens': [2053, 2178], 'Kuklik-Roos': [2055], 'Bechet': [2057], 'J.M.': [2058], 'Laux': [2059], 'Bachl': [2061], 'Korndoerfer': [2063], 'Schlee': [2065], 'Hölzel': [2067], 'Malamoussi': [2069], 'Chapman': [2071], 'R.D.': [2072], 'Nimmerjahn': [2073], 'F.': [2074], 'Mautner': [2075], 'Hillen': [2077, 2176], 'Bujard': [2079], 'Feuillard': [2081], 'Stringent': [2083], 'doxycycline-dependent': [2084], 'activities': [2088], 'one-vector': [2092], '2005;': [2096, 4027], '33:': [2097], 'e137Crossref': [2098], '(116)': [2101], 'alternative': [2107], 'trans-silencer': [2108], 'CtBP-recruiting': [2111], 'PLDLS': [2112], 'motif': [2114], '(21Molloy': [2115], 'Barral': [2117], 'P.M.': [2118], 'Bremner': [2119], 'Gallimore': [2121], 'P.H.': [2122], 'Grand': [2123], 'R.J.': [2124, 2641, 3217], 'Structural': [2125], 'determinants': [2126, 4052], 'outside': [2127], 'PXDLS': [2129], 'affect': [2131], 'interaction': [2133], 'adenovirus': [2135], 'E1A,': [2136], 'C-terminal': [2137, 2144], 'interacting': [2138], 'Drosophila': [2141], 'repressors': [2142], 'protein.Biochim.': [2146], 'Biophys.': [2147], 'Acta.': [2148], '2001;': [2149], '1546:': [2150], '55-70Crossref': [2151], '(19)': [2154], 'relaxed': [2159], 'effector': [2160], 'specificity': [2161, 3433, 4049], '(22Krueger': [2162], 'Danke': [2164], 'Pfleiderer': [2166], 'Schuh': [2168], 'Jäck': [2170], 'H.M.': [2171], 'Lochner': [2172], 'S.': [2173, 2605, 3211, 3229, 3257], 'Gmeiner': [2174], 'system': [2183, 2693, 2809], 'four': [2185], 'distinct': [2186, 3702], 'levels.J.': [2188], 'Med.': [2190], '8:': [2192, 3354, 3756], '1037-1047Crossref': [2193], '(28)': [2196], 'together': [2199, 3599], 'IRES-coupled': [2202], 'puromycin-resistance': [2203], 'gene.': [2204], 'To': [2205, 2945], 'generate': [2206], 'vector,': [2210, 2437], 'pri-mir-34a': [2212], 'cDNA': [2213, 3892, 3904, 3911, 4104, 4111], 'excised': [2216], 'SfiI': [2218, 2227], 'ligated': [2222], 'into': [2223, 2584, 4119], 'sites.': [2228], 'insert': [2230], 'orientation': [2231], 'portion': [2235], 'verified': [2237, 4149], 'sequencing.': [2239, 4151], 'Cells': [2240], 'seeded': [2242, 2439, 4186], 'six-well': [2244], 'plates': [2245], '×': [2247, 2315, 2348, 2430, 2741, 2790, 3024, 4192], '105': [2248, 2431, 3025], 'cells/well)': [2249], 'cultured': [2251], 'presence': [2254, 2376], 'absence': [2256], 'ng/ml': [2259, 2482], 'doxycycline,': [2260], 'respectively.': [2261, 4182], 'flow': [2263, 2767, 2869], 'cytometry,': [2264], 'trypsinized': [2267], '40': [2269, 2498, 2515, 3890], 'mRFP': [2272, 2285, 2412], '72': [2276], 'fixed': [2289, 2335, 3471], 'phosphate-buffered': [2291, 2325, 2361], 'saline': [2292, 2326], '3.5%': [2294], '(w/v)': [2295, 2379], 'paraformaldehyde': [2296], '0.5%': [2298], '(v/v)': [2299, 2338, 2755, 2813, 2820, 2825, 2883, 2889, 2893, 2900, 2904], 'Nonidet': [2300], 'P-40': [2301], '(Fluka)': [2302], '30': [2304, 2770, 3114], 'min': [2305, 2318, 2351, 2764, 2839, 2854, 2880, 2886, 