The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation

Name: Work Video:
Duration: 3 min 30 s
Étienne Caron; Krystel Vincent; Marie‐Hélène Fortier; Jean‐Philippe Laverdure; Alexandre Bramoullé; Marie‐Pierre Hardy; Grégory Voisin; Philippe P. Roux; Sébastien Lemieux; Pierre Thibault; Claude Perreault
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610, 653, 689, 728, 935, 1000, 1110, 1284, 1392, 1520, 1706, 1719, 1731, 1742, 1984, 2137, 2212, 2253, 2281, 2347, 2374, 2432, 2512, 2671, 2697, 2747, 2753, 3681, 3829, 4001], 'this': [54, 79, 113, 138, 163, 188, 213, 255, 298, 334, 373, 410, 435, 469, 494, 519, 544, 569, 611, 654, 690, 729, 832, 1740, 1766, 2610, 2919, 3482, 3512, 3615, 3640, 4035], 'author': [55, 80, 114, 139, 164, 189, 214, 256, 299, 335, 374, 411, 436, 470, 495, 520, 545, 570, 612, 655, 691, 730, 912], 'Krystel': [56, 58, 412, 414, 735], 'Vincent': [57, 59, 413, 415], 'Marie-Hélène': [81, 83, 437, 439, 737], 'Fortier': [82, 84, 438, 440, 1535, 1626, 3030, 3204], 'Chemistry,': [101, 322, 457, 678, 787], 'Jean-Philippe': [115, 117, 471, 473, 739], 'Laverdure': [116, 118, 472, 474], 'Alexandre': [140, 142, 496, 498, 741], 'Bramoullé': [141, 143, 497, 499], 'Marie-Pierre': [165, 167, 521, 523, 743], 'Hardy': [166, 168, 522, 524], 'Grégory': [190, 192, 546, 548, 745], 'Voisin': [191, 193, 547, 549], 'Philippe': [215, 218, 571, 574, 747], 'P': [216, 219, 572, 575, 748], 'Roux': [217, 220, 573, 576], 'Pathology': [237, 593, 796], 'Cell': [239, 595, 798, 2249], 'Biology,': [240, 596, 799], 'Sébastien': [257, 259, 613, 615, 750], 'Lemieux': [258, 260, 614, 616], 'Computer': [277, 633, 811], 'Science': [278, 634, 812], 'Operations': [280, 636, 814], 'Research,': [281, 637, 815], 'Arts': [284, 640, 818], 'Sciences,': [286, 642, 820], 'Pierre': [300, 304, 656, 660, 752], 'Thibault': [301, 305, 657, 661, 753], 'Corresponding': [302, 338, 658, 694], 'Author': [303, 339, 659, 695, 731], 'Claude': [336, 340, 692, 696, 756], 'Perreault': [337, 341, 693, 697, 757], 'Information': [732], 'Caron1,2,‡,': [734], 'Vincent1,‡,': [736], 'Fortier1,3,‡,': [738], 'Laverdure1,': [740], 'Bramoullé1,': [742], 'Hardy1,': [744], 'Voisin1,': [746], 'Roux1,4,': [749], 'Lemieux1,5,': [751], '1,3': [754], '1,2': [758], '1Institute': [759], '2Department': [773], '3Department': [785], '4Department': [794], '5Department': [809], '‡These': [827], 'authors': [828], 'contributed': [829, 3285], 'equally': [830], 'work.': [833], '*Corresponding': [834], 'authors.': [835], 'PO': [847], 'Box': [848], '6128': [849], 'Station': [850], 'Centre-Ville,': [851], 'H3C': [855], '3J7.': [856], 'Tel.:': [857, 871], '+1': [858, 863, 872, 877], '514': [859, 864, 873, 878], '343': [860, 865, 874, 879], '6910;': [861], 'Fax:': [862, 876], '6843;': [866], 'E-mail:': [867, 881], '[email': [868, 882], 'protected]': [869, 883], 'or': [870, 1200, 1734, 2233, 2811, 3737], '6126;': [875], '5839;': [880], 'Molecular': [884], 'Systems': [885], 'Biology': [886], '(2011)7:533https://doi.org/10.1038/msb.2011.68': [887], 'PDFDownload': [888], 'PDF': [889], 'article': [891], 'text': [892], 'main': [894], 'figures.': [895], 'Peer': [896], 'ReviewDownload': [897], 'a': [898, 927, 966, 1006, 1050, 1142, 1185, 1579, 1699, 1747, 1784, 1848, 1965, 2218, 2408, 2424, 2615, 2634, 2686, 2887, 3091, 3390, 3485, 3517, 3537, 3557, 3726, 3779, 3864, 3951, 4052, 4107, 4142, 4191], 'summary': [899], 'editorial': [902, 906], 'decision': [903, 907], 'process': [904], 'including': [905, 1819, 2646], 'letters,': [908], 'reviewer': [909], 'comments': [910], 'responses': [913], 'feedback.': [915], 'ToolsAdd': [916], 'favoritesDownload': [918], 'CitationsTrack': [919], 'CitationsPermissions': [920], 'Figures': [921], '&': [922], 'Info': [923], 'Self/non-self': [924], 'discrimination': [925, 1246, 1254, 2787], 'is': [926, 971, 996, 1121, 1129, 1577, 1694, 1702, 1712, 1770, 1783, 1807, 2014, 2317, 2345, 2391, 2886, 3649], 'fundamental': [928, 1714, 2888], 'requirement': [929], 'life.': [931], 'Endogenous': [932], 'peptides': [933, 956, 1108, 1313, 1421, 2510, 2537, 2804, 2837, 3566], 'presented': [934, 1109, 1283, 1344, 2431, 2511, 2696], 'major': [936, 1111, 1285], 'histocompatibility': [937, 1112, 1286], 'complex': [938, 1113, 1287, 2081, 3651], 'class': [939, 1114, 1288], '(MHC': [941, 1290], 'I)': [942, 1291], 'molecules': [943, 