TCPA v3.0: An Integrative Platform to Explore the Pan-Cancer Analysis of Functional Proteomic Data

Name: Work Video:
Duration: 3 min 30 s
Mei-Ju May Chen; Jun Li; Yumeng Wang; Rehan Akbani; Yiling Lu; Gordon B. Mills; Han Liang
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3463, 3485, 3528, 3570, 3620, 3702, 3737, 3769, 3781, 3788, 3966, 4038, 4042, 4086, 4264, 4277, 4318, 4383, 4415, 4437, 4466, 4478, 4498, 4577, 4596, 4608, 4638, 4677, 4701, 4717, 4725, 4760, 4782, 4809, 4862, 4891, 4893, 4912, 4917, 5005, 5132, 5149, 5165, 5213, 5248, 5346], 'understanding': [15, 180, 342], 'their': [16, 181, 343, 1852, 2897, 3287, 3490, 3510, 3767, 3980, 4167, 4402, 4801, 5112, 5187], 'effects': [17, 122, 182, 287, 345, 2404, 3762, 3953, 4472], 'on': [18, 116, 125, 183, 281, 290, 346, 910, 1340, 1444, 1757, 1930, 1984, 3349, 3766, 3935, 4148, 4157, 4461, 4473, 4603, 5199], 'cancer': [19, 32, 83, 149, 184, 197, 248, 314, 347, 573, 585, 624, 691, 867, 916, 947, 1038, 1079, 1751, 1766, 2111, 2142, 2171, 2256, 2407, 2442, 2453, 2468, 2507, 2531, 2669, 2881, 3017, 3203, 3246, 3275, 3460, 3482, 3533, 3541, 3548, 3680, 3694, 3710, 3741, 3989, 4081, 4171, 4198, 4217, 4279, 4322, 4329, 4433, 4629, 4649, 4715, 4736, 4814, 4837, 4868, 4895, 4922, 5037, 5083, 5196, 5225, 5312, 5329], 'development.': [20, 185, 348], 'Using': [21, 186, 535, 561, 934], 'this': [22, 91, 187, 256, 2349, 3318, 5205, 5316], 'platform,': [23, 188, 564], 'we': [24, 58, 189, 223, 565, 802, 960, 2619, 2715, 3324, 3347, 3500, 3639, 3801, 4029, 4160, 4189, 4427, 4514, 4591, 4689, 4790, 4821, 5046, 5088, 5154, 5208], 'have': [25, 59, 190, 224, 566, 908, 961, 3193, 4457, 5142, 5209], 'characterized': [26, 191, 567], '∼8,000': [27, 192, 568], 'patient': [28, 193, 569, 1016, 1075, 1723, 2665, 2792, 2796, 2965, 3530, 4804, 4830, 4878], 'samples': [29, 194, 430, 570, 1067, 1076, 2666, 3531, 4021], 'of': [30, 56, 90, 97, 108, 123, 132, 195, 221, 255, 262, 273, 288, 297, 424, 429, 466, 479, 588, 689, 768, 774, 925, 931, 954, 990, 1137, 1143, 1177, 1186, 1249, 1252, 1260, 1481, 1488, 1518, 1614, 1642, 1719, 1760, 1827, 1988, 2110, 2164, 2170, 2183, 2189, 2283, 2414, 2427, 2452, 2506, 2592, 2711, 2719, 2758, 2778, 2878, 3073, 3164, 3236, 3317, 3330, 3459, 3489, 3509, 3617, 3650, 3667, 3693, 3727, 3751, 3760, 3763, 3779, 4069, 4094, 4123, 4145, 4182, 4259, 4385, 4547, 4556, 4615, 4644, 4683, 4697, 4721, 4744, 4757, 4777, 4795, 4915, 4972, 4996, 5050, 5072, 5126, 5195, 5233, 5272, 5290, 5302, 5319], '32': [31, 196, 572, 1078, 2668], 'types': [33, 198, 574, 773, 917, 930, 989, 1080, 1142, 1641, 2172, 2454, 2469, 2508, 2532, 2670, 2718, 2757, 2882, 3247, 3276, 3711, 4027, 4199, 4434, 4838, 4869, 4896], 'through': [34, 199, 575, 2982, 3004, 3100, 3120, 3183, 3255, 3310, 4487], 'The': [35, 47, 200, 212, 362, 367, 391, 396, 576, 808, 1059, 1341, 1366, 1445, 1848, 1931, 1944, 2144, 2191, 2243, 2280, 2295, 2374, 2425, 2444, 2539, 2562, 2582, 2589, 2681, 2735, 2773, 3062, 3147, 3270, 3936, 4207, 4452, 4560, 4612, 4738, 5173, 5344], 'Cancer': [36, 48, 201, 213, 363, 368, 392, 397, 577, 752, 809, 872, 1121, 1194, 1342, 1446, 1815, 1932, 2081, 3430, 3937], 'Genome': [37, 202, 364, 393, 578, 753, 1122, 1343, 1447, 1816, 1933, 2082, 3431, 3938], 'Atlas': [38, 50, 203, 215, 579, 754, 811, 1123, 1515, 1572, 1817, 2083, 2727, 3432, 5341], 'built': [40, 205, 4597], 'widely': [42, 207], 'used,': [43, 208], 'open-access': [44, 209, 805], 'bioinformatic': [45, 210, 5325], 'resource,': [46, 211, 807], 'Proteome': [49, 214, 369, 398, 810, 873], '(TCPA).': [51, 216, 812], 'To': [52, 217, 789, 956, 1968, 2400, 2707, 3313, 3337, 4151, 4420, 4583], 'maximize': [53, 218, 957, 2708], 'the': [54, 88, 95, 105, 120, 148, 219, 253, 260, 270, 285, 313, 562, 765, 792, 819, 871, 888, 904, 911, 942, 951, 1024, 1041, 1066, 1134, 1250, 1258, 1261, 1504, 1512, 1563, 1569, 1578, 1585, 1612, 1714, 1717, 1727, 1761, 1772, 1828, 1970, 1985, 1994, 2134, 2159, 2162, 2168, 2181, 2187, 2198, 2202, 2227, 2230, 2233, 2238, 2267, 2272, 2352, 2358, 2385, 2402, 2409, 2412, 2422, 2428, 2434, 2450, 2473, 2483, 2493, 2504, 2511, 2525, 2537, 2546, 2552, 2593, 2602, 2611, 2709, 2712, 2749, 2782, 2807, 2822, 2826, 2838, 2846, 2876, 2880, 2906, 2914, 2952, 3071, 3093, 3217, 3233, 3274, 3279, 3283, 3295, 3311, 3315, 3327, 3331, 3339, 3486, 3507, 3520, 3546, 3556, 3576, 3609, 3614, 3647, 3659, 3664, 3668, 3718, 3724, 3821, 3860, 3992, 4007, 4011, 4020, 4024, 4032, 4052, 4059, 4067, 4096, 4142, 4154, 4180, 4202, 4422, 4429, 4554, 4564, 4579, 4586, 4604, 4619, 4642, 4652, 4656, 4674, 4681, 4687, 4718, 4742, 4768, 4792, 4849, 4853, 4884, 5008, 5051, 5059, 5070, 5093, 5123, 5200, 5231, 5234, 5258, 5270, 5300, 5304, 5328, 5333, 5360], 'utility': [55, 220, 1183, 1251, 2710, 3316, 5232], 'TCPA,': [57, 222, 366, 395], 'developed': [60, 225, 803, 968, 3320], 'new': [62, 227, 1025, 2651, 5174, 5206, 5317], 'module': [63, 92, 228, 257, 969, 975, 2596, 2633, 2738, 2776, 5177, 5237], 'called': [64, 229, 970], '"TCGA': [65, 230, 971], 'Pan-Cancer': [66, 231, 972, 1514, 1571, 2726, 5340], 'Analysis,"': [67, 232], 'which': [68, 233, 884, 949, 1072, 2129, 2361, 2510, 2744, 2918, 3579, 3808, 4116, 4219, 4517, 4632, 4666, 5268], 'provides': [69, 234, 832, 976, 3224, 5178], 'comprehensive': [70, 235, 977], 'protein-centric': [71, 236, 978, 1049, 2631], 'analyses': [72, 237, 913, 924, 979, 1666, 2584, 5137], 'that': [73, 238, 417, 823, 980, 1033, 1053, 3683, 4563, 4823, 5027, 5048, 5216, 5257], 'integrate': [74, 239, 981], 'expression': [76, 241, 1009, 1535, 2240, 2753, 2789, 2811, 2830, 2833, 2992, 3026, 3035, 3072, 3106, 3132, 3234, 3343, 3552, 3574, 3773, 3790, 3844, 4068, 4125, 4485, 4874, 4995, 5094, 5106, 5171], 'data': [77, 81, 242, 246, 794, 822, 843, 869, 895, 927, 986, 994, 998, 1061, 1369, 1508, 1552, 1565, 1638, 1650, 2200, 2641, 2656, 2723, 2916, 4026, 4566, 5141, 5262, 5335, 5345], 'other': [79, 244, 929, 988, 1564, 1640, 2717, 2756, 3168, 3202, 3244, 4060, 4710, 4719, 4769], 'TCGA': [80, 245, 1070, 1513, 1570, 1586, 2664, 2725, 3867, 5140, 5167, 5339, 5361], 'across': [82, 247, 571, 1037, 1077, 2667, 3015, 3245, 3532, 3739, 4197, 4432, 4812, 5036, 5191], 'types.': [84, 249, 1039, 3018, 3542, 3742, 4737, 4815, 5038, 5197], 'We': [85, 250, 1741, 2308, 3983, 4002, 5252, 5296, 5314, 5355], 'further': [86, 251, 1371, 2386, 2543, 2573, 3325, 5229], 'demonstrate': [87, 252, 3314, 5122, 5230], 