InnateDB: facilitating systems‐level analyses of the mammalian innate immune response

Name: Work Video:
Duration: 3 min 30 s
David J. Lynn; Geoffrey L. Winsor; Calvin C. Chan; Nicolas Richard; Matthew R. Laird; Aaron Barsky; Jennifer L. Gardy; Fiona Roche; Timothy H.W. Chan; Naisha Shah; Raymond Lo; Misbah Naseer; Jaimmie Que; Melissa Yau; M. Acab; Dan Tulpan; Matthew D. Whiteside; Avinash Chikatamarla; Bernadette Mah; Tamara Munzner; Karsten Hokamp; Robert E. W. Hancock; Fiona S. L. Brinkman
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730, 754, 780, 803, 831, 857, 887, 926, 950, 976, 1002, 1028, 1052, 1076, 1102, 1128, 1154, 1177, 1197, 1227, 1257], 'Geoffrey': [57, 60, 679, 682, 1264], 'L': [58, 61, 183, 186, 608, 614, 680, 683, 805, 808, 1230, 1236, 1265, 1277, 1318], 'Winsor': [59, 62, 681, 684], 'Calvin': [83, 85, 705, 707, 1267], 'Chan': [84, 86, 239, 243, 706, 708, 861, 865], 'Nicolas': [109, 111, 731, 733, 1269], 'Richard': [110, 112, 732, 734], 'Matthew': [133, 136, 455, 458, 755, 758, 1077, 1080, 1271, 1300], 'R': [134, 137, 756, 759, 1272], 'Laird': [135, 138, 757, 760], 'Aaron': [159, 161, 781, 783, 1274], 'Barsky': [160, 162, 782, 784], 'Computer': [165, 539, 787, 1161, 1351], 'Science,': [166, 540, 788, 1162, 1352], 'Jennifer': [182, 185, 804, 807, 1276], 'Gardy': [184, 187, 806, 809], 'Fiona': [210, 213, 606, 612, 832, 835, 1228, 1234, 1279, 1316], 'M': [211, 214, 833, 836, 1280], 'Roche': [212, 215, 834, 837], 'Timothy': [236, 240, 858, 862, 1282], 'H': [237, 241, 859, 863, 1283], 'W': [238, 242, 578, 582, 860, 864, 1200, 1204, 1284, 1313], 'Naisha': [266, 268, 888, 890, 1286], 'Shah': [267, 269, 889, 891], 'Raymond': [305, 307, 927, 929, 1288], 'Lo': [306, 308, 928, 930], 'Misbah': [329, 331, 951, 953, 1290], 'Naseer': [330, 332, 952, 954], 'Jaimmie': [355, 357, 977, 979, 1292], 'Que': [356, 358, 978, 980], 'Melissa': [381, 383, 1003, 1005, 1294], 'Yau': [382, 384, 1004, 1006], 'Michael': [407, 409, 1029, 1031, 1296], 'Acab': [408, 410, 1030, 1032], 'Dan': [431, 433, 1053, 1055, 1298], 'Tulpan': [432, 434, 1054, 1056], 'D': [456, 459, 1078, 1081, 1301], 'Whiteside': [457, 460, 1079, 1082], 'Avinash': [481, 483, 1103, 1105, 1303], 'Chikatamarla': [482, 484, 1104, 1106], 'Bernadette': [507, 509, 1129, 1131, 1305], 'Mah': [508, 510, 1130, 1132], 'Tamara': [533, 535, 1155, 1157, 1307], 'Munzner': [534, 536, 1156, 1158], 'Karsten': [556, 558, 1178, 1180, 1309], 'Hokamp': [557, 559, 1179, 1181], 'Smurfit': [560, 1182], 'Institute': [561, 1183, 1362, 3093], 'Genetics,': [563, 1185, 1364], 'Trinity': [564, 1186, 1365], 'College': [565, 1187, 1366], 'Dublin,': [566, 567, 1188, 1189, 1367, 1368], 'Ireland': [568, 1190, 1369], 'Robert': [576, 580, 1198, 1202, 1311], 'E': [577, 581, 1199, 1203, 1312], 'Hancock': [579, 583, 1201, 1205], 'S': [607, 613, 1229, 1235, 