1116, 1292, 1419, 1477, 2516, 2543], 'represent': [944, 1293, 3797], 'essence': [946, 1295], 'self': [948, 1276, 1297], 'CD8': [950, 1299, 1325, 1720], 'T': [951, 1300, 1326, 1721], 'lymphocytes.': [952], 'These': [953, 1123, 1310, 2993, 3570], '(MIPs)': [957, 1314], 'are': [958, 1343, 1356, 1645, 1728, 2222, 2266, 2286, 2336, 2822, 2995, 3157, 3208, 3327, 3606, 3665, 4021, 4122, 4156], 'collectively': [959, 1357], 'referred': [960, 1358, 2997], 'as': [962, 1360, 1558, 2217, 2999, 3027, 3536], 'immunopeptidome.': [964, 981, 1170, 1656, 3111, 3632], 'From': [965], 'systems-level': [967, 1040, 1173, 2375, 3616, 4103], 'perspective,': [968], 'very': [969, 1543, 4022], 'little': [970, 1544], 'known': [972, 3996], 'about': [973, 1545, 2973], 'origin,': [975], 'composition': [976, 1165, 1210, 1550, 1670], 'plasticity': [978, 2361, 2366, 2667, 3657], 'Here,': [982, 2086], 'we': [983, 1012, 1038, 1148, 1223, 1540, 1854, 1938, 1991, 2040, 2087, 2898, 2921, 2939, 3494, 3514, 3876, 3922, 4008, 4037, 4078, 4188], 'show': [984, 1125, 2830, 3281], 'that': [985, 1014, 1042, 1126, 1150, 1175, 1208, 1319, 1384, 1505, 1513, 1574, 1653, 1882, 1994, 2027, 2042, 2089, 2127, 2505, 2589, 2805, 2890, 2948, 3071, 3089, 3184, 3284, 3344, 3465, 3573, 3605, 3619, 3643, 3655, 3849, 3861, 3882, 3958, 4010, 4020, 4080, 4106, 4138, 4232, 4259], 'immunopeptidome,': [987, 2670], 'therefore': [989, 1673, 2406, 2664], 'nature': [991], 'immune': [994, 1237, 1257, 1822], 'self,': [995], 'plastic': [997, 1130, 1703], 'moulded': [999], 'metabolic': [1002, 1056, 1191, 1220, 1232, 1708, 2660, 2880, 2910, 4147], 'activity.': [1003], 'By': [1004, 4071], 'using': [1005, 3682, 3938, 4072], 'quantitative': [1007, 1143], 'high-throughput': [1008, 1144, 1640, 2409], 'mass': [1009, 1102, 1145, 1446], 'spectrometry-based': [1010, 1146], 'approach,': [1011, 1147], 'found': [1013, 1149, 3054, 3077, 4231, 4262], 'altering': [1015], 'metabolism': [1017], 'via': [1018, 2020], 'inhibition': [1020, 1151, 2130, 2303, 2333, 2863, 3101, 3622], 'mammalian': [1023, 1154, 1228, 1757], 'target': [1024, 1155, 1758, 4127], 'rapamycin': [1026, 1157, 1760, 1769, 1840, 1860, 1909, 1931, 1943, 1961, 1985, 2004, 2052, 2061, 2110, 2158, 2198, 2237, 2329, 2437, 2527, 2553, 2560, 2600, 2663, 2719, 2856, 2927, 2954, 3128, 3181, 3891, 3976, 4129], 'results': [1027, 1159, 1611, 2025, 2125, 2321, 3087, 3847], 'dynamic': [1029, 1161, 2607], 'changes': [1030, 1105, 1162, 1216, 2641, 2867, 2881, 3105, 3626, 3670, 4012, 4148], 'MIPs': [1035, 1342, 1385, 1458, 1506, 1562, 1600, 2430, 2462, 2488, 2594, 2638, 2648, 2680, 2695, 2738, 2790, 2848, 3021, 3176, 3183, 4168], 'landscape.': [1036], 'Moreover,': [1037, 1443], 'provide': [1039, 1172, 1224], 'evidence': [1041, 1174], 'projects': [1045, 1180, 2878, 4141], 'at': [1046, 1059, 1181, 1194, 1345, 2094, 2681, 2843, 2913, 3059, 3081], 'representation': [1051, 1186, 3115, 3169, 4144], 'biochemical': [1053, 1188, 3840, 4118], 'networks': [1054, 1189, 3841, 4119], 'events': [1057, 1192, 1318], 'regulated': [1058, 1193, 1808, 2912, 4000], 'multiple': [1060, 1195], 'levels': [1061, 1196, 2164, 2568], 'inside': [1062, 1203], 'cell.': [1064, 1140, 1205], 'Our': [1065], 'findings': [1066], 'open': [1067, 1428], 'up': [1068, 1948, 2064, 2439], 'new': [1069], 'perspectives': [1070], 'systems': [1072], 'immunology': [1073], 'predictive': [1075], 'biology.': [1076], 'Indeed,': [1077], 'predicting': [1078], 'variations': [1079, 2902, 4112], 'response': [1084, 1218, 1274, 2598, 2611], 'cell-intrinsic': [1086], '-extrinsic': [1088], 'factors': [1089], 'could': [1090, 3877], 'be': [1091, 1518, 1674, 2372, 3056, 3079, 3134, 3659, 3903, 3998], 'relevant': [1092, 1676], 'rational': [1095], 'design': [1096, 2703], 'immunotherapeutic': [1098], 'interventions.': [1099], 'Synopsis': [1100], 'Quantitative': [1101], 'spectrometry': [1103, 1447], 'reveals': [1104], 'when': [1117, 3137], 'mTOR': [1119, 1782, 1805, 1842, 1866, 2080, 2862, 3100, 3621, 3673, 3713, 3738, 3814, 3844, 3857, 3862, 3908, 3991, 4002, 4029, 4057, 4091, 4162, 4186, 4195, 4252, 4289], 'pathway': [1120, 2177], 'perturbed.': [1122], 'data': [1124, 2586, 4134, 4257], 'provides': [1132], 'information': [1133], 'on': [1134, 1612, 1639, 1841, 1861, 1955, 1979, 2319, 2651, 2928, 3040, 3203, 3382, 3892, 3927, 4066, 4204], 'internal': [1136], 'state': [1137], 