'value': [89, 254], 'by': [93, 258, 694, 826, 964, 1375, 1736, 2152, 2278, 2304, 2421, 2449, 2545, 2558, 2607, 2616, 2852, 2973, 3001, 3079, 3088, 3115, 3178, 3250, 3282, 3723, 3776, 3869, 4076, 4102, 4178, 4200, 4301, 4378, 4524, 4753, 4799, 5238], 'examining': [94, 259], 'correlations': [96, 261, 1715, 1971, 2145, 2397, 2418, 2514, 2827, 3160, 3661, 3825, 3849, 3972, 4034, 4168, 4181, 4605, 4646, 4707, 4731, 4802, 5041], 'RPPA': [98, 263, 563, 793, 828, 842, 894, 926, 1060, 1368, 1637, 1762, 2199, 2490, 2640, 2654, 2713, 4565, 4796, 5073, 5261], 'proteins': [99, 133, 264, 298, 2193, 2345, 4071, 4535, 4609, 5091, 5308], 'with': [100, 152, 265, 317, 928, 1558, 1689, 2154, 2173, 2237, 2291, 2376, 2461, 2527, 2566, 2627, 2657, 2791, 2951, 2964, 3022, 3033, 3108, 3161, 3242, 3506, 3646, 3674, 3749, 3795, 3850, 3979, 4022, 4131, 4442, 4673, 4708, 4728, 4767, 4803, 4828, 4876, 4883, 5000, 5042, 5097, 5108, 5220], 'significantly': [101, 266, 380, 409, 1989, 3129, 3829, 4444, 4540], 'mutated': [102, 267, 381, 410, 1976, 1990, 2135, 3094, 3125, 3491, 3529, 3557, 3577, 3714], 'genes,': [103, 268, 1977, 3169, 4188], 'assessing': [104, 269, 4800], 'predictive': [106, 271], 'power': [107, 272, 5071], 'somatic': [109, 274, 376, 405, 1000, 1002, 1522, 3080, 3345, 3764], 'copy-number': [110, 275, 377, 406, 1003], 'alterations,': [111, 276], 'DNA': [112, 277, 1006, 1520, 1524, 1652, 1954, 2215, 2818, 3109, 3697, 3786, 3967, 4103], 'methylation,': [113, 278, 1007, 1525, 1653, 2216, 3787, 4048], 'mRNA': [115, 280, 1008, 1655, 2218, 2239, 3789, 3843, 3960, 4050, 4077, 4488], 'expression,': [118, 127, 283, 292, 1012, 1656, 1658, 4159], 'inferring': [119, 284], 'regulatory': [121, 286, 4403, 4430, 4499, 4518, 4581], 'miRNAs': [124, 289, 2369, 2375, 2389, 2445, 4192, 4212, 4481, 4521], 'constructing': [128, 293], 'co-expression': [130, 295, 2484, 4600], 'network': [131, 296, 477, 1773, 1980, 2477, 4601, 4613, 4621, 4654], 'pathways,': [135, 300, 3719, 4688, 4703], 'identifying': [137, 302], 'clinically': [138, 303, 5150], 'relevant': [139, 304, 2695, 3288], 'markers.': [141, 306], 'This': [142, 307, 813, 974, 2650, 3007], 'upgraded': [143, 308], 'TCPA': [144, 309, 906, 963, 1043, 2621, 3335, 5156, 5320, 5352], '(v3.0)': [145, 310, 1044], 'will': [146, 311], 'provide': [147, 312, 922, 3756, 4567], 'research': [150, 315, 800, 5330], 'community': [151, 316], 'more': [154, 319, 1690, 3970], 'tool': [156, 321], 'for': [157, 322, 475, 508, 542, 623, 1184, 1257, 1485, 1500, 1648, 1670, 1764, 2201, 2634, 2893, 3206, 3228, 3278, 3496, 4010, 4019, 4084, 4090, 4128, 5040, 5065, 5182, 5284, 5327], 'studying': [158, 323], 'making': [162, 327], 'translational': [163, 328, 4491, 4548, 5124], 'impacts.': [164, 329], 'Functional': [330], 'is': [332, 938, 1054, 2742, 2890, 3077, 3273, 3774, 4213, 4553, 4669, 4998], 'phenotypic': [344], '(RPPAs)': [352], '1The': [353], 'abbreviations': [354, 383], 'used': [355, 384, 1631, 1711, 2131, 2347], 'are:': [356, 385], 'RPPA,': [357, 386, 1659], 'reverse-phase': [358, 387, 536, 695, 1489], 'arrays;': [360, 389], 'TCGA,': [361, 390], 'Atlas;': [365, 370, 394, 399], 'FDR,': [371, 400], 'false': [372, 401, 1737], 'discovery': [373, 402, 1738], 'rate;': [374, 403], 'SCNAs,': [375, 404, 2816, 3785], 'alterations;': [378, 407], 'SMGs,': [379, 408, 3732], 'genes.1The': [382], 'genes.': [411, 2373], 'cutting-edge': [414], 'technology': [416, 1181], 'can': [418, 1028, 2849, 2859, 2919, 2957, 3009, 3306, 4072, 4482], 'quantitatively': [419], 'assess': [420, 2265, 3338, 4141], 'large': [422, 3495], 'number': [423, 1560, 2169, 2451, 2505, 3726, 4093, 5289], 'markers': [426, 1032, 1358, 1721, 2488, 2660, 2683, 3014, 3240, 3285, 4798, 4826, 5054, 5075, 5128, 5222], 'in': [427, 431, 550, 844, 896, 903, 914, 1065, 1264, 1616, 1771, 1832, 1864, 2140, 2213, 2289, 2331, 2348, 2384, 2405, 2440, 2464, 2472, 2509, 2529, 2536, 2549, 2587, 2599, 2871, 2905, 2923, 3036, 3052, 3082, 3133, 3197, 3266, 3334, 3353, 3515, 3539, 3544, 3555, 3565, 3575, 3608, 3613, 3653, 3678, 3690, 3708, 3712, 3817, 3826, 4064, 4078, 4169, 4175, 4228, 4267, 4305, 4327, 4405, 4531, 4631, 4647, 4662, 4665, 4711, 4732, 4787, 4818, 4833, 4866, 4888, 4920, 5012, 5076, 5100, 5114, 5129, 5223, 5299], 'thousands': [428], 'cost-effective,': [433], 'sensitive,': [434], 'high-throughput': [436], 'manner': [437, 5103], '(1.Sheehan': [438], 'K.M.': [439], 'Calvert': [440], 'V.S.': [441], 'Kay': [442], 'E.W.': [443], 'Lu': [444, 594, 682, 854, 1162, 1206, 1332, 1436, 1468, 1922, 3594, 3927], 'Y.': [445, 522, 595, 683, 855, 1161, 1163, 1207, 1333, 1437, 1469, 1600, 1776, 1923, 3928, 4239, 4255, 4257, 4335, 4341, 4359, 4361, 4365, 4369, 4993], 'Fishman': [446], 'D.': [447, 671, 673, 1780, 1792, 1810, 2017, 2062, 2095, 3366, 3411, 3444, 4937], 'Espina': [448], 'V.': [449, 731, 1100, 2319], 'Aquino': [450], 'J.': [451, 593, 638, 849, 1233, 1235, 1297, 1401, 1590, 1802, 1887, 2025, 2038, 2093, 3374, 3387, 3442, 3595, 3892, 4241, 4245, 4269, 4331, 4337, 4373], 'Speer': [452], 'R.': [453, 455, 534, 597, 642, 725, 733, 735, 851, 1094, 1102, 1104, 1159, 1229, 1279, 1383, 1473, 1869, 2105, 2550, 2588, 3454, 3874, 4343, 4989], 'Araujo': [454], 'Mills': [456, 531, 616, 684, 858, 1168, 1244, 1334, 1438, 1476, 1813, 1924, 2102, 3451, 3929], 'G.B.': [457, 532, 617, 685, 859, 1169, 1245, 1335, 1439, 1477, 1814, 1925, 2103, 3452, 3930], 'Liotta': [458], 'L.A.': [459, 528, 658, 1319, 1423, 1909, 3914], 'Petricoin': [460], '3rd,': [461], 'E.F.': [462], 'Wulfkuhle': [463], 'J.D.': [464, 679, 1305, 1409, 1895, 3900], 'Use': [465], 'reverse': [467, 1253], 'phase': [468, 1173, 1254], 'microarrays': [470, 507], 'reference': [472], 'standard': [473], 'development': [474, 549], 'molecular': [476, 766, 932, 991, 1135, 1507, 1643, 1825, 2568, 2720, 2761, 3291, 5212], 'analysis': [478, 1185, 1774, 2261, 2387, 3805, 4164], 'metastatic': [480, 2676], 'ovarian': [481], 'carcinoma.Mol.': [482], 'Cell.': [483, 698], 'Proteomics.': [484, 1269], '2005;': [485], '4:': [486, 2335], '346-355Abstract': [487], 'Full': [488, 490, 702, 704, 779, 781, 1148, 1150, 1838, 1840, 2119, 2121, 3468, 3470, 4504, 4506], 'Text': [489, 491, 703, 705, 780, 782, 1149, 1151, 1839, 1841, 2120, 2122, 3469, 3471, 4505, 4507], 'PDF': [492, 706, 783, 1152, 1842, 2123, 2927, 3472, 4508], 'PubMed': [493, 516, 556, 632, 707, 784, 879, 1153, 1199, 1273, 1349, 1453, 1495, 1622, 1843, 