1317], 'Brinkman': [609, 615, 1231, 1237, 1319], 'Information': [1259], '1,2,': [1263], 'Winsor1,': [1266], 'Chan2,': [1268, 1285], 'Richard1,': [1270], 'Laird1,': [1273], 'Barsky3,': [1275], 'Gardy2,': [1278], 'Roche1,': [1281], 'Shah1,2,': [1287], 'Lo1,': [1289], 'Naseer2,': [1291], 'Que2,': [1293], 'Yau2,': [1295], 'Acab1,': [1297], 'Tulpan1,': [1299], 'Whiteside1,': [1302], 'Chikatamarla2,': [1304], 'Mah2,': [1306], 'Munzner3,': [1308], 'Hokamp4,': [1310], 'Hancock2': [1314], '1': [1320, 2862], '1Department': [1321], '2Centre': [1334], '3Department': [1349], '4Smurfit': [1361], '*Corresponding': [1370], 'authors.': [1371], 'Bology': [1375], 'Room': [1378], 'SSB': [1379], '8166,': [1380], '8888': [1384], 'Drive,': [1386], 'V5A': [1391], '1S6.': [1392], 'Tel.:': [1393, 1405], '+778': [1394, 1398, 1406], '782': [1395, 1399, 1407, 1411], '2061;': [1396], 'Fax:': [1397, 1409], '5583;': [1400, 1412], 'E-mail:': [1401, 1413], '[email': [1402, 1414], 'protected]': [1403, 1415], 'or': [1404, 2083, 2112, 2307, 2393, 2428, 2610, 3107, 3721, 3737, 3776, 4143], '5646;': [1408], '778': [1410], 'Systems': [1417], '(2008)4:218https://doi.org/10.1038/msb.2008.55': [1419], 'PDFDownload': [1420], 'PDF': [1421], 'article': [1423], 'text': [1424], 'main': [1426], 'figures.': [1427], 'ToolsAdd': [1428], 'to': [1429, 1480, 1578, 1602, 1643, 1802, 1807, 1832, 1851, 1890, 1909, 1929, 1941, 1990, 2027, 2034, 2043, 2088, 2102, 2115, 2133, 2139, 2173, 2191, 2253, 2264, 2270, 2349, 2356, 2404, 2416, 2452, 2513, 2525, 2529, 2578, 2589, 2600, 2671, 2755, 2966, 2971, 3000, 3012, 3117, 3123, 3145, 3184, 3203, 3300, 3312, 3438, 3469, 3599, 3641, 3648, 3657, 3726, 3747, 3766, 3779, 3797, 3803, 3855, 3985, 4107, 4115, 4139, 4161, 4176, 4194], 'favoritesDownload': [1430], 'CitationsTrack': [1431], 'CitationsPermissions': [1432], 'ShareFacebookTwitterLinked': [1433], 'InMendeleyWechatReddit': [1434], 'Figures': [1435], '&': [1436], 'Info': [1437], 'Although': [1438], 'considerable': [1439], 'progress': [1440, 1682, 2794], 'has': [1441, 1477, 1619, 1683, 2024, 2291, 2633, 2653, 2795, 3084, 3236, 3394, 3694, 3882, 3948, 3982], 'been': [1442, 1478, 1548, 1621, 1684, 2025, 2063, 2293, 2634, 2654, 2796, 3070, 3085, 3639, 3681, 3983], 'made': [1443, 1685, 2797], 'in': [1444, 1450, 1469, 1525, 1584, 1606, 1623, 1657, 1665, 1686, 1945, 1974, 2010, 2120, 2142, 2148, 2156, 2195, 2316, 2379, 2401, 2425, 2464, 2502, 2520, 2621, 2659, 2702, 2727, 2769, 2777, 2798, 3231, 3242, 3275, 3316, 3345, 3411, 3420, 3460, 3517, 3576, 3619, 3703, 3784, 3806, 3868, 3952, 3999, 4030, 4038, 4146, 4165, 4174, 4198], 'dissecting': [1445], 'signaling': [1447, 1701, 2813, 3893, 3903, 3906, 4068], 'pathways': [1448, 1494, 1523, 1702, 1744, 1750, 1907, 1972, 2042, 2186, 2267, 2274, 2304, 2396, 2427, 2486, 2497, 2516, 2537, 2814, 2908, 2914, 