'Using': [1141, 2934, 3511], '(mTOR)': [1158, 1761], 'We': [1171, 1206, 1738, 1764, 2405, 3004, 4230], '(transcriptional': [1197], 'co-': [1199], 'post-translational': [1201], 'level)': [1202], 'demonstrate': [1207], 'perturbations': [1221, 2907], 'insights': [1225, 1468], 'into': [1226, 1469, 3725], 'how': [1227, 1930], 'cells': [1229, 1327, 1351, 1717, 1823, 1846, 1941, 2033, 2145, 2230, 2243, 2434, 2456, 2627, 2653, 2712, 2744, 2785, 2821, 2946, 2951, 2979, 3152, 3156, 3195], 'communicate': [1230], 'their': [1231], 'status': [1233], 'adaptive': [1236], 'system.': [1238], 'Introduction': [1239], 'While': [1240, 1908], 'unicellular': [1241], 'eukaryotes': [1242], 'primarily': [1243, 1255], 'employ': [1244], 'self/non-self': [1245, 1253], 'avoid': [1248], 'self-mating,': [1249], 'multicellular': [1250], 'organisms': [1251], 'use': [1252], 'defense': [1258], '(Boehm,': [1259], '2006).': [1260, 1604, 2085], 'Failure': [1261], 'respond': [1263], 'non-self': [1265], 'can': [1266, 1517, 2370], 'lead': [1267], 'death': [1269], 'from': [1270, 1387, 1508, 2312, 2452, 2629, 2731, 2739, 2791, 3096, 3546, 3556, 3598, 3603, 3839, 3852, 3885, 4018, 4051, 4117], 'infection': [1271], 'whereas': [1272], 'untoward': [1273], 'paves': [1277], 'way': [1279], 'autoimmunity.': [1281], 'Peptides': [1282], 'lymphocytes': [1301, 1722], '(Rammensee': [1302], 'et': [1303, 1307, 1339, 1366, 1399, 1403, 1460, 1486, 1490, 1494, 1498, 1524, 1528, 1532, 1536, 1602, 1623, 1627, 1631, 1683, 1801, 1825, 1829, 1833, 1875, 1897, 1905, 1925, 2009, 2083, 2378, 2382, 2402, 2413, 2418, 2467, 2472, 2794, 2799, 3031, 3205, 3873, 3945, 4004, 4068, 4206], 'al,': [1304, 1308, 1340, 1367, 1400, 1404, 1461, 1487, 1491, 1495, 1499, 1525, 1529, 1533, 1537, 1603, 1624, 1628, 1632, 1684, 1802, 1826, 1830, 1834, 1876, 1898, 1906, 1926, 2010, 2084, 2379, 2383, 2403, 2414, 2419, 2468, 2473, 2795, 2800, 3032, 3206, 3874, 3946, 4005, 4069, 4207], '1993;': [1305, 1492], 'Klein': [1306, 1338], '2009).': [1309, 1341, 1907, 2404], 'I-associated': [1312], 'regulate': [1315], 'all': [1316, 1509, 1816, 2732], 'key': [1317, 1691, 2166], 'occur': [1320], 'during': [1321, 2046], 'lifetime': [1323], 'thymus': [1330], 'periphery': [1333], '(Goldrath': [1334], 'Bevan,': [1336], '1999;': [1337], 'most': [1349, 2393, 2509, 2536, 3018, 3187, 3592], 'nucleated': [1350], 'jawed': [1353], 'vertebrates': [1354], '(Istrail': [1365], '2004).': [1368], 'Classic': [1369], 'reductionist': [1370], 'approaches': [1371, 1644], 'have': [1372, 1407, 1449, 1465, 1502, 1571, 1608, 1880], 'established': [1373], 'broad': [1375], 'outlines': [1376], 'MIP': [1379, 1414, 1483, 1515, 1620, 2156, 2620, 3553], 'processing': [1380, 2174], 'system': [1381], 'shown': [1383, 1881, 2071], 'derive': [1386, 1507], 'degradation': [1388, 3871], 'endogenous': [1390], 'proteins': [1391, 1556, 1587, 1595, 2167, 2209], 'proteasome': [1394, 4285], 'other': [1396, 3613, 4170], 'peptidases': [1397], '(Yewdell': [1398], '2003;': [1401], 'Hammer': [1402], '2007).': [1405], 'They': [1406, 1501], 'also': [1408, 1432, 1503, 1572, 1992, 2069, 3076, 3388], 'highlighted': [1409, 2823, 3209], 'complexity': [1411, 3636], 'repertoire.': [1415], 'Thus,': [1416, 2109, 3085, 4132], 'present': [1420], 'encoded': [1422, 1434], 'not': [1423, 1566, 1578, 1589, 2161, 2234, 2548, 2574, 2812, 2892, 3595, 3878, 3902], 'only': [1424, 2371, 3045, 3069, 3090], 'primary': [1427], 'reading': [1429, 1437], 'frames': [1430, 1438], 'but': [1431, 2054, 2099, 2117, 2573, 4281], 'those': [1433], 'alternate': [1436], '(Starck': [1439], 'Shastri,': [1441], '2011).': [1442, 1462, 1633], 'progresses': [1444], '(MS)': [1448], 'allowed': [1450, 2457], 'increasingly': [1451], 'sophisticated': [1452], 'comprehensive': [1454, 2394, 4053], 'large-scale': [1455, 1606, 2399], 'analyses': [1456, 1464, 1607, 2153, 2376, 3218, 3571], '(Mester': [1459], 'Large-scale': [1463], 'yielded': [1466, 1609, 3425], 'unprecedented': [1467], 'peptide': [1471], 'specificities': [1472], 'motifs': [1474], 'diversity': [1480, 2678], 'repertoire': [1484, 1516, 1621, 4166], '(Hunt': [1485], '1992;': [1488], 'Engelhard': [1489], 'Bonner': [1493], '2002;': [1496], 'Weinzierl': [1497, 1531], '2008).': [1500, 1538, 1927], 'demonstrated': [1504], 'compartments': [1511], 'modified': [1519], 'neoplastic': [1521, 1726, 1820], 