1939, 2124, 2337, 3473, 3633, 3944, 4313, 4394, 4509, 4927, 4979, 5019], 'Scopus': [494, 517, 557, 633, 708, 785, 880, 1154, 1200, 1274, 1350, 1454, 1496, 1623, 1844, 1940, 2125, 2338, 3474, 3634, 3945, 4314, 4395, 4510, 4928, 4980, 5020], '(269)': [495], 'Google': [496, 519, 559, 635, 710, 787, 882, 1156, 1202, 1276, 1352, 1456, 1498, 1625, 1846, 1942, 2127, 2340, 3476, 3636, 3947, 4275, 4316, 4397, 4512, 4930, 4982, 5022], 'Scholar,': [497, 520, 636, 711, 1157, 1203, 1277, 1457, 4931, 4983], '2.Spurrier': [498], 'B.': [499, 1165, 2027, 3376, 4291, 4367, 4898], 'Ramalingam': [500], 'S.': [501, 503, 524, 648, 1213, 1299, 1331, 1403, 1435, 1889, 1921, 2015, 2034, 3364, 3383, 3894, 3926, 4253, 4347, 4904, 4933, 4941, 4943, 4954, 4960], 'Nishizuka': [502], 'lysate': [506], 'analysis.Nat.': [511], 'Protoc.': [512], '2008;': [513], '3:': [514], '1796-1808Crossref': [515], '(154)': [518], '3.Lu': [521], 'Ling': [523, 647, 1298, 1402, 1888, 3893], 'Hegde': [525], 'A.M.': [526, 727, 1096, 1209], 'Byers': [527, 657, 1318, 1422, 1908, 3913], 'Coombes': [529, 1220, 1478], 'K.': [530, 1221, 1295, 1399, 1784, 1885, 2099, 3448, 3890], 'Akbani': [533, 596, 641, 732, 850, 1101, 1472, 1865, 3870], 'as': [539, 1013, 1015, 2700, 3176, 3686, 3734, 4051, 4106, 4114, 4193, 4225, 4261, 4298, 5031, 5158], 'pharmacodynamic': [540], 'assays': [541], 'proteomics,': [544], 'biomarker': [545, 4266], 'discovery,': [546], 'drug': [548], 'cancer.Semin.': [551], 'Oncol.': [552], '2016;': [553, 5016], '43:': [554], '476-483Crossref': [555], '(39)': [558], 'Scholar).': [560, 788, 1353, 1626, 1847, 1943, 2341, 3637, 4398], '(TCGA)': [580], 'project': [581, 1516], '>650': [583], 'independent': [584], 'lines': [587, 693], '19': [589, 4191], 'lineages': [591], '(4.Li': [592], 'Ju': [598, 645, 1214, 1288, 1392, 1878, 3883], 'Z.': [599, 646, 1215, 1289, 1393, 1459, 1798, 1804, 1879, 2036, 3385, 3603, 3884], 'Roebuck': [600, 651, 1462, 1593], 'P.L.': [601, 1463], 'Liu': [602, 643, 1218, 1290, 1394, 1460, 1597, 1880, 2043, 3392, 3885, 4286, 4354, 4360, 4368, 4374], 'W.': [603, 640, 644, 662, 853, 1219, 1291, 1395, 1461, 1881, 3886, 4247, 4985], 'Yang': [604, 1292, 1396, 1882, 3887, 4252, 4352, 4992], 'J.Y.': [605, 1293, 1397, 1883, 2068, 3417, 3888], 'Broom': [606, 1324, 1428, 1914, 3919], 'B.M.': [607, 1325, 1429, 1915, 3920], 'Verhaak': [608, 1326, 1430, 1916, 3921], 'R.G.': [609, 1327, 1431, 1917, 3922], 'Kane': [610], 'D.W.': [611], 'Wakefield': [612], 'C.': [613, 715, 1084, 2011, 2048, 2066, 3360, 3397, 3415, 3589, 4281, 4339, 4351, 4939], 'Weinstein': [614, 856, 1322, 1426, 1474, 1601, 1912, 3917], 'J.N.': [615, 681, 857, 1323, 1427, 1475, 1602, 1913, 3918], 'Liang': [618, 686, 860, 1328, 1432, 1603, 1822, 1918, 2055, 2076, 3404, 3425, 3923, 4340], 'H.': [619, 687, 749, 861, 1118, 1329, 1433, 1604, 1800, 1806, 1823, 1919, 2077, 3426, 3924, 4251], 'TCPA:': [620], 'A': [621, 1246, 1336, 1440, 1926, 2475, 3931], 'resource': [622, 5326], 'data.Nat.': [627], 'Methods.': [628], '2013;': [629], '10:': [630, 4273], '1046-1047Crossref': [631], '(314)': [634], '5.Li': [637], 'Zhao': [639, 852, 4242], 'Vellano': [649], 'C.P.': [650], 'P.': [652, 1309, 1413, 1594, 1899, 2030, 3379, 3904, 4966, 4991], 'Yu': [653], 'Q.': [654, 2040, 3389], 'Eterovic': [655], 'A.K.': [656], 'Davies': [659, 1216, 1470], 'M.A.': [660, 1217, 1471], 'Deng': [661], 'Gopal': [663], 'Y.N.': [664], 'Chen': [665, 1799, 1803, 2098, 3447], 'G.': [666, 2097, 3446, 4353], 'von': [667], 'Euw': [668], 'E.M.': [669, 2044, 2075, 3393, 3424], 'Slamon': [670], 'Conklin': [672], 'Heymach': [674, 1310, 1414, 1900, 3905], 'J.V.': [675, 1311, 1415, 1901, 3906], 'Gazdar': [676], 'A.F.': [677], 'Minna': [678, 1304, 1408, 1894, 3899], 'Myers': [680], 'Characterization': [688], 'human': [690, 1266, 2697], 'arrays.Cancer': [697], '2017;': [699, 876, 4310, 4976], '31:': [700, 1493], '225-239Abstract': [701], '(141)': [709], '6.Hoadley': [712], 'K.A.': [713, 1082], 'Yau': [714, 1083], 'Hinoue': [716, 1085], 'T.': [717, 1086, 4345, 4349], 'Wolf': [718, 1087], 'D.M.': [719, 1088], 'Lazar': [720, 1089, 2100, 3449], 'A.J.': [721, 1090, 2101, 3450], 'Drill': [722, 1091], 'E.': [723, 1092, 2013, 2070, 3362, 3419, 4947, 4969, 4987], 'Shen': [724, 1093], 'Taylor': [726, 1095], 'Cherniack': [728, 1097], 'A.D.': [729, 1098], 'Thorsson': [730, 1099], 'Bowlby': [734, 1103], 'Wong': [736, 1105], 'C.K.': [737, 1106], 'Wiznerowicz': [738, 1107], 'M.': [739, 1108, 1167, 1227, 1285, 1389, 1875, 3880, 4357, 4962], 'Sanchez-Vega': [740, 1109], 'F.': [741, 1110, 1223, 1231, 1287, 1315, 1321, 1391, 1419, 1425, 1821, 1877, 1905, 1911, 2042, 3391, 3882, 3910, 3916, 4333, 4363], 'Robertson': [742, 1111], 'A.G.': [743, 1112], 'Schneider': [744, 1113], 'B.G.': [745, 1114], 'Lawrence': [746, 1115, 2086, 3435], 'M.S.': [747, 1116, 1211, 2087, 3436], 'Noushmehr': [748, 1117], 'Malta': [750, 1119], 'T.M.': [751, 1120], 'N.': [755, 1124, 1317, 1421, 1467, 1907, 2050, 2091, 3399, 3440, 3912, 4900], 'Stuart': [756, 1125, 2092, 3441], 'J.M.': [757, 1126, 2058, 3407], 'Benz': [758, 1127], 'C.C.': [759, 1128], 'Laird': [760, 1129], 'P.W.': [761, 1130], 'Cell-of-origin': [762, 1131], 'patterns': [763, 1036, 1132, 3986, 4740, 4887, 5095], 'dominate': [764, 1133], 'classification': [767, 1136], '10,000': [769, 1138], 'tumors': [770, 1139, 2673, 4110], 'from': [771, 995, 1069, 1140, 1511, 1555, 1568, 1584, 1731, 2004, 2197, 2314, 2642, 2662, 2724, 3831, 3864, 3996, 4046, 5204, 5359], '33': [772, 1141], 'cancer.Cell.': [775, 1144], '2018;': [776, 1145, 1835, 2116, 3465, 4272], '173:': [777, 1146], '291-304.e296Abstract': [778, 1147], '(1050)': [786, 1155], 'better': [790, 3028, 3049, 4100, 4152, 4584], 'utilize': [791], 'serve': [796, 5030], 'broad': [798, 5193], 'biomedical': [799, 5183], 'community,': [801], 'an': [804, 3225, 3757, 4162, 4226, 4262, 4299], 'bioinformatics': [806], 'web-based': [814], 'platform': [815, 829, 1052, 1609, 2626, 5162], 'not': [816, 921, 4537], 'only': [817, 918, 2459, 4534, 5263, 5286], 'releases': [818], 'most': [820, 2234, 3521, 3811, 4070], 'updated': [821, 962], 'are': [824, 2834, 2883, 2938, 3264, 3480, 3493, 3791, 4626, 5297, 5336, 5348], 'generated': [825, 1982, 2362, 2480, 2615, 2939], 'our': [827, 3865], 'but': [830, 3954, 4536], 'also': [831, 3950, 5349], 'user-friendly': [834], 'interface': [835, 2591], 'allowing': [836], 'users': [837, 1027, 2746, 2894, 2956, 