2897], 'ice.': [2307], 'Fixed': [2308], 'collected': [2311, 2344], 'centrifugation': [2313, 2346], '(200': [2314, 2347], 'g,': [2316, 2349], '5': [2317, 2350, 2429, 2742, 2746, 2763, 2795, 2879, 3023], '4': [2320, 2353, 2972], '°C)': [2321, 2354], 're-suspended': [2323], 'FACS': [2328, 2394], '70%': [2337], 'ethanol': [2339], 'overnight': [2340], '−20': [2342], '°C,': [2343], 'followed': [2355], 'washing': [2358], 'step': [2359], 'saline,': [2362], 'stained': [2364, 2573, 3940], '0.6': [2366], 'mg/ml': [2367, 2385, 2473], 'propidium': [2368], 'iodide': [2369], '(MP': [2370], 'Biochemicals,': [2371], 'Solon,': [2372], 'OH)': [2373], '0.1%': [2378, 2754, 2812, 2819, 2882, 2888, 2899, 2912], 'Triton': [2380], 'X-100': [2381], '(Sigma)': [2382], '0.5': [2384], 'RNaseA': [2386], '(Sigma).': [2387], 'RNA': [2388, 3897], 'digestion': [2389], 'carried': [2391, 2723, 3094, 4285], 'out': [2392, 2724, 3095, 4286], 'before': [2393, 2906], 'room': [2397], 'temperature': [2398], '1': [2400, 4191], 'h.': [2401, 3891], 'content': [2404], '10,000': [2406, 3082], 'detection': [2410], '25,000': [2414], 'per': [2416, 3195], 'sample': [2417], 'analyzed': [2419, 2676], 'FACScalibur': [2422], 'device': [2423], '(BD': [2424], 'Bioscience).': [2425], 'An': [2426], 'aliquot': [2427], 'cells,': [2433], 'harboring': [2434], 'onto': [2440, 2731], '10-cm': [2441], 'dishes': [2442], 'grown': [2444], 'light': [2446, 2452], 'DMEM': [2447], '(PAN': [2448], 'Biotech)': [2449], 'supplemented': [2450], 'l-arginine': [2453], '(84': [2454, 2494, 2511], 'mg/l)': [2455, 2459], 'l-lysine': [2457], '(40': [2458], 'dialyzed': [2463], 'FBS': [2464], '(Hyclone,': [2465], 'Thermo': [2466], 'Scientific),': [2467], 'units/ml': [2469], 'penicillin': [2470], '0.1': [2472], 'streptomycin.': [2474], 'Sixteen': [2475], 'hours': [2476], 'pri-miR-34a': [2478, 3875], 'labeled': [2486, 3440, 3622, 3673, 3913], 'shifting': [2488], 'heavy': [2491, 3488], 'mg/l': [2495, 2499, 2512], '13C615N4-l-arginine': [2496], '13C615N2-l-lysine),': [2500], 'whereas': [2501], 'noninduced': [2503], 'shifted': [2507], 'medium-heavy': [2509], 'media': [2510], '13C6-l-arginine': [2513], 'mg/L': [2516], '2H4-l-lysine).': [2517], 'All': [2518], 'purchased': [2522], 'Cambridge': [2524], 'Isotope': [2525], 'Laboratories.': [2526], 'After': [2527, 3035], '24': [2528], 'h,': [2529], 'lysed': [2532], 'RIPA': [2534], 'buffer': [2535], 'lysates': [2537], 'subjected': [2539, 2552, 2592], 'one-dimensional': [2541], 'SDS-PAGE.': [2542], 'total,': [2544], 'three': [2545], 'independent': [2546], 'experiments': [2548], 'performed': [2550, 3430, 3656], 'further': [2554], 'separated': [2558], '4–12%': [2561], 'NuPageTM': [2562], 'Bis-Tris': [2563], 'gradient': [2564], 'gel': [2565], '(Invitrogen)': [2566], 'according': [2567, 3931, 3943, 4163], "manufacturer's": [2570, 3934, 3946, 4165], 'instructions': [2571, 4166], 'colloidal': [2575], 'Coomassie': [2576], 'Brilliant': [2577], 'Blue': [2578], 