'transformation': [1522], '(Schirle': [1523], '2000;': [1526], 'Hickman': [1527], '2004;': [1530], '2007;': [1534, 1625], 'Nevertheless,': [1539], 'still': [1541], 'know': [1542], 'genesis': [1547], 'molecular': [1549, 1669], 'immunopeptidome:': [1553], 'why': [1554], 'do': [1555, 1565, 1588, 3601], 'such': [1557], 'STT3B': [1559], 'yield': [1560], 'abundant': [1561, 1586, 3074], 'while': [1563, 1592, 3591], 'others': [1564], '(Perreault,': [1567], '2010)?': [1568], 'MS': [1569, 2386], 'studies': [1570, 1637, 1879, 2358, 4155], 'revealed': [1573, 2588, 3343, 3389, 3572, 4258], 'random': [1580, 4096], 'sample': [1581], 'proteome:': [1584], 'many': [1585], 'generate': [1590, 1596], 'MIPs,': [1591], 'some': [1593, 3886], 'low-abundance': [1594], 'large': [1597], 'amounts': [1598], '(Milner': [1601], 'Furthermore,': [1605, 1804], 'conflicting': [1610], 'relation': [1614], 'between': [1615, 2642, 2770, 2815, 3273, 3305, 3433, 3489, 3504, 3520, 3700, 3747, 3773, 3801, 3809, 3918, 4042, 4178], 'transcriptome': [1617, 2870, 2930, 2942, 3108, 3490, 3629, 4183], '(Weinzierl': [1622], '2008;': [1629, 1899, 2415, 2469, 2796], 'Mester': [1630], 'Therefore,': [1634, 4007], 'further': [1635, 3914], 'systematic': [1636], 'based': [1638, 2318, 3202, 4065, 4203], 'technologies': [1641], 'needed': [1646, 4157], 'order': [1648, 3478, 3912], 'elucidate': [1650], 'mechanisms': [1652], 'mould': [1654], 'In-depth': [1657], 'mechanistic': [1658], 'understanding': [1659], 'biogenesis': [1663], 'would': [1664, 1672, 3901], 'allow': [1665], 'prediction': [1666], 'its': [1668, 1707, 1791, 3656], 'highly': [1675, 4123], 'development': [1679], 'immunotherapies': [1681], '(Zarling': [1682], '2006;': [1685, 2380], 'Sette': [1686], 'Rappuoli,': [1688], '2010).': [1689, 1803, 1835, 1877, 2474, 2801, 3947, 4006, 4070], 'A': [1690, 2765, 2958, 3761, 3818], 'unresolved': [1692], 'question': [1693, 1741, 2889], 'whether': [1695, 2901, 3481, 4160], 'particular': [1700], 'affected': [1705, 1932], 'state.': [1709], 'This': [1710, 2475, 3948, 4102], 'issue': [1711], 'importance': [1715], 'because': [1716, 1768, 1781], 'targeted': [1718], '(i.e.': [1723, 4130], 'infected': [1724], 'cells)': [1727], 'metabolically': [1729], 'perturbed': [1730, 2131], 'intracellular': [1732, 2879, 4146], 'parasite/viruses': [1733], 'various': [1735], 'transforming': [1736], 'events.': [1737], 'addressed': [1739, 2894], 'studying': [1743], 'mouse': [1748], 'lymphoma': [1749], 'line': [1751, 2258], '(EL4)': [1752], 'treated': [1753, 1939, 2193, 2232, 2952], 'with': [1754, 1942, 1964, 2194, 2236, 2387, 2552, 2614, 2662, 2715, 2953, 3010], 'classic': [1756], 'inhibitor,': [1762], 'rapamycin.': [1763, 2038], 'selected': [1765, 3552], 'model': [1767], 'exquisitely': [1772], 'specific': [1773, 2458], 'inhibitor': [1774], 'serine/threonine': [1777], 'kinase': [1778], 'mTOR,': [1779, 3921], 'central': [1785], 'regulator': [1786], 'homeostasis': [1789], 'through': [1790], 'involvement': [1792], 'promoting': [1794], 'anabolic': [1795], 'inhibiting': [1797, 2139], 'catabolic': [1798], 'processes': [1799, 2911, 3291, 3307, 3318, 3397, 3424, 3456], '(Sengupta': [1800], 'signaling': [1806, 1843, 1934, 4030, 4060, 4198, 4290], 'numerous': [1810, 2593], 'physiological': [1811], 'pathological': [1813], 'conditions': [1814, 2734], 'types,': [1818], '(Araki': [1824], '2009;': [1827, 1903], '2010;': [1831], 'Sengupta': [1832], 'Results': [1836], 'effect': [1838, 3889], 'EL4': [1845, 1862, 1936, 1940, 2032, 2121, 2144, 2189, 2229, 2305, 2433, 2455, 2711, 2743, 2784, 2820, 2932, 2945, 2950, 2978], 'As': [1847, 1952, 1988], 'prelude': [1849], 'our': [1851, 2152, 4133], 'peptidomic': [1852], 'studies,': [1853], 'first': [1855, 1865, 2048, 2922, 3515, 3923], 'assessed': [1856], 'effects': [1858, 2299], 'cells.': [1863, 2122, 2190, 2306, 2933], 'complex,': [1867], 'mTORC1,': [1868, 2116], 'phosphorylates': [1869], 'both': [1870, 2673, 3293, 3321, 3469], 'S6K1': [1871, 1895, 1915, 1956, 2140, 2185], '4E-BP1': [1873, 1893, 1922, 1980, 1997, 2013, 2142, 2187], '(Dowling': [1874], 'Recent': [1878], 'rapamycin,': [1883], 'previously': [1884, 1989], 'thought': [1885], 'completely': [1887, 1911], 'inhibit': [1888, 2073], 'mTORC1': [1889, 1933, 2129, 2302], 'activity,': [1890], 'differentially': [1891, 2138, 2183, 2807, 2962, 3000, 3019, 3057, 3135, 3188], 'affects': [1892], '(Choo': [1896, 