3201, 3343, 3373, 3516, 3656, 3969, 4063, 4069, 4144, 4189], 'involved': [1449, 1524, 1703, 1973, 2009, 2400, 2424, 2519, 2815, 3344, 3618, 4145], 'response,': [1454, 1654, 1691, 2199, 2737, 2766, 2803, 3235, 4202], 'it': [1455, 1886, 2510, 3180], 'is': [1456, 1504, 1645, 1730, 1914, 1956, 1989, 2095, 2511, 2665, 2699, 2757, 2894, 3208, 3327, 3598, 3750, 3759, 3845, 3850, 4003, 4118], 'now': [1457, 1796, 1830, 2666, 2960, 2998], 'apparent': [1458, 1889, 3183], 'that': [1459, 1484, 1497, 1734, 1892, 1913, 1933, 2187, 2250, 2440, 2487, 2498, 2517, 2668, 2898, 3186, 3304, 3476, 3699, 3710, 3885, 4002, 4121, 4155, 4190], 'can': [1462, 1641, 2311, 2483, 2739, 2753, 3477], 'no': [1463, 2611], 'longer': [1464], 'be': [1465, 2312, 2741, 3479], 'productively': [1466], 'thought': [1467], 'terms': [1470, 3412, 3997], 'simple': [1472, 1742, 2906, 3963], 'linear': [1473, 1743, 2907, 3964], 'pathways.': [1474], 'InnateDB': [1475, 1503, 1560, 1954, 1988, 2044, 2149, 2200, 2236, 2256, 2317, 2343, 2353, 3325, 3353, 3391, 3449, 3524, 3567, 3597, 3658, 3879, 3958, 3978, 4031, 4203], '(www.innatedb.ca)': [1476, 1955, 3326], 'developed': [1479, 1952, 3323], 'facilitate': [1481, 3439], 'will': [1485, 1595, 1934, 2575, 3305], 'provide': [1486, 1852, 1930, 1991, 3103, 3114, 3146, 3301, 3600], 'better': [1487, 1771, 2935], 'insight': [1488, 3528], 'into': [1489, 1559, 2235, 2342, 2365, 2411, 2584, 2636, 3384, 3970], 'complex': [1491, 1747, 2911], 'networks': [1492, 1748, 2389, 2912, 4142], 'interactions': [1496, 1521, 1546, 1905, 1970, 2008, 2040, 2074, 2107, 2137, 2184, 2223, 2249, 2423, 3199, 3240, 3258, 3341, 3369, 3534, 3590, 3617, 3654, 3698, 3712, 3771, 3801, 3934, 4061, 4187, 4226], 'govern': [1498], 'response.': [1502, 2648, 2663, 3130, 3446, 4113, 4169], 'a': [1505, 1599, 1607, 1648, 1663, 1931, 1938, 1946, 1957, 1992, 2018, 2081, 2109, 2193, 2296, 2328, 2366, 2405, 2418, 2601, 2742, 2760, 2775, 3074, 3267, 3277, 3302, 3309, 3317, 3328, 3385, 3483, 3562, 3569, 3601, 3627, 3718, 3773, 3851, 3971, 4000, 4014, 4057, 4073, 4196], 'publicly': [1506, 1845, 1958, 2231, 2280, 3139, 3245, 3329, 3539, 4234], 'available,': [1507], 'manually': [1508, 1993, 2064, 3381, 3602, 3682], 'curated,': [1509, 2152, 3274, 4034], 'integrative': [1510, 3571], 'biology': [1511, 1805, 2969, 3572], 'database': [1512, 1960, 2348, 3331], 'human': [1515, 1535, 1976, 2000, 2207, 2220, 3347, 3498, 3545, 3609, 4210, 4223], 'mouse': [1517, 1537, 2002, 2209, 2222, 3060, 3547, 3611, 4212, 4225], 'molecules,': [1518], 'experimentally': [1519, 1968, 1998, 3339, 3607, 3932], 'verified': [1520, 1969, 1999, 3340, 3608, 3933], 'immunity,': [1527, 1911, 3205, 4148], 'along': [1528, 2547], 'with': [1529, 2075, 2491, 2548, 2620, 2708, 3379, 3549, 3713, 4005], 'centralized': [1530, 1995, 3386, 3570, 3604, 4058], 'annotation': [1531, 2037, 