3067, 3152, 3229, 5240], 'analyze': [839, 865, 2639, 5166], 'visualize': [841, 2637, 2942], 'rich': [846], 'context': [847], '(7.Li': [848], 'Explore,': [862], 'visualize,': [863], 'proteomic': [868, 1180, 1338, 1442, 1928, 3933], 'using': [870, 4201, 4439, 5138, 5273], 'Atlas.Cancer': [874], 'Res.': [875, 1618, 4271], '77:': [877], 'e51-e54Crossref': [878], '(60)': [881], 'Scholar),': [883, 2128, 4513, 5023], 'has': [885, 2909, 4220], 'substantially': [886], 'reduced': [887], 'computational': [889], 'barriers': [890], 'analyzing': [892], 'complex': [893], 'large-scale': [897], 'sample': [898, 2138, 3097, 3487], 'sets.': [899], 'However,': [900], 'analytic': [901, 1051, 2553, 2595, 2632, 2737, 2775, 2847, 3322, 5176, 5201, 5236], 'modules': [902], 'previous': [905, 3866], 'versions': [907], 'focused': [909, 3348], 'protein-based': [912], 'individual': [915], 'do': [920], 'integrative': [923, 4163], 'data.': [933, 1549, 2219, 5172], 'those': [935, 1688, 2460, 3032, 4129, 4440], 'modules,': [936], 'it': [937, 2889, 3047], 'difficult': [939], 'explore': [941, 1611, 5164], 'similarities': [943], 'differences': [945], 'among': [946, 2486, 2993, 3092, 3662, 4589, 4628, 4779, 5058], 'types,': [948, 2408, 3204, 3534, 3549, 3681, 3990, 4082, 4630, 4716], 'limits': [950, 5269], 'full': [952], 'potential': [953, 3012, 3561, 3761, 4121, 4194, 4783, 5125], 'TCPA.': [955], 'its': [958, 3105, 3165, 4056], 'utility,': [959], 'adding': [965], 'newly': [967, 2629, 3319], 'Analysis."': [973], 'association': [982], 'studies': [983], 'between': [984, 1636, 1716, 1972, 2146, 2297, 2411, 2515, 2751, 2809, 2828, 3341, 3525, 4606, 4659, 4785], 'clinical': [993, 1505, 1539, 1645, 2570, 2722, 2759, 2793, 3289, 4793, 5214], 'TCGA.': [996], 'These': [997, 3754, 4138, 4399, 4772, 5227], 'include': [999], 'mutations,': [1001, 1523, 3346], 'alterations': [1004], '(SCNAs),': [1005], 'miRNA': [1011, 1657, 2312, 2403, 3173, 4155, 4424, 4574, 5292], 'well': [1014], 'survival,': [1017, 1545, 2797], 'tumor': [1018, 1542, 1579, 1695, 2798, 2994, 4325, 4807, 5044, 5061, 5078, 5098, 5109, 5115, 5134], 'subtype,': [1019, 1696, 2799, 4808], 'disease': [1021, 4810], 'stage.': [1022], 'With': [1023], 'module,': [1026, 3323, 5207], 'easily': [1029, 2860, 2921], 'identify': [1030, 4006, 4573, 5147], 'show': [1034, 1969, 2482, 3027, 5217], 'interesting': [1035], 'Overall,': [1040], 'current': [1042, 5259], 'represents': [1045, 2167, 2186, 2497, 2503, 4635, 4641, 4680], 'comprehensive,': [1047], 'cutting-edge,': [1048], 'pan-cancer': [1050, 1337, 1441, 1634, 1927, 2583, 2594, 2644, 2655, 2736, 2774, 2898, 3321, 3332, 3868, 3932, 5168, 5175, 5235, 5260], 'freely': [1055], 'available': [1056, 5337, 5350], 'at': [1057, 1745, 2377, 2465, 4712, 4733, 4834, 5338, 5351], 'http://tcpaportal.org.': [1058], 'were': [1062, 1364, 1370, 1509, 1553, 1566, 1582, 1630, 1667, 1679, 1685, 1710, 1734, 1754, 1862, 1948, 2002, 2130, 2150, 2194, 2224, 2247, 2252, 2275, 2287, 2302, 2346, 2355, 2382, 2398, 2419, 2446, 2470, 2518, 2533, 2542, 2555, 2572, 2585, 2605, 2614, 3504, 3644, 3671, 3705, 3747, 4751, 5055, 5294], 'first': [1063, 2195, 2309, 2556, 3271, 4592], 'quantified': [1064, 2661], 'collected': [1068, 1583, 2716, 4030], 'project,': [1071], 'included': [1073, 1947, 2383], '7,694': [1074, 2663], '(6.Hoadley': [1081], '8.Tibes': [1158], 'Qiu': [1160], 'Hennessy': [1164], 'Andreeff': [1166], 'Kornblau': [1170], 'S.M.': [1171, 1313, 1417, 1903, 3908, 4956], 'Reverse': [1172], 'array:': [1175], 'Validation': [1176], 'novel': [1179, 5245], 'primary': [1187, 2672], 'leukemia': [1188], 'specimens': [1189], 'hematopoietic': [1191], 'stem': [1192], 'cells.Mol.': [1193], 'Ther.': [1195], '2006;': [1196], '5:': [1197, 1347, 1451, 1937, 3942], '2512-2521Crossref': [1198], '(522)': [1201], '9.Hennessy': [1204], 'B.T.': [1205], 'Gonzalez-Angulo': [1208], 'Carey': [1210], 'Myhre': [1212], 'Meric-Bernstam': [1222, 1320, 1424, 1910, 3915], 'Bedrosian': [1224], 'I.': [1225, 2052, 3401], 'McGahren': [1226], 'Agarwal': [1228], 'Zhang': [1230, 1286, 1390, 1466, 1805, 1876, 3881, 4282, 4288, 4366, 4372], 'Overgaard': [1232], 'Alsner': [1234], 'Neve': [1236], 'R.M.': [1237], 'Kuo': [1238], 'W.L.': [1239], 'Gray': [1240], 'J.W.': [1241, 2323], 'Borresen-Dale': [1242], 'A.L.': [1243], 'technical': [1247], 'assessment': [1248], 'study': [1259, 3356], 'proteome': [1263], 'non-microdissected': [1265], 'breast': [1267, 3134, 3198, 4921, 5066], 'cancers.Clin.': [1268], '2010;': [1270], '6:': [1271], '129-151Crossref': [1272], '(177)': [1275], '10.Akbani': [1278], 'Ng': [1280, 1384, 1785, 1870, 2029, 3378, 3875], 'P.K.': [1281, 1385, 1786, 1871, 3876], 'Werner': [1282, 1386, 1872, 3877], 'H.M.': [1283, 1387, 1873, 3878, 4285], 'Shahmoradgoli': [1284, 1388, 1874, 3879], 'Yoshihara': [1294, 1398, 1884, 3889], 'Li': [1296, 1400, 1801, 1886, 3891, 4234, 4250], 'Seviour': [1300, 1404, 1890, 3895], 'E.G.': [1301, 1405, 1891, 3896], 'Ram': [1302, 1406, 1892, 3897], 'P.T.': [1303, 1407, 1893, 3898], 'Diao': [1306, 1410, 1595, 1896, 3901], 'L.': [1307, 1411, 1592, 1596, 1598, 1808, 1897, 2046, 2107, 3395, 3456, 3902, 4233, 4243, 4375, 4902, 4935, 4945], 'Tong': [1308, 1412, 1898, 3903], 'Hill': [1312, 1416, 1902, 3907], 'Dondelinger': [1314, 1418, 1904, 3909], 'Städler': [1316, 1420, 1906, 3911], 'Mukherjee': [1330, 1434, 1920, 3925], 'perspective': [1339, 1443, 1929, 2646, 3934], 'Atlas.Nat.': [1344, 1448, 1934, 3939], 'Commun.': [1345, 1449, 1935, 3940, 4975], '2014;': [1346, 1450, 1936, 3941, 4924], '3887Crossref': [1348, 1452, 1938, 3943], '(352)': [1351, 1455, 1941, 3946], 'In': [1354, 1575, 1998, 2158, 2492, 2821, 2901], 'total,': [1355, 1999], '258': [1356, 2658, 2675, 5052], '(including': [1359, 1651], 'total': [1360, 2192, 2207, 2344, 2686, 3730], 'phosphorylated': [1362, 2688], 'proteins)': [1363, 2689], 'assayed.': [1365], 'raw': [1367, 5334], 'standardized': [1372], 'normalized': [1374], 'SuperCurve,': [1376], 'median': [1377], 'polish,': [1378], 'replicate-based': [1380], 'normalization': [1381], '(10.Akbani': [1382, 1868, 3873], '11.Ju': [1458], 'Siwak': [1464], 'D.R.': [1465], 'K.R.': [1479], 'Development': [1480], 'robust': [1483, 5033], 'classifier': [1484], 'quality': [1486], 'control': [1487], 'arrays.Bioinformatics.': [1491], '2015;': [1492, 1619, 2334], '912-918Crossref': [1494], '(33)': [1497], 'Scholar)': [1499, 3477, 4276, 4317], 