1924], 'Choo': [1900], 'Blenis,': [1902], 'Thoreen': [1904], 'treatment': [1910, 2005, 2062, 2105, 2111, 2159, 2528, 2551], 'sustainably': [1913], 'inhibits': [1914, 1921, 2184], 'activation,': [1916], 'it': [1917], 'partly': [1918], 'variably': [1920], 'phosphorylation': [1923, 2091], 'To': [1928, 2917, 4032, 4172], 'evaluate': [1929, 3915, 4034, 4159], 'cells,': [1937], 'different': [1945, 2491], 'time': [1946, 2202, 2522, 2760, 2845], 'durations': [1947], '48': [1950, 2107, 2113, 2239, 2326, 2441, 2555, 2728, 2853, 2956, 3125, 3178], 'h.': [1951, 2108, 2240, 2556, 2729, 2957], 'expected,': [1953], 'Thr-389': [1954], 'was': [1957, 1998, 2029, 2096, 2102, 2251, 2279, 2504, 2547, 2612, 3072, 3075, 3143, 3430, 3534, 3679, 3694, 3723, 3787, 3821], 'fully': [1958], 'dephosphorylated': [1959, 1983], 'upon': [1960], 'treatment,': [1962, 2053], 'correlating': [1963], 'decrease': [1966], 'size': [1969, 2136, 2250], '(Figure': [1970, 1986, 2006, 2058, 2146, 2443, 2496, 2529, 2980, 3034, 3063, 3349, 3368, 3398, 3405, 3443, 3475, 3509, 3588, 3933, 4100, 4214, 4223, 4244], '1A': [1971], 'B).': [1973, 3066], 'In': [1974, 2531, 2604, 3227, 3242, 3477, 3612, 3895], 'contrast,': [1975, 2532], 'Ser-65': [1976], 'Thr-37/46': [1978], 'were': [1981, 2192, 2210, 2231, 2244, 2310, 2713, 2735, 2745, 2763, 2806, 2849, 2965, 2988, 3053, 3131, 3185, 3219, 3234, 3256, 3362, 3466, 3579, 3959, 4086, 4237, 4261], 'partially': [1982], '1A).': [1987], 'reported,': [1990], 'noted': [1993], 'abundance': [1995, 2428, 2484, 2507, 2534, 2591, 2621, 2675, 2693, 2762, 2778, 2833, 3119, 3142, 3173], 'decreased': [1999, 2045, 2098], 'after': [2000, 2104, 2325, 2523, 2550, 2852, 3124, 3177], '24': [2001, 2066, 2726], 'h': [2002, 2050, 2067, 2114, 2327, 2442, 2525, 2722, 2854, 3126, 3179], '1A)': [2007], '(Dilling': [2008], '2002).': [2011], 'Because': [2012], 'critically': [2015], 'involved': [2016, 2168, 3420], 'cap-dependent': [2018], 'translation': [2019, 2028], 'eIF4E,': [2023], 'these': [2024, 2124, 3086], 'suggested': [2026, 3848], 'maintained': [2030], 'presence': [2036], 'Accordingly,': [2039, 2557], 'observed': [2041, 2088], 'protein': [2043, 2132, 2277, 3868, 3893], 'synthesis': [2044, 2133, 2278, 3869], '12': [2049], 'progressively': [2055, 2596], 'recovered': [2056, 2100], 'thereafter': [2057], '1C).': [2059], 'Prolonged': [2060], 'has': [2068, 2891, 3863], 'been': [2070, 2893], 'assembly': [2075], 'mTORC2,': [2077], 'second': [2079], '(Sarbassov': [2082], 'mTORC2-mediated': [2090], 'AKT': [2093], 'Ser-473': [2095], 'transiently': [2097], 'increased': [2103, 2520, 2595], 'inhibited': [2115], 'activated': [2118], 'mTORC2': [2119], 'Collectively,': [2123], 'showed': [2126, 2639], 'rapamycin-mediated': [2128, 2301, 3620, 4011], '1D).': [2147], 'Of': [2148], 'direct': [2149], 'relevance': [2150], 'landscape,': [2157], 'did': [2160, 3594], 'affect': [2162], 'expression': [2163, 3043], 'antigen': [2173], 'presentation': [2176], '(Supplementary': [2178, 2463, 2578, 2601, 2654, 3376, 3567, 3967, 4062, 4200], 'Figure': [2179, 2181, 2323, 2579, 2602, 2689, 3098, 3352, 3408, 3661, 3968, 4226], 'S1).': [2180], '1.Rapamycin': [2182], 'versus': [2186], 'Cells': [2191, 2730], '20': [2195, 2716], 'ng/ml': [2196, 2717], 'indicated': [2201, 2208], 'periods.': [2203], '(A)': [2204, 2701, 3112, 3675], 'Levels': [2205], 'determined': [2211], 'western': [2213], 'blotting.': [2214], 'β-Actin': [2215], 'served': [2216], 'loading': [2219], 'control.': [2220], 'Data': [2221, 2265, 2284], 'representative': [2223, 2267, 2287, 3282], 'three': [2225, 2269, 2289, 2840], 'independent': [2226, 2270, 2290], 'experiments.': [2227, 2271, 2291], '(B)': [2228, 2827, 3166], '(ctrl)': [2235], 'One': [2241], 'thousand': [2242], 'counted': [2245], 'each': [2247, 2844], 'condition.': [2248], 'measured': [2252, 2280, 4038], 'light': [2254], 'microscopy.': [2255], 'red': [2257, 3161, 3795], 'corresponds': [2259, 3764], 'average': [2262], 'size.': [2264], '*P<0.0005': [2272], "(Student's": [2273, 2294], 't-test).': [2274, 2295], '(C)': [2275, 3267], 'Relative': [2276], '[3H]-leucine': [2282], 'incorporation.': [2283], '(mean±s.d.)': [2285], '*P<0.01,': [2292], '**P<0.005': [2293], '(D)': [2296, 3299], 'Model': [2297], 'Proteins': [2307], 'reactions': [2309], 'curated': [2311], 'literature.': [2314], 'Color': [2315], 