'G-250.': [2579], 'Gel': [2580], 'lanes': [2581], 'cut': [2583], '20': [2585, 2885, 4210], 'slices,': [2586], 'immediately': [2589], 'destained,': [2590], 'washed,': [2591, 3939], 'tryptic': [2594, 3432], 'digestion,': [2595], 'prepared': [2597], 'LC/MS': [2599], '(23Wiese': [2604], 'Gronemeyer': [2606], 'Ofman': [2608], 'Kunze': [2610], 'Grou': [2612], 'C.P.': [2613], 'Almeida': [2614], 'J.A.': [2615], 'Eisenacher': [2616], 'Stephan': [2618], 'Hayen': [2620], 'Schollenberger': [2622], 'Korosec': [2624], 'Waterham': [2626], 'H.R.': [2627], 'Schliebs': [2628], 'Erdmann': [2630], 'Berger': [2632], 'Meyer': [2634], 'H.E.': [2635], 'Just': [2636], 'Azevedo': [2638], 'J.E.': [2639], 'Wanders': [2640], 'Warscheid': [2642], 'Proteomics': [2644], 'mouse': [2647], 'kidney': [2648], 'peroxisomes': [2649], 'mass': [2652, 2948, 2960, 3161, 3418, 3448, 3519, 3638, 3808, 3824], 'spectrometry': [2653, 3419], 'correlation': [2656], 'profiling.Mol.': [2657], '2045-2057Abstract': [2662], '(175)': [2670], 'Tryptic': [2673], 'digests': [2674], 'nano': [2678, 2783], '(HPLC)/electrospray': [2683], '(ESI)-tandem': [2685], '(MS/MS)': [2687], 'UltiMateTM': [2690], '3000': [2691], 'HPLC': [2692, 2721], '(Dionex': [2694], 'LC': [2695, 2750, 2784, 2799], 'Packings,': [2696], 'Idstein,': [2697], 'Germany)': [2698], 'online': [2699], 'coupled': [2700], 'linear': [2703, 2832, 3058], 'trap': [2704, 3060], 'quadrupole': [2705], '(LTQ)-Orbitrap': [2706], 'XL': [2707, 2916], 'instrument': [2708, 2917, 2938], '(Thermo': [2709, 2925, 2993, 4113], 'Fisher': [2710, 2926, 2994], 'Scientific,': [2711], 'Bremen,': [2712], 'Germany).': [2713], 'Separation': [2714], 'peptides': [2716, 2802, 3567, 3580, 3682], 'nanoflow': [2718], 'reversed-phase': [2719], 'capillary': [2720, 2970, 2974], 'follows:': [2726, 2878, 2965], 'peptide': [2727, 3156, 3177, 3499, 3514, 3609, 3623, 3633, 3697, 3722, 3803], 'mixtures': [2728], 'loaded': [2730], 'one': [2732, 3435, 3549], 'two': [2734, 3439, 3545], 'C18': [2735, 2781], 'μ-pre-columns': [2736], '(0.3': [2737], 'mm': [2738], 'inner': [2739, 2788], 'diameter': [2740, 2789], 'mm,': [2743, 2792], 'particle': [2744, 2793], 'size': [2745, 2794], 'μm;': [2747, 2796], 'PepMap,': [2748, 2797], 'Dionex': [2749, 2798], 'Packings)': [2751, 2800], 'equilibrated': [2752, 2860], '(TFA),': [2758], 'washed': [2759, 2851, 2876], 'preconcentrated': [2761], 'rate': [2768, 2870, 3493], 'μl/min.': [2771], 'precolumn': [2773], 'then': [2775, 2850], 'switched': [2776], 'RP': [2782], 'column': [2785, 2848, 2908], '(75': [2786], 'μm': [2787], '150': [2791, 2838, 3090], 'eluted': [2804], 'binary': [2807], 'solvent': [2808, 2835, 2842, 2857, 2863], 'consisting': [2810], 'formic': [2814, 2821], '(solvent': [2816, 2827], 'A)': [2817], '84%': [2824, 2903], 'acetonitrile': [2826, 2905], 'B)': [2828], 'following': [2831, 3135, 3660], 'gradient:': [2833], '5–40%': [2834], 'B': [2836, 2843, 2858, 2864], '40–95%': [2841], '2': [2845, 2992], 