'downstream': [1501], 'analyses.': [1502, 2561, 2734], 'All': [1503, 1562, 1726, 2271, 2551, 2601, 2845, 3301, 5332], 'obtained': [1510, 2003, 2310, 5203], 'consisting': [1517, 4756], '(i)': [1519, 1647, 2781, 4618], 'data:': [1521, 1530, 1540, 1646], 'SCNAs;': [1527], '(ii)': [1528, 1669, 2803, 4651], 'RNA': [1529, 3162, 3586], 'RNA-seq': [1531], 'miRNA-seq-based': [1533], 'gene': [1534, 2813, 3085, 3611, 4124, 4484], 'data;': [1536], '(iii)': [1538, 1682, 2820], 'stage,': [1541, 1697, 2800], 'grade,': [1543], 'overall': [1544, 2966, 3029, 3758, 4829], 'progression-free': [1547, 2968, 3050], 'survival': [1548, 1701, 1724, 2943, 2969, 3030, 3051, 4805, 4831, 4879], 'Specifically,': [1550, 2950, 3696, 3842], 'SCNA': [1551], 'downloaded': [1554, 3309], 'Synapse': [1556], '(https://www.synapse.org/)': [1557], 'accession': [1559], 'syn5049520.1.': [1561], 'retrieved': [1567], 'website': [1573, 5342, 5353], '(https://gdc.cancer.gov/about-data/publications/pancanatlas).': [1574, 5343], 'addition,': [1576, 2902], 'all': [1577, 2610, 2691, 2755, 2879, 3545, 3663, 3717, 3744, 3820, 4023, 4031, 4080, 4705, 4729, 5310], 'subtype': [1580], 'information': [1581, 4569], 'marker': [1587, 2962, 3076, 3158, 4672, 4856, 5035], 'publications': [1588], '(12.Li': [1589], 'Han': [1591, 1807], 'Yuan': [1599], 'TANRIC:': [1605], 'An': [1606], 'interactive': [1607, 2625, 2853, 5161], 'open': [1608], 'function': [1613, 4224], 'lncRNAs': [1615], 'cancer.Cancer': [1617], '75:': [1620], '3728-3737Crossref': [1621], '(377)': [1624], 'Multiple': [1627], 'statistical': [1628, 2560, 3497], 'methods': [1629], 'examine': [1633, 2748, 2958, 3069, 3154, 3231], 'associations': [1635, 2750, 2808, 3263, 3340, 4588, 5219], 'continuous': [1649], 'SCNA,': [1654, 2214, 4047], 'pathway': [1661, 1752, 1831, 1861, 1996, 3770, 4594, 4637, 4676, 4780, 5011], 'scores),': [1662], "Spearman's": [1663, 2258, 2395, 2512, 3116, 3179, 3251, 4446], 'rank': [1664, 2259, 2396, 2513, 3117, 3180, 3252, 4447], 'correlation': [1665, 2176, 2203, 2236, 2260, 2281, 3196, 3993, 4057, 4448, 4528], 'performed;': [1668, 1680], 'dichotomous': [1671], 'variables': [1672], '(e.g.': [1673, 1694, 5063], 'wild': [1674], 'type': [1675, 1767, 5084], 'versus': [1676, 4186], 'mutated),': [1677], 't-tests': [1678, 2153], 'ANOVA': [1683], 'tests': [1684], 'applied': [1686, 1770], 'than': [1691, 3031, 3959], 'two': [1692, 2467, 2516, 3238, 4209, 4616, 4691, 4749, 4770], 'levels': [1693, 1718, 1763, 1974, 3235, 3508], 'grade).': [1699], 'For': [1700, 2254, 2391, 2523, 2929, 3019, 3123, 3186, 3258, 5280], 'analysis,': [1702, 2944], 'both': [1703, 2266, 2567, 2685], 'Cox': [1704, 2975, 4845], 'proportional-hazards': [1705, 2976, 4846], 'model': [1706, 2977], 'log-rank': [1708, 2979, 4842], 'test': [1709, 2896, 3091, 3837, 4843, 5186], 'calculate': [1713], 'times.': [1725], 'p': [1728, 2273, 3299, 3838], 'values': [1729, 2274, 3839], 'derived': [1730], 'multiple': [1732, 2221, 3709], 'comparisons': [1733], 'adjusted': [1735, 2277], 'rate': [1739], '(FDR).': [1740], 'reported': [1742, 4222, 4886], 'significant': [1743, 2175, 2519, 3304, 3328, 3537, 4033, 4471, 4645, 4684, 4863, 5218], 'results': [1744, 2554, 2604, 2848, 2877, 3305, 3333, 3755, 4139, 4400, 4561, 4773, 5025, 5121, 5202, 5347], 'FDR': [1746, 2155], '<': [1747, 2156, 2178, 2521, 3840, 4036, 4450, 4840], '0.1.': [1748, 2157], 'Eleven': [1749], 'core': [1750, 1950, 4726], 'scores': [1753, 4595], 'calculated': [1755, 2431, 4593], 'based': [1756, 1983, 4602], '(signed)': [1758], 'average': [1759, 3861], 'each': [1765, 1860, 2141, 2165, 2184, 2255, 2392, 2495, 2501, 2903, 3243, 3259, 4633, 4639, 4663, 4667, 4678, 4709], 'before': [1768], 'being': [1769], '(13.Wang': [1775], 'Xu': [1777, 3596, 4244, 4246], 'X.': [1778, 1796, 4237, 4249, 4283, 4355, 4371], 'Maglic': [1779], 'Dill': [1781], 'M.T.': [1782], 'Mojumdar': [1783], 'Jeong': [1787, 2031, 3380], 'K.J.': [1788, 2032, 3381], 'Tsang': [1789], 'Y.H.': [1790], 'Moreno': [1791], 'Bhavana': [1793], 'V.H.': [1794], 'Peng': [1795], 'Ge': [1797], 'Du': [1809], 'Creighton': [1811], 'C.J.': [1812], 'Research': [1818, 2084, 3433, 5362], 'Network': [1819, 2085, 3434], 'Camargo': [1820], 'Comprehensive': [1824, 2108, 3457], 'characterization': [1826, 2109, 3458], 'Hippo': [1829, 2704], 'cancer.Cell': [1833, 4307], 'Rep.': [1834, 5015], '25:': [1836], '1304-1317.e5Abstract': [1837], '(190)': [1845], 'members': [1850, 4661, 4781], 'directions': [1854, 2463], '(i.e.': [1855, 2763], 'up-': [1856], 'or': [1857, 2438, 2866, 2926, 2967, 2986, 2997, 3103, 3167, 3172, 3290, 4049, 4111, 4134, 4490, 4844], 'down-regulation)': [1858], 'within': [1859, 3987, 5080], 'defined': [1863], 'et': [1866, 2006, 3871], 'al.': [1867, 2007, 3872], '11': [1945, 1995, 3540, 3547], 'apoptosis,': [1949, 3701, 4722, 4758], 'reactive,': [1951], 'cycle,': [1953], 'damage': [1955, 3698], 'response,': [1956, 3699], 'epithelial-mesenchymal': [1957, 4723], 'transition,': [1958, 4724], 'hormone': [1959, 1961], 'a,': [1960], 'b,': [1962], 'PI3K/Akt,': [1963, 2701, 4698], 'Ras/MAPK,': [1964, 2702], 'RTK,': [1965, 4700], 'TSC/mTOR.': [1967], 'bipartite': [1979, 2160], 'was': [1981, 2241, 2262, 2430, 2479, 2597, 3519, 3553, 3721, 4099, 4764], 'mutational': [1986, 2814, 3648], 'status': [1987, 3649, 3677], 'genes': [1991, 2113, 2212, 2354, 2381, 3174, 3462, 3484, 4130, 4185], '(SMGs)': [1992], 'scores.': [1997], '299': [2000, 3350], 'SMGs': [2001, 2149, 3351, 3479, 3503, 3728, 3746], 'Bailey': [2005], '(14.Bailey': [2008, 3357], 'M.H.': [2009, 3358], 'Tokheim': [2010, 3359], 'Porta-Pardo': [2012, 3361], 'Sengupta': [2014, 3363], 'Bertrand': [2016, 3365], 'Weerasinghe': [2018, 3367], 'A.': [2019, 2021, 2064, 2089, 3368, 3370, 3413, 3438, 3599, 4949, 4964], 'Colaprico': [2020, 3369], 'Wendl': [2022, 3371], 'M.C.': [2023, 3372], 'Kim': [2024, 3373], 'Reardon': [2026, 3375], 'Kwok-Shing': [2028, 3377], 'Cao': [2033, 3382], 'Wang': [2035, 2041, 3384, 3390, 4284, 4332, 4336, 4358], 'Gao': [2037, 2039, 3386, 3388], 'Mularoni': [2045, 3394], 'Rubio-Perez': [2047, 3396], 'Nagarajan': [2049, 3398], 'Cortés-Ciriano': [2051, 3400], 'Zhou': [2053, 3402], 'D.C.': [2054, 3403], 'W.W.': [2056, 3405], 'Hess': [2057, 3406], 'Yellapantula': [2059, 3408], 'V.D.': [2060, 3409], 'Tamborero': [2061, 3410], 'Gonzalez-Perez': [2063, 3412], 'Suphavilai': [2065, 3414], 'Ko': [2067, 3416], 'Khurana': [2069, 3418], 'Park': [2071, 