'code': [2316], '1': [2324], 'treatment.': [2330, 2857, 3129, 3182], 'Activation': [2331], 'components/reactions': [2335], 'depicted': [2337, 3158], 'green': [2339, 2350, 3163], 'red,': [2341], 'respectively.': [2342, 2992, 3165, 3266], 'Partial': [2343], 'inactivation': [2344], 'represented': [2346, 3828], 'thinner': [2349], 'lines.': [2351], 'Download': [2352, 2354, 2858, 2860, 3333, 3335, 3833, 3835], 'figure': [2353, 2859, 3334, 3834], 'PowerPoint': [2355, 2861, 3336, 3836], 'High-throughput': [2356], 'MS-based': [2357, 2410], 'unveil': [2359], 'estimated': [2373], '(Benoist': [2377], 'Germain': [2381], '2011),': [2384], 'high': [2388, 2775], 'accuracy': [2389], 'analyzers': [2390], 'versatile': [2396], 'tool': [2397], 'proteomics': [2400], '(Yates': [2401], 'used': [2407, 3535, 3695, 3788, 3822], 'approach': [2411], '(Fortier': [2412, 2466, 2793], 'Verteuil': [2417, 2471, 2798], '2010)': [2420], 'profile': [2422], 'time-sequential': [2425], 'manner': [2426], 'exposed': [2435], '2A;': [2444], 'Supplementary': [2445, 2498, 2630, 3036, 3351, 3407, 3410, 3935, 4216, 4225], 'Information).': [2446], 'Subtraction': [2447], "'contaminant": [2449], "peptides'": [2450], 'eluted': [2451], 'β2m': [2453], 'mutant': [2454, 2783, 2819], 'identification': [2459, 2478, 2705], 'genuine': [2461, 2789], 'Table': [2464, 2499, 2631, 2655, 3037, 3377, 3411, 3568, 3936, 4063, 4201, 4217], 'S1)': [2465], 'resulted': [2476], 'quantification': [2480, 2708], 'relative': [2483, 2624, 2707, 2832, 3118, 3153, 3172, 3192, 4094], '422': [2486, 3175], 'unique': [2487, 3012, 3561], 'associated': [2489, 2538, 3235, 3257, 3363], 'allelic': [2494], 'products': [2495], '2B;': [2497], 'S2).': [2500, 2632, 2656, 3038], 'salient': [2502], 'finding': [2503, 3641], 'classical': [2513], 'Ia': [2515, 2699], '(H2Db': [2517], 'H2Kb)': [2519], 'over': [2521], '12–48': [2524], '2B).': [2530], 'non-classical': [2540], 'Ib': [2542], '(Qa1': [2544], 'Qa2)': [2546], 'augmented': [2549], 'exposure': [2558], 'led': [2561], 'increase': [2564], 'H2Db': [2570], 'H2Kb': [2572], 'Qa1': [2575], 'Qa2': [2577], 'S2B).': [2580], 'Clustering': [2581], 'analysis': [2582, 3381, 3617, 3926, 3949, 4104], 'time-series': [2585], 'sets': [2587, 3548], 'S2A).': [2603], 'general,': [2605], 'range': [2608], 'modest': [2613], 'median': [2616], 'fold': [2617, 2640, 3139, 3198], 'change': [2618, 2968, 3024], '2.1': [2623], 'untreated': [2626, 2944, 3194], '(calculated': [2628], 'Nonetheless,': [2633], 'subset': [2635], '222': [2637], '2': [2643], '15,': [2645], '6': [2647, 3237, 3395], 'detected': [2649, 2850], 'exclusively': [2650], 'rapamycin-treated': [2652, 2740, 3151], 'Perturbation': [2657], 'activity': [2661], 'unveiled': [2665], 'increasing': [2672], 'time-dependent': [2687], 'manner.': [2688], '2.Rapamycin': [2690], 'increases': [2691], 'molecules.': [2700], 'Experimental': [2702], 'MIPs.': [2710], 'incubated': [2714], '0': [2721], '(ctrl),': [2723], '6,': [2724], '12,': [2725], 'experimental': [2733], 'harvested': [2736], 'simultaneously.': [2737], 'ctrl': [2742, 3155], 'isolated': [2746], 'mild': [2748], 'acid': [2749], 'elution': [2750], 'analyzed': [2752], 'nanoLC–MS–MS/MS.': [2754], 'Heat': [2755], 'maps': [2756], 'displaying': [2757], 'm/z,': [2758], 'retention': [2759], 'generated.': [2764], 'logarithmic': [2766], 'intensity': [2767], 'scale': [2768], 'distinguishes': [2769], 'low': [2771], '(dark': [2772], 'red)': [2773], '(bright': [2776], 'yellow)': [2777], 'species.': [2779], 'Analysis': [2780, 3337, 3413], 'β2m-': [2782, 2818], 'allows': [2786], 'contaminants': [2792], 'Examples': [2802], 'expressed': [2808, 2963, 3001, 3020, 3058, 3136, 3189], '(red': [2809], 'line)': [2810, 2814], '(green': [2813], 'WT': [2816], 'boxes.': [2826, 3213, 3332], 'Volcano': [2828, 3113, 3167], 'plots': [2829], '416': [2835], 'H2b-associated': [2836, 3565], 'identified': [2838, 2966, 3452, 3530], 'biological': [2841], 'replicates': [2842], 'point.': [2846], 'Six': [2847], 'uniquely': [2851], 'induces': [2864, 3102, 3623], 'functionally': [2865, 3103, 3608, 3624], 'coherent': [2866, 3104, 3625], 'Whether': [2874], 'accurately': [2877], 'yet.': [2895], 'More': [2896], 'precisely,': [2897], 'asked': [2899], 'herein': [2900], 'reflected': [2906], 'rapamycin-sensitive': [2909], 'transcript': [2915, 3061, 3083], 'level.': [2916, 3084], 'address': [2918], 