'min.': [2846], '3': [2853], '95%': [2856], '5%': [2862], '(20': [2865], 'min)': [2866], '300': [2872, 3003], 'nl/minute.': [2873], 'Precolumns': [2874], 'TFA,': [2884], 'TFA': [2890, 2901], '50%': [2892], 'acetonitrile,': [2894], 're-equilibrated': [2910], 'TFA.': [2913], 'LTQ-Orbitrap': [2915], 'equipped': [2919], 'nano-electrospray': [2922], 'ion': [2923, 3059, 3117], 'source': [2924], 'Scientific)': [2927, 2995], 'distal': [2929], 'coated': [2930], 'SilicaTips': [2931], '(FS360–20-10-D,': [2932], 'New': [2933], 'Objective,': [2934], 'Woburn,': [2935], 'MA).': [2936], 'externally': [2940], 'calibrated': [2941], 'compounds.': [2944], 'provide': [2946], 'accuracy,': [2949], 'lock': [2950], 'masses': [2951], 'routinely': [2953], 'internal': [2956], 'calibration.': [2957], 'general': [2959], 'spectrometric': [2961, 3139, 3825], 'parameters': [2962], 'spray': [2966], 'voltage,': [2967, 2971, 2980], '1.5': [2968], 'kV;': [2969], 'V;': [2973], 'temperature,': [2975], '200': [2976], '°C;': [2977], 'tube': [2978], 'lens': [2979], 'data-dependent': [2984], 'MS/MS': [2985, 3185], 'analyses,': [2986], 'software': [2988, 3145], 'XCalibur': [2989], '2.0': [2990], 'SR': [2991], 'used.': [2997], 'scan': [2999, 3068], 'spectra': [3001, 3186], '(m/z': [3002], 'resolution': [3006], '60,000': [3008], 'm/z': [3010], '400)': [3011], 'acquired': [3013], 'orbitrap.': [3016, 3071], 'Automatic': [3017], 'gain': [3018, 3074], 'set': [3021, 3080, 3121, 3479, 3564, 3578, 3991], 'ions': [3026, 3046, 3083, 3129, 3455], 'maximum': [3029, 3086], 'fill': [3030, 3087], 'time': [3031, 3088, 3112], '750': [3033], 'ms.': [3034], 'brief': [3037], 'survey': [3038], 'scan,': [3039], 'six': [3041, 3193, 3558], 'intense': [3043], 'multiply': [3044], 'charged': [3045], 'fragmentation': [3050], 'low': [3052], 'energy': [3053, 3100], 'collision-induced': [3054], 'dissociation': [3055], 'simultaneous': [3061], 'completion': [3064], 'automatic': [3073], 'LTQ': [3078], 'milliseconds.': [3091, 3115], 'Fragmentation': [3092, 3124], 'normalized': [3098], 'collision': [3099], '35%': [3102], 'q': [3106], '=': [3107], '0.25': [3108], 'threshold': [3119], '5000.': [3123], 'precursor': [3128, 3454], 'dynamically': [3131], 'excluded': [3132, 3684], '45': [3136], 's.': [3137], 'Mass': [3138], 'data': [3140, 3845, 4071], 'processed': [3142], 'MaxQuant': [3146, 3153, 3511, 3601, 3630, 3691, 3779, 3800, 3833], '(version': [3147, 3310], '1.0.13.13)': [3148], '(24Cox': [3149, 3507, 3626, 3796], 'enables': [3154, 3512, 3631, 3801], 'rates,': [3158, 3516, 3635, 3805], 'individualized': [3159, 3517, 3636, 3806], 'p.p.b.