3420], 'P.J.': [2072, 3421], 'Van': [2073, 3422, 4967], 'Allen': [2074, 3423], 'MC3': [2078, 3427], 'Working': [2079, 3428], 'Group,': [2080, 3429], 'Godzik': [2088, 3437], 'Lopez-Bigas': [2090, 3439], 'Wheeler': [2094, 3443], 'Getz': [2096, 3445], 'Karchin': [2104, 3453], 'Ding': [2106, 3455, 4988], 'driver': [2112, 3461, 3483], 'mutations.Cell.': [2115, 3464], '174:': [2117, 3466], '1034-1035Abstract': [2118, 3467], '(206)': [2126, 3475], 'define': [2133], 'wild-type': [2137, 3096, 3527], 'groups': [2139, 3492], 'type.': [2143, 2443], 'assessed': [2151], 'network,': [2161], 'thickness': [2163], 'edge': [2166, 2185, 2502, 4640, 4679], '(FDR': [2177, 2520, 4035, 4449, 4839], '0.1),': [2179], 'color': [2182], 'direction': [2188, 2436], 'correlations.': [2190, 2844, 4685], 'extracted': [2196], 'analysis.': [2204, 2350, 4529], 'Among': [2205, 3716, 4686, 4848], '191': [2206, 2343], 'proteins,': [2208, 4095, 4426, 4590], '187': [2209], 'had': [2210], 'matched': [2211, 2244, 2356], 'When': [2220], 'methylation': [2222, 3110, 3968, 4104], 'probes': [2223], 'mapped': [2225], 'same': [2228, 3858], 'gene,': [2229], 'one': [2231, 4695, 5254], 'showing': [2232, 2455, 2913, 3535, 4704, 5092], 'negative': [2235, 2456, 2462, 3971, 4445, 4541], 'selected.': [2242], 'protein-gene': [2245], 'pairs': [2246, 2365, 3828, 3833, 4441], 'named': [2248], '"cis-pairs"': [2249], 'others': [2251], '"trans-pairs."': [2253], 'type,': [2257], 'performed': [2263, 4161], 'cis-': [2268, 2284, 2298], 'trans-pairs.': [2270], 'then': [2276, 2447, 3294], 'FDR.': [2279], 'coefficients': [2282], 'trans-pairs': [2286], 'plotted': [2288], 'histograms': [2290], 'corresponding': [2292, 3296, 3511, 4580], 'density': [2293], 'curves.': [2294], 'difference': [2296, 2410, 2426, 3538], 'trans-': [2300], 'distributions': [2301, 2413], 'tested': [2303, 2972, 3000, 3087, 3114, 3177, 3249], "Student's": [2305, 3089], 't': [2306, 3090, 3836], 'test.': [2307, 2424], 'predicted': [2311, 4075, 4183], 'targets': [2313, 4576, 5293], 'TargetScanHuman': [2315], '7.2': [2316], '(http://www.targetscan.org/vert_72/)': [2317], '(15.Agarwal': [2318], 'Bell': [2320], 'G.W.': [2321], 'Nam': [2322], 'Bartel': [2324], 'D.P.': [2325, 4494], 'Predicting': [2326], 'effective': [2327, 3226], 'microRNA': [2328], 'target': [2329, 2380, 4184, 4425], 'sites': [2330], 'mammalian': [2332], 'mRNAs.Elife.': [2333], 'e05005Crossref': [2336], '(4426)': [2339], 'Only': [2342, 4089], 'Next,': [2351, 3638], 'RPPA-associated': [2353], 'miRNA-target': [2359], 'list,': [2360], '1,345': [2363], 'miRNA-gene': [2364, 2393], 'including': [2366, 2795, 3170], '223': [2367], 'mature': [2368], '179': [2371], 'coding': [2372, 3171], 'least': [2378, 2466, 4713, 4734, 4835], 'five': [2379, 4321, 4836], '(119': [2388], 'retained).': [2390], 'pair,': [2394], 'calculated.': [2399], 'evaluate': [2401], 'different': [2406, 3016, 3830, 4146, 4170, 4624, 4648, 4813], 'miRNA—target-protein': [2415], 'miRNA—nontarget-protein': [2417], 'examined': [2420, 3326, 3501, 4516, 4791], 'Kolmogorov-Smirnov': [2423], 'means': [2429], 'determine': [2433], 'regulation': [2435, 3563, 4156], '(repression': [2437], 'activation)': [2439], 'ranked': [2448], 'direction,': [2457], 'displayed': [2471, 2606], 'heatmap.': [2474], 'nested': [2476, 2612, 2911, 4599], 'visualization': [2478], 'relationships': [2485, 4658], 'pathways.': [2491, 2706, 3567, 4746, 4771, 5313], 'networks,': [2494], 'node': [2496, 4634, 4668], 'pathway/protein,': [2499], 'nodes': [2517], '0.1).': [2522, 4451], 'simplicity,': [2524], 'edges': [2526], 'significance': [2528, 4914], '<10': [2530], 'filtered': [2534], 'out': [2535], 'network.': [2538], 'complete': [2540, 4692], 'graphs': [2541, 4693], 'identified': [2544, 3352, 4190, 5210], '"igraph"': [2547], 'package': [2548], 'precomputed': [2557, 3303], 'univariate': [2559, 2974], 'result': [2563, 2907, 3612], 'data,': [2564, 2571, 2714, 2794], 'along': [2565, 5107], 'converted': [2574], 'JSON': [2576], 'format': [2577], 'curated': [2579], 'into': [2580, 2885], 'CouchDB.': [2581], 'conducted': [2586, 3802], 'web': [2590], 'implemented': [2598], 'JavaScript.': [2600], 'table': [2603, 2908, 3268], 'DataTables,': [2608], 'plots': [2613, 2937], 'HighCharts.': [2617], 'Here': [2618, 5153], 'present': [2620, 4774, 5155], 'v3.0,': [2622], 'user-friendly,': [2624, 5160], 'integrated': [2630, 2884], 'researchers': [2635, 5184], 'multi-omic': [2645, 5139, 5189], '(Fig.': [2647, 2678, 2728, 2739, 2770, 3059, 3144, 3213, 3221, 4000, 4418, 4558, 4610, 4870, 4880, 5085, 5117], '1,': [2648, 2679, 2729, 2740, 2771, 3060, 3145, 3214, 3222], 'i).': [2649], 'release': [2652], 'includes': [2653], '(7,436': [2671], 'samples)': [2677], 'ii).': [2680], '(include': [2684], 'cover': [2690, 5264], 'major': [2692, 5255, 5311], 'cancer,': [2698], 'such': [2699, 3733, 4551], 'iii)': [2730], 'allow': [2732], 'multidimensional': [2733], 'iv)': [2741], 'protein-centric,': [2743], 'enables': [2745, 3066], 'features': [2762, 3823, 5215], 'clinical,': [2764], 'DNA,': [2765], 'RNA,': [2766], 'data)': [2769], 'v-viii).': [2772], 'consists': [2777, 4614], 'four': [2779, 4025], 'submodules:': [2780], '"Clinical': [2783, 2953], 'relevance"': [2784, 2954], 'submodule': [2785, 2841, 3008, 3065, 3150, 3220], 'shows': [2786, 2990, 3048, 3159, 4622, 4655], 'how': [2787, 3641, 4623], 'correlates': [2790, 2963, 3107], 'grade.': [2802], '"Protein-DNA': [2804, 3063], 'correlation"': [2805, 2824, 2840, 3064, 3149, 3219], 'evaluates': [2806], 'status,': [2815], 'methylation.': [2819], '"Protein-RNA': [2823, 3148], 'submodule,': [2825, 2955, 3260], 'mRNA/miRNA': [2832], 'examined;': [2835], '(iv)': [2837], '"Protein-protein': [2839], 'assesses': [2842], 'be': [2850, 2920, 3307, 3581, 4073, 4118, 5322], 'visualized': [2851, 2981, 3003, 3099, 3119, 3182, 3254], 'tables': [2854], 'under': [2855], 'separated': [2856], 'tabs.': [2857], 'Users': [2858], 'sort': [2861], 'search': [2863, 2867, 2873], 'any': [2864, 2868, 3237], 'column': [2865, 3272], 'keyword': [2869], 'globally': [2870], 'box.': [2874], 'Because': [2875, 4480], 'single': [2887], 'table,': [2888], 'very': [2891], 'simple': [2892], 'hypotheses': [2899, 5190], 'directly.': [2900, 3799], 'row': [2904], 'plot': [2912], 'original': [2915], 'points,': [2917], 'exported': [2922], 'either': [2924, 4486], 'PNG': [2925], 'format.': [2928], 'example,': [2930, 3020, 