'question,': [2920], 'defined': [2923], 'impact': [2925], 'NimbleGen': [2935], 'MM8': [2936], '385K': [2937], 'microarrays,': [2938], 'compared': [2940, 3006], 'total': [2959], '1353': [2961, 3008], 'transcripts': [2964, 2976, 3123], '(fold': [2967, 3023, 3190], '>2.0;': [2969], 'P<0.05),': [2970], 'which': [2971, 3499], 'represents': [2972], '3%': [2974], '3A).': [2981], 'Among': [2982], 'these,': [2983], '903': [2984], '450': [2986], 'mRNAs': [2987, 3255, 3361], 'under-': [2989, 3252, 3358], 'overexpressed,': [2991], 'genes': [2994, 3002, 3014, 3049, 3224, 3232, 3249, 3276, 3283, 3296, 3312, 3324, 3348, 3387, 3404, 3419, 3442, 3474, 3508, 3529, 3555, 3563, 3578, 3604, 3664, 3704, 3711, 3734, 3804, 3812, 3853, 3900, 3932, 3957, 4019, 4047, 4085, 4213, 4236, 4280], 'hereafter': [2996], '(DEGs).': [3003], 'next': [3005], 'DEGs': [3009, 3326, 3415, 3436, 3470, 3523, 3585, 3706, 3736, 3806, 4222, 4260], '98': [3011, 3384, 3929, 4210], 'source': [3013, 3048, 3223, 3231, 3275, 3295, 3311, 3323, 3386, 3403, 3418, 3441, 3473, 3528, 3554, 3562, 3577, 3663, 3703, 3710, 3733, 3803, 3811, 3931, 3956, 4046, 4084, 4180, 4212, 4235, 4272, 4279, 4297], 'coding': [3015, 3250, 3356], '(DEMs)': [3022], '>2.5;': [3025, 3196], 'P<0.05:': [3026], 'described': [3028, 4076], '2008)': [3033, 3207], '3B;': [3035, 3934, 4215], 'Based': [3039], 'microarray': [3041, 4256], 'gene': [3042], 'data,': [3044], 'two': [3046, 3505, 4275], 'DEM': [3047, 3070, 3222, 3230, 3274, 3294, 3310, 3322, 3385, 3402, 3417, 3440, 3472, 3527, 3576, 3702, 3709, 3732, 3802, 3810, 3930, 3955, 4045, 4083, 4179, 4211, 4234, 4271, 4278, 4296], '(Tmod1': [3050], 'Dhcr7)': [3052], 'level': [3062], '3A': [3064], 'Interestingly,': [3067], 'less': [3073], 'downregulated': [3080], 'indicate': [3088], 'minority': [3092], 'DEMs': [3094, 3593, 3837, 3850, 3883, 3919], 'originate': [3095, 3596, 3602, 4017], 'DEGs.': [3097, 3226, 3278, 3298, 3314, 3611], '3.Rapamycin-mediated': [3099], 'plot': [3114, 3168], '42': [3121], '586': [3122], 'Transcripts': [3130, 3146], 'considered': [3132], 'difference': [3140, 3191, 3199], '>2.0': [3144], '(P<0.05).': [3145], 'over-': [3147], 'underexpressed': [3149], 'boxes,': [3164], 'P<0.05;': [3197], 'P-value': [3201], 'blue': [3212], '(C,': [3214], 'D)': [3215], 'GO': [3216, 3379], 'enrichment': [3217, 3287, 3393], 'performed': [3220], 'all,': [3228, 3243], '38': [3229, 3401, 3439, 3526, 3550, 3575], '(blue)': [3233], 'significantly': [3238, 3262, 3370], 'enriched': [3239, 3263, 3371, 3422, 3467], 'processes.': [3241], '101': [3244, 3345], '(green)': [3245], '70': [3247, 3347], '(red)': [3248], 'overexpressed': [3254, 3360], '7': [3259, 3365, 4240, 4268], '8': [3261, 3367], 'processes,': [3265, 3373], 'Venn': [3268, 3300], 'diagram': [3269, 3301], 'showing': [3270, 3302], 'no': [3271, 3431, 4282], 'overlap': [3272, 3304, 3432], 'Dashed': [3279], 'boxes': [3280], 'four': [3289, 3316, 3453], 'functional': [3303, 3450, 3487, 3502, 3698, 3717, 3791, 3965, 4143, 4242], 'overrepresented': [3308, 3319, 3449], 'listed': [3328], 'dashed': [3331], 'Gene': [3339], 'Ontology': [3340], '(GO)': [3341], 'annotations': [3342], '3C;': [3350, 3406, 4224], 'S3B': [3353, 4227], 'C)': [3355, 3783], '3D)': [3369, 3399], 'respectively': [3374], '(P<0.05)': [3375, 3392], 'S3).': [3378, 3412], 'term': [3380], 'significant': [3391, 3486], 'implicating': [3400], 'S3A;': [3409], 'several': [3426], 'findings.': [3427], 'First,': [3428], 'there': [3429], '171': [3435, 3522, 3584, 4221], '3C).': [3444], 'Second,': [3445], 'cross-comparison': [3446], 'groups': [3451], 'distinct': [3454], '(protein': [3457], 'transport,': [3458], 'cycle/proliferation,': [3460], 'DNA': [3461], 'replication': [3462], 'transcription)': [3464], '3D).': [3476], 'determine': [3480], 'result': [3483], 'implies': [3484], 'relationship': [3488, 3917], 'variations,': [3493], 'developed': [3495, 3680], 'all-pairs-shortest-path': [3497, 3677, 3692, 3721, 3785], 'matrix,': [3498, 3513], 'scores': [3500, 3545, 3684, 3827], 'connectivity': [3503, 3518, 3544, 3762, 3792, 3799, 3826, 4040], 'lists': [3506], '4A).': [3510], 'calculated': [3516, 4079], 'score': [3519, 3763, 3800, 4041], 'above.': [3531], 'Then,': [3532], 'bootstrapping': [3533], 'statistical': [3538], 'sampling': [3539], 'method': [3540], 'calculate': [3542, 3697, 3790, 3824], 