-range': [3160, 3518, 3637, 3807], 'accuracies': [3162, 3520, 3639, 3809], 'quantification.Nat.': [3166, 3524, 3643, 3813], 'Biotechnol.': [3167, 3525, 3644, 3814], '1367-1372Crossref': [3170, 3528, 3647, 3817], '(9145)': [3173, 3531, 3650, 3820], 'identification,': [3180], 'peak': [3182], 'lists': [3183], 'filtered': [3188], 'peaks': [3194], 'Da': [3197, 3458], 'interval': [3198], 'International': [3203], 'Protein': [3204, 3687], 'Index': [3205], '(25Wood': [3206], 'L.D.': [3207], 'Parsons': [3208], 'D.W.': [3209], 'Jones': [3210], 'Lin': [3212], 'Sjöblom': [3214], 'Leary': [3216], 'Shen': [3218], 'Boca': [3220], 'S.M.': [3221], 'Barber': [3222], 'Ptak': [3224], 'Silliman': [3226], 'Szabo': [3228], 'Dezso': [3230], 'Ustyanksky': [3232], 'Nikolskaya': [3234], 'Nikolsky': [3236], 'Karchin': [3238], 'Wilson': [3240], 'P.A.': [3241], 'Kaminker': [3242], 'J.S.': [3243, 3409], 'Zhang': [3244], 'Croshaw': [3246], 'Willis': [3248], 'Dawson': [3250], 'Shipitsin': [3252], 'Willson': [3254], 'J.K.': [3255], 'Sukumar': [3256], 'Polyak': [3258], 'Park': [3260], 'B.H.': [3261], 'Pethiyagoda': [3262], 'C.L.': [3263], 'Pant': [3264], 'P.V.': [3265], 'Ballinger': [3266], 'D.G.': [3267], 'Sparks': [3268], 'A.B.': [3269], 'Hartigan': [3270], 'Smith': [3272], 'D.R.': [3273], 'Suh': [3274], 'Papadopoulos': [3276], 'Buckhaults': [3278], 'Markowitz': [3280], 'S.D.': [3281], 'Parmigiani': [3282], 'Kinzler': [3284], 'K.W.': [3285], 'Velculescu': [3286], 'V.E.': [3287], 'Vogelstein': [3288], 'genomic': [3291], 'landscapes': [3292], 'breast': [3295], 'cancers.Science.': [3298], '318:': [3300], '1108-1113Crossref': [3301], '(2564)': [3304], 'database': [3309, 3369], '3.52)': [3311], '73,928': [3313], '175': [3317], 'contaminants': [3320], 'reversed': [3323], 'sequences': [3324, 4154], 'had': [3328], 'added': [3330], '(26Pan': [3331, 3733], 'Olsen': [3333, 3735], 'J.V.': [3334, 3736], 'Daub': [3335, 3737], 'Global': [3339, 3741], 'effects': [3340, 3742], 'kinase': [3342, 3744], 'inhibitors': [3343, 3745], 'signaling': [3345, 3747], 'networks': [3346, 3748], 'quantitative': [3349, 3751], 'phosphoproteomics.Mol.': [3350, 3752], '2796-2808Abstract': [3355, 3757], '(170)': [3363, 3765], 'Species': [3366], 'restriction': [3367], 'searches': [3370, 3395], 'justified': [3374], 'fact': [3377], 'work': [3386], 'colon': [3390], 'adenocarcinoma': [3391], 'Database': [3394], 'Mascot': [3397, 3827], '[version': [3398], '2.2,': [3399], 'Matrix': [3400], 'Science': [3401], '(27Perkins': [3402], 'D.N.': [3403], 'Pappin': [3404], 'D.J.': [3405], 'Creasy': [3406], 'D.M.': [3407], 'Cottrell': [3408], 'Probability-based': [3410], 'searching': [3414], 'databases': [3416], 'data.Electrophoresis.': [3420], '1999;': [3421], '20:': [3422], '3551-3567Crossref': [3423], '(6761)': [3426], 'Scholar)]': [3428], 'allowing': [3434], 'missed': [3436], 'cleavage': [3437], 'well': [3444], 'initial': [3447], 'tolerance': [3449], '7': [3451], 'ppm': [3452], '0.4': [3457], 'fragment': [3460], 'ions.': [3461], 'Oxidation': [3462], 'methionine': [3464], 'considered': [3466, 3538], 'variable': [3468], 'modification;': [3469], 'no': [3470], 'modifications': [3472], 'included.': [3474, 4087], '2H4-lysine': [3475], '13C6-arginine': [3477], 'labels': [3482], '13C6-15N4-arginine': [3484], '13C6-15N2-lysine': [3486], 