3124, 3187, 5281], 'Kaplan-Meier': [2931, 2984], 'plots,': [2932, 2934], 'box': [2933, 3005, 3101], 'scatter': [2936, 3121, 3184, 3256], 'help': [2941, 3010, 4140, 4572], 'protein-mutation,': [2945], 'protein-mRNA': [2947], 'correlations,': [2948, 4542], 'respectively.': [2949], 'whether': [2959, 2987, 3070, 3104, 3155, 3232, 3502], 'time': [2970], '(as': [2971, 2999, 3086, 3113, 3248], 'test;': [2980], 'plot),': [2985], 'differential': [2991], 'stages,': [2995], 'grades,': [2996], 'subtypes': [2998, 5062], 'ANOVA;': [3002], 'plots).': [3006, 3122, 3185, 3257], 'discover': [3011], 'prognostic': [3013, 4265, 4855, 4864, 4913, 5034], 'patients': [3021], 'high': [3023, 4872], 'PTEN': [3024, 3126], 'low': [3034], 'kidney': [3037, 3053, 4406], 'renal': [3038, 3054, 4229, 4407], 'clear': [3039, 3055, 4408], 'carcinoma,': [3041, 3136, 3209, 4410, 4414], 'low-grade': [3042, 3137], 'glioma,': [3043, 3138], 'mesothelioma,': [3045], 'while': [3046, 4468], 'carcinoma': [3057, 3143, 3200, 4231, 4387, 4417, 4973], 'alone': [3058], 'v).': [3061], 'affected': [3078, 3775], 'mutations': [3081, 3607, 3765], 'specific': [3084, 4016, 5250], 'groups;': [3098], 'plots)': [3102], 'SCNAs': [3112, 3949, 4112], 'correlation;': [3118, 3181, 3253], 'leads': [3127], 'lower': [3130], 'invasive': [3135, 3199, 5067], 'uterine': [3140], 'corpus': [3141], 'endometrial': [3142], 'vi).': [3146], 'allows': [3151], 'abundance': [3163, 3797, 3852, 4013, 4098], 'own': [3166], '(both': [3175], 'CYCLINB1': [3188], '(protein': [3189], 'marker)': [3190], 'KIF2C': [3192], 'positive': [3195, 3848, 3952, 4706, 4730], 'except': [3205, 4083], 'cholangiocarcinoma,': [3207], 'thyroid': [3208], 'uveal': [3211, 4087], 'melanoma': [3212], 'vii).': [3215], 'Finally,': [3216, 4789], '"Protein': [3218], 'viii)': [3223], 'way': [3227], 'correlate': [3241], 'these': [3261, 3302, 4520, 4745, 4748, 5024, 5120], 'pairwise': [3262], 'presented': [3265], 'view.': [3269], 'observed': [3277, 3984, 4211, 5089], 'associations,': [3280], 'followed': [3281], 'features,': [3292, 3783], 'statistic': [3297], 'value.': [3300], 'directly': [3308, 4302], 'portal.': [3312], 'findings': [3329, 5228], 'v3.0.': [3336], 'recent': [3355], 'because': [3478], 'usually': [3481], 'sizes': [3488], 'sufficiently': [3494], 'tests.': [3498], 'First,': [3499], 'associated': [3505, 3645, 3748, 4999], 'proteins.': [3512], 'As': [3513, 3652, 3815, 4062, 4173, 4816, 5039], 'shown': [3514, 3816, 4063, 4174, 4817], 'Fig.': [3516, 3654, 3818, 4065, 4176, 4819], '2A,': [3517], 'p53': [3518, 3550], 'differentially': [3522, 5056], 'expressed': [3523, 5057], 'TP53': [3526, 3656, 3675, 3684, 3713], 'Intriguingly,': [3543], 'up-regulated': [3554, 3707], 'group,': [3558, 3578], 'suggesting': [3559, 3682, 4543, 5069, 5111], 'feedback-loop': [3562], 'involved': [3564], 'p53-related': [3566], 'ARID1A,': [3568], 'PTEN,': [3569], 'ATM': [3571], 'showed': [3572, 3658, 3824, 3845, 3951, 3969, 4470, 4539, 4859], 'decreased': [3573], 'might': [3580], 'partly': [3582], 'due': [3583, 4119], 'nonsense-mediated': [3585], 'degradation': [3587], '(16.Yang': [3588], 'Asthagiri': [3590], 'A.R.': [3591], 'Iyer': [3592], 'R.R.': [3593, 3605], 'D.S.': [3597], 'Ksendzovsky': [3598], 'Brady': [3600], 'R.O.': [3601], 'Zhuang': [3602], 'Lonser': [3604], 'Missense': [3606], 'NF2': [3610], 'quantitative': [3615], 'loss': [3616], 'merlin': [3618], 'minimally': [3621], 'affect': [3622], 'intrinsic': [3624], 'function.Proc.': [3625], 'Natl.': [3626], 'Acad.': [3627], 'Sci.': [3628], 'U.S.A.': [3629], '2011;': [3630], '108:': [3631], '4980-4985Crossref': [3632], '(43)': [3635], 'investigated': [3640], 'cancer-related': [3642, 5278], 'SMGs.': [3651, 3665], '2B,': [3655], 'again': [3657], 'strongest': [3660], 'Most': [3666], 'surveyed': [3670], 'highly': [3672, 3706], 'correlated': [3673, 4627, 4766, 4827, 4875, 5096], 'mutation': [3676], 'many': [3679, 3740, 5049, 5211], 'serves': [3685], 'master': [3688], 'regulator': [3689], 'cascades': [3692], 'cells.': [3695], 'TSC/mTOR,': [3700, 4699, 4759], 'cycle': [3704], 'samples.': [3715], 'RTK': [3720, 3752, 4761], 'regulated': [3722, 4377], 'largest': [3725], '(in': [3729, 4215, 4320], 'seven': [3731, 3745, 4216], 'BRAF,': [3735], 'EPAS1,': [3736], 'KIT)': [3738], 'Interestingly,': [3743, 4530, 4747], 'down-regulation': [3750], 'pathway.': [3753], 'view': [3759], 'activities.': [3771], 'Protein': [3772], 'variety': [3778], 'genomic': [3780], 'transcriptomic': [3782], 'where': [3784, 4762], 'expected': [3792], 'associate': [3794], 'change': [3798], 'Thus,': [3800, 4018], 'comparative': [3804], 'see': [3807], 'feature': [3809, 4045], 'contributes': [3810], 'expression.': [3814, 4150], '3A,': [3819], 'three': [3822, 3835], 'cis': [3827], 'trans': [3832], '(all': [3834], '2.2e-16).': [3841], 'much': [3846], 'stronger': [3847], '(the': [3853, 3961, 3973], 'averaged': [3854, 3962, 3974], 'ρ': [3855, 3862, 3963, 3975, 4039], '=': [3856, 3964, 3976], '0.30;': [3857], 'computed': [3863], 'Scholar));': [3948], 'lesser': [3957], 'extent': [3958], '0.11);': [3965], '−0.09),': [3977], 'consistent': [3978, 4861], 'gene-silencing': [3981], 'role.': [3982], 'similar': [3985], 'particular': [3988, 5082], 'although': [3991], 'strength': [3994], 'varied': [3995], '3B).': [4001], 'next': [4003, 4515], 'wanted': [4004], 'best': [4008, 4053, 4074, 4854], 'predictor': [4009, 4054], 'given': [4014], 'protein.': [4017], 'available,': [4028], '0.1': [4037], '≥': [4040], '0.3)': [4041], 'selected': [4043], 'if': [4055], 'dominated': [4058], 'two.': [4061], '3C,': [4066], 'almost': [4079], 'cholangiocarcinoma': [4085], 'melanoma.': [4088], 'small': [4092, 5288], 'inferred': [4101, 4428], '(such': [4105, 4113], 'testicular': [4107], 'germ': [4108], 'sarcoma),': [4115], 'may': [4117, 4522], 'noise': [4122], 'quantification,': [4126], 'especially': [4127], 'close': [4132], 'paralogs': [4133], 'complicated': [4135], 'splicing': [4136], 'isoforms.': [4137], 'relative': [4143], 'importance': [4144], 'cis-elements': [4147], 'understand': [4153], 'investigate': [4166], 'contexts.': [4172, 5226], '4A,': [4177], 'comparing': [4179], 'nontarget': [4187], 'key': [4195], 'regulators': [4196], 'KS-test-based': [4203], '(see': [4205], 'Methods).': [4206], 'top': [4208], 'frequently': [4210], 'hsa-miR-18a-5p': [4214], 'types),': [4218, 4323], 'been': [4221], 'oncogene': [4227, 4263, 