'control': [3543, 3825], '105': [3547], 'randomly': [3551], 'database': [3558, 3689, 3942], '891': [3560], 'encoding': [3564], 'S4).': [3569, 3969], 'tightly': [3580, 3607, 3666, 3904], 'interconnected': [3581, 3960, 4088], '(bootstrapping;': [3586, 4098], 'P=0.004)': [3587], '4B).': [3589], 'Hence,': [3590, 3910], 'directly': [3597, 3999], 'DEGs,': [3599], 'they': [3600], 'connected': [3609, 3667, 3842, 3854, 3905, 4024, 4124], 'words,': [3614], 'demonstrates': [3618, 4105], 'Given': [3633], 'tremendous': [3635], 'transcriptome,': [3639], 'suggests': [3642], 'than': [3652], 'anticipated': [3653], 'might': [3658, 4016], 'extensive.': [3660], '4.DEM': [3662], 'transcriptomic': [3669], 'network.': [3674, 3858, 3909, 4031, 4253], 'An': [3676], 'matrix': [3678, 3693, 3722, 3730, 3786, 4075], 'computed': [3683], '(S)': [3685], 'STRING': [3688], '(http://string-db.org/).': [3690], 'associations': [3699], '(1)': [3701], '(2)': [3708], 'network': [3714, 3739, 3756, 3815, 3941, 3952, 3972, 4061, 4092, 4163, 4193, 4199], 'components.': [3715], 'Each': [3716], 'association': [3718, 3755], 'transformed': [3724], 'distance': [3727, 3746, 3772], '(D).': [3728], 'shows': [3731], '(rows),': [3735], 'components': [3740, 3816, 3984, 4026, 4049, 4093, 4121, 4249], '(columns),': [3741], 'shortest': [3744, 3770], 'path': [3745, 3771], 'every': [3748, 3774], 'pair': [3749, 3775], 'nodes': [3751, 3777], '(genes/proteins)': [3752], '(e.g.': [3757, 3985, 3990], 'Dw-z': [3758], 'Dx-y).': [3760], 'mean': [3767], 'given': [3780], 'matrix.': [3781], '(B,': [3782], 'scores.': [3793], 'lines': [3796], '(B),': [3807], '(C).': [3817], 'bootstrap': [3819], 'procedure': [3820], 'Gaussian': [3831], 'distributions.': [3832], 'arise': [3838, 4116], 'above': [3846], 'originated': [3851, 3884], 'However,': [3859], 'considering': [3860], 'pervasive': [3865], 'role': [3866], '(Caron': [3872, 4003], '2010),': [3875, 4208], 'discard': [3879], 'possibility': [3881], 'non-specific': [3887], 'generic': [3888], 'metabolism.': [3894], 'latter': [3897], 'case,': [3898], 'DEM-coding': [3899], 'conducted': [3924], 'S2)': [3937, 4218], 'interaction': [3940], 'STITCH': [3943], '(Kuhn': [3944], 'uncovered': [3950], 'containing': [3953, 4270], '30': [3954, 4044, 4082], 'organized': [3962], 'within': [3963], 'discrete': [3964, 4241], 'modules': [3966, 3989, 4247, 4269, 4276], 'Strikingly,': [3970], 'included': [3973, 4248], 'chemicals': [3975], 'everolimus': [3978], '(rapamycin': [3979], 'analog)': [3980], 'addition': [3982], 'Rictor,': [3986], 'Sgk1)': [3987], 'signaling,': [3992], 'translation,': [3993], 'lipid': [3994], 'biosynthesis)': [3995], 'reasoned': [4009], 'closely': [4023], 'systematically': [4033], 'assumption,': [4036], 'extracted': [4050], 'map': [4054], 'interactome': [4058, 4196], 'S5': [4064, 4202], 'all-pair-shortest-path': [4074], 'above,': [4077], 'strongly': [4087], 'assignments': [4097], 'P<10−5)': [4099], '4C).': [4101], 'substantial': [4108], 'fraction': [4109], 'rapamycin-induced': [4111], 'whose': [4120], 'mTOR).': [4131], 'reinforce': [4135], 'notion': [4137], 'surface.': [4152], 'Further': [4153], 'immunopeptidomic': [4154], 'regulates': [4164], 'contexts.': [4171], 'visualize': [4173], 'organization': [4175], 'relationships': [4177], 'genes,': [4181], 'network,': [4187], 'integrated': [4189], 'global': [4192], 'C).': [4229], '33': [4233], 'constituents': [4238], 'subnetworks': [4243], '5A).': [4245], 'All': [4246], 'Integration': [4254], '5': [4264], 'out': [4265], 'genes.': [4273], 'Notably,': [4274], 'contained': [4277], 'DEGs:': [4283], 'core': [4288], 'modules.': [4291], 'Overall,': [4292], '82%': [4293]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W1969124154', 'counts_by_year': [{'year': 2024, 'cited_by_count': 8}, {'year': 2023, 'cited_by_count': 10}, {'year': 2022, 'cited_by_count': 8}, {'year': 2021, 'cited_by_count': 16}, {'year': 2020, 'cited_by_count': 13}, {'year': 2019, 'cited_by_count': 8}, {'year': 2018, 'cited_by_count': 6}, {'year': 2017, 'cited_by_count': 6}, {'year': 2016, 'cited_by_count': 10}, {'year': 2015, 'cited_by_count': 11}, {'year': 2014, 'cited_by_count': 4}, {'year': 2013, 'cited_by_count': 11}, {'year': 2012, 'cited_by_count': 4}], 'updated_date': '2024-12-12T16:21:39.744227', 'created_date': '2016-06-24'}
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