'labels.': [3489], 'false': [3491], 'discovery': [3492], '<': [3495], '1%': [3496], 'level,': [3502], 'calculated': [3503], 'applied.': [3535], 'identified': [3539, 3566, 3681], 'when': [3540], 'supported': [3541], 'least': [3544, 3548], 'peptides,': [3546], 'unique,': [3552], 'minimum': [3555], 'length': [3556], 'acids.': [3560], 'case': [3562, 3586], 'assignable': [3569], 'completely': [3574], 'another': [3582], '(e.g.': [3584], 'isoforms': [3589], 'distinguishable': [3591], 'unique': [3593, 3666], 'peptides),': [3594], 'grouped': [3598], 'reported': [3603, 3689], 'group.': [3607, 3706], 'Relative': [3608], 'MaxQuant,': [3614], 'based': [3615, 3664], 'two-dimensional': [3617], 'centroid': [3618], 'intensities': [3619], 'species': [3624], '(see': [3625], 'details),': [3654], 'automatically': [3657], 'settings:': [3661], '"razor"': [3668], 'peptides;': [3669], '"Re-quantify"': [3670], '"Filter': [3672], 'acids"': [3675], 'enabled;': [3677], 'low-scoring': [3678], 'versions': [3679], 'quantification.': [3686], 'ratios': [3688, 3698, 3723, 3785, 3793], 'median': [3694, 3789], 'assigned': [3699], 'variability': [3708], '(in': [3709], '%)': [3710], 'deviation': [3715], 'natural': [3718], 'logarithms': [3719], 'calculate': [3726], 'ratio': [3729], 'multiplied': [3730], 'Systematic': [3768], 'deviations': [3769], 'mixing': [3772], 'errors': [3773], 'corrected': [3775], 'algorithm': [3780], 'normalizing': [3782], 'log-transformed': [3792], 'zero': [3795], 'Raw': [3823], 'files,': [3826], 'search': [3828], '(dat/msm': [3830], 'files),': [3831], 'output': [3834], 'files': [3835, 3954], 'stored': [3837], 'scientific': [3840], 'file': [3841], 'sharing': [3842], 'network': [3843], 'repository': [3846], 'Tranche.': [3847], 'Data': [3848], 'associated': [3849], 'manuscript': [3852], 'downloaded': [3855], 'Tranche': [3858], 'website': [3859], 'www.ProteomeCommons.org': [3860], 'hash:': [3863], 'drMpxhWY0iVgjjrlc': [3864], 'LC8v8BI25dXgU2bX1t/V1PJBdmvrRI3fexqMYEpfOGonyiWgLMG60': [3865], 'DKG/n4eq7d8H1biWERyuwAAAAAAAA9lw==': [3866], 'will': [3868], 'provided': [3870, 3972], 'request.': [3872], 'Expression': [3873, 3948, 3957], 'bearing': [3881], 'ng/μl': [3887], 'total': [3896], 'amplified': [3899], 'GeneChip': [3902, 3916], 'WT': [3903, 3917], 'Amplification': [3905], 'Kit': [3906], '(Affymetrix,': [3907], 'Santa': [3908], 'Clara,': [3909], 'CA).': [3910], 'terminal': [3918], 'kit': [3920, 4112, 4162], 'hybridized': [3922], 'Affymetrix': [3924], 'Human': [3925], 'Exon': [3926], 'ST': [3927], '1.0': [3928], 'arrays': [3929], '(Affymetrix)': [3930], 'instructions.': [3935], 'Arrays': [3936], 'hybridized,': [3938], 'scanned': [3942], 'recommendations.': [3947], 'values': [3949], 'derived': [3951], 'CEL': [3953], 'Console': [3958], 'implemented': [3959], 'Affymetrix.': [3961], 'normalization': [3963, 4218], 'method': [3964], 'choice': [3966], 'robust-multichip': [3969], 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