4300], '(17.Zhou': [4232], 'Z.W.': [4235], 'Pan': [4236, 4346], 'Lai': [4238, 4256], 'Quan': [4240], 'Guan': [4248], 'Gui': [4254], 'Identification': [4258], 'miR-18a-5p': [4260], 'RCC.Am.': [4268], 'Transl.': [4270], '1874-1886PubMed': [4274], 'lung': [4278, 4306, 4411], '(18.Liang': [4280], 'X.M.': [4287], 'X.J.': [4289], 'Zheng': [4290, 4344], 'Qian': [4292], 'G.R.': [4293], 'Ma': [4294], 'Z.L.': [4295], 'MicroRNA-18a-5p': [4296], 'functions': [4297], 'targeting': [4303], 'IRF2': [4304], 'Death': [4308], 'Dis.': [4309], '8:': [4311, 4977], 'e2764Crossref': [4312], '(95)': [4315], 'hsa-miR-532-5p': [4319, 4469], 'suppressor': [4326], 'liver': [4328], '(19.Han': [4330], 'Lan': [4334], 'Nie': [4338], 'Song': [4342], 'Pei': [4348], 'Xie': [4350], 'Zhu': [4356], 'Meng': [4362, 4370], 'Cui': [4364], 'KIFC1': [4376], 'miR-532–3p': [4379], 'promotes': [4380], 'epithelial-to-mesenchymal': [4381], 'transition': [4382], 'metastasis': [4384], 'hepatocellular': [4386, 4416], 'via': [4388, 5007], 'gankyrin/AKT': [4389], 'signaling.Oncogene.': [4390], '2019;': [4391], '38:': [4392], '406-420Crossref': [4393], '(52)': [4396], 'supported': [4401], 'roles': [4404], 'squamous': [4412], '4A).': [4419], 'pinpoint': [4421], 'high-confidence': [4423], 'networks': [4431], '(Figs.': [4435], '4B': [4436], '4C)': [4438], 'miRNA,': [4453], 'hsa-miR-18a-5p,': [4454], 'appeared': [4455], 'strong': [4459], 'effect': [4460, 4546], 'ATM,': [4462], 'c-KIT,': [4463], 'HER2,': [4464], 'ERα,': [4465], 'Gab2,': [4467], 'targets,': [4475], 'ETS-1,': [4476], 'ACRL1,': [4477], 'N-Cadherin.': [4479], 'regulate': [4483], 'decay': [4489], 'repression': [4492], '(20.Bartel': [4493], 'MicroRNAs:': [4495], 'Target': [4496], 'recognition': [4497], 'functions.Cell.': [4500], '2009;': [4501], '136:': [4502], '215-233Abstract': [4503], '(15903)': [4511], 'mechanisms': [4519], 'involve': [4523], 'performing': [4525], 'parallel': [4526], 'miRNA-mRNA': [4527], 'some': [4532, 5090], 'cases,': [4533], 'mRNAs': [4538], 'dominating': [4545], 'inhibition.': [4549], 'One': [4550], 'example': [4552], 'case': [4555], 'hsa-miR-532–5p': [4557], '4D).': [4559], 'suggest': [4562, 5026], 'additional': [4568], 'gain': [4570], 'direct': [4575], 'elucidate': [4578, 5277], 'mechanisms.': [4582], 'characterize': [4585], '5).': [4611], 'parts:': [4617], 'inner': [4620], 'recurrence': [4643, 4682], 'types;': [4650], 'outer': [4653], 'zoom-in': [4657], 'pathway,': [4664], 'linked': [4675, 4752], 'found': [4690, 4822, 5047], '(cliques):': [4694], 'consisted': [4696, 4720], 'Ras/MAPK': [4702], '20': [4714], 'reactive': [4727], '15': [4735], 'clique': [4739, 4755], 'highlight': [4741], 'coordination': [4743], 'cliques': [4750], 'another': [4754], 'apoptosis': [4763], 'negatively': [4765], 'summary': [4776], 'interactions': [4778], 'crosstalk': [4784], 'cancer.': [4788], 'relevance': [4794], 'time,': [4806], 'stage': [4811], '6A,': [4820], '21': [4824, 4850], 'times': [4832], '0.1,': [4841], 'model).': [4847], 'markers,': [4852, 5267], 'fibronectin': [4857, 4873, 4916, 4997, 5028], '(FN1)': [4858], 'pattern': [4865], 'nine': [4867], '6B):': [4871], 'worse': [4877], '6C).': [4881], 'Consistent': [4882], 'previously': [4885], 'breast,': [4889], 'colorectal,': [4890], 'head': [4892], 'neck': [4894], '(21.Fernandez-Garcia': [4897], 'Eiró': [4899], 'Marín': [4901], 'Gonzalez-Reyes': [4903], 'González': [4905], 'L.O.': [4906], 'Lamelas': [4907], 'M.L.': [4908], 'Vizoso': [4909], 'F.J.': [4910], 'Expression': [4911], 'matrix': [4918], 'metalloproteases': [4919], 'metastasis.Histopathology.': [4923], '64:': [4925], '512-522Crossref': [4926], '(112)': [4929], '22.Gopal': [4932], 'Veracini': [4934], 'Grall': [4936], 'Butori': [4938], 'Schaub': [4940], 'Audebert': [4942], 'Camoin': [4944], 'Baudelet': [4946], 'Radwanska': [4948], 'Beghelli-de': [4950], 'la': [4951], 'Forest': [4952], 'Divonne': [4953], 'Violette': [4955], 'Weinreb': [4957], 'P.H.': [4958], 'Rekima': [4959], 'Ilie': [4961], 'Sudaka': [4963], 'Hofman': [4965], 'Obberghen-Schilling': [4968], 'Fibronectin-guided': [4970], 'migration': [4971], 'collectives.Nat.': [4974], '14105Crossref': [4978], '(103)': [4981], '23.Yi': [4984], 'Xiao': [4986], 'Luo': [4990], 'High': [4994], 'poor': [5001], 'prognosis,': [5002], 'proliferation': [5004], 'malignancy': [5006], 'NF-kappaB/p53-apoptosis': [5009], 'colorectal': [5013], 'cancer.Oncol.': [5014], '36:': [5017], '3145-3153Crossref': [5018], '(49)': [5021], 'could': [5029], 'established': [5043, 5060], 'subtypes,': [5045], 'PAM50': [5064], 'carcinoma),': [5068], 'defining': [5077, 5133], 'heterogeneity': [5079], '6D).': [5086], 'Also,': [5087], 'stages': [5099], 'monotonic': [5102], '(continuously': [5104], 'increased/decreased': [5105], 'stage),': [5110], 'involvement': [5113], 'progression': [5116], '6E).': [5118], 'Together,': [5119], 'improving': [5130], 'prognosis': [5131], 'heterogeneity.': [5135], 'Pan-cancer': [5136], 'demonstrated': [5143], 'tremendous': [5144], 'potentials': [5145], 'biologically': [5148], 'meaningful': [5151], 'patterns.': [5152], 'v3.0': [5157], 'RPPA-based': [5169], 'unique': [5180], 'opportunity': [5181], 'protein-driven': [5188], 'range': [5194], 'Based': [5198], 'diverse': [5224], 'helping': [5239], 'confirm': [5241], 'known': [5242, 5291], 'mechanisms,': [5243], 'reveal': [5244], 'biological': [5246], 'insights,': [5247], 'test/refine': [5249], 'hypotheses.': [5251], 'recognize': [5253], 'limitation': [5256], '∼260': [5265], 'scope': [5271], 'mechanism.': [5279], 'when': [5282], 'searching': [5283], 'cis-regulators,': [5285], 'identified.': [5295], 'now': [5298], 'process': [5301], 'expanding': [5303], 'list': [5305], '500': [5307], 'covering': [5309], 'expect': [5315], 'version': [5318], 'valuable': [5324], 'community.': [5331], '(http://tcpaportal.org).': [5354], 'gratefully': [5356], 'acknowledge': [5357], 'contributions': [5358], 'Network.': [5363]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2952817552', 'counts_by_year': [{'year': 2024, 'cited_by_count': 4}, {'year': 2023, 'cited_by_count': 18}, {'year': 2022, 'cited_by_count': 15}, {'year': 2021, 'cited_by_count': 13}, {'year': 2020, 'cited_by_count': 12}, {'year': 2019, 'cited_by_count': 3}, {'year': 2018, 'cited_by_count': 1}], 'updated_date': '2024-12-25T21:43:19.733031', 'created_date': '2019-06-27'}
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