2214, 2290, 3284, 3651, 3812, 3990, 4217], 'on': [1532, 2038, 2204, 2215, 3014, 3425, 3542, 3652, 3696, 4207, 4218], 'broader': [1534, 3582], 'interactomes.': [1538, 2210, 4213], 'To': [1539, 1770, 1924, 2015, 2050, 2211, 2239, 2934, 3295, 3388, 3624, 3668, 3877, 4170, 4214], 'date,': [1540, 2051, 3389, 3669, 3878], 'than': [1542, 1659, 2053, 2217, 2272, 2771, 3365, 3397, 3403, 3671, 4220], '3500': [1543, 2054, 3404, 3672], 'immunity-relevant': [1545, 2056, 2266, 3406, 3589, 3674, 3848], 'have': [1547, 1800, 1951, 2062, 2192, 2964, 3010, 3069, 3273, 3322, 3488, 3638, 3680, 3708, 3929, 4195], 'contextually': [1549], 'annotated': [1550, 3241, 3256, 3702], 'through': [1551, 2045, 2066, 2318, 2678, 3090, 3659, 3684], 'review': [1553, 2028, 2068, 3268, 3642, 3686], '1000': [1555, 2060, 2071, 3398, 3678, 3689], 'plus': [1556], 'publications.': [1557, 2072, 3690], 'Integrated': [1558, 2479], 'are': [1561, 1795, 1829, 2086, 2099, 2150, 2188, 2251, 2414, 2441, 2473, 2488, 2499, 2518, 2597, 2617, 2674, 2676, 2959, 2997, 3436, 3700, 3724, 3740, 3763, 3886, 4032, 4104, 4131, 4191], 'novel': [1562, 2380, 2579, 3432], 'bioinformatics': [1563, 1827, 1895, 2336, 2553, 2995, 3189, 3430], 'resources,': [1564], 'including': [1565, 1692, 1717, 2804, 2881, 3895, 4079], 'network': [1566, 1573, 1590, 2338, 2369, 3433, 3463, 3975], 'visualization': [1567, 2339, 3434], 'software,': [1568], 'pathway': [1569, 1592, 1849, 2282, 2371, 2480, 2508, 3108, 3143, 3465, 3910, 3915], 'analysis,': [1570, 2509], 'orthologous': [1571], 'interaction': [1572, 1589, 1847, 2085, 2123, 2233, 2368, 2388, 3106, 3141, 3247, 3252, 3462, 3705, 3723, 3787, 3824, 3831, 3849, 3974, 3989, 4016], 'construction': [1574], 'ability': [1577], 'overlay': [1579], 'user-supplied': [1580], 'gene': [1581, 2004, 2111, 2287, 2363, 2504, 2861, 3456, 3491, 3613, 3775], 'expression': [1582, 3457, 3492], 'data': [1583, 1605, 1944, 2147, 2203, 2300, 2359, 2378, 2460, 3033, 3122, 3315, 3383, 3458, 3475, 3541, 4029, 4206], 'an': [1585, 1637, 2655, 2749, 3461, 3846, 4109], 'intuitively': [1586], 'displayed': [1587], 'molecular': [1588, 1904, 2007, 2248, 2367, 2387, 3105, 3198, 3239, 3257, 3533, 3616, 4015], 'context,': [1593, 2372, 3466], 'which': [1594, 2472, 2672, 2723, 3083, 3207, 3421], 'enable': [1596, 1935, 2240, 3124, 3306], 'biologists': [1597, 1936, 3307], 'without': [1598, 1937, 2683, 3308], 'computational': [1600, 1939, 3310], 'background': [1601, 1940, 3311], 'explore': [1603, 1942, 3313], 'their': [1604, 1943, 2143, 2183, 2247, 2503, 3314, 3473, 3807, 4186], 'systems-oriented': [1609, 1948, 3319], 'manner.': [1610], 'Synopsis': [1611], 'The': [1612, 2090, 2734, 3691, 3754, 3977], 'importance': [1613, 2091, 2693, 3755], 'long': [1620], 'recognized': [1622, 2701], 'front': [1625], 'line': [1626, 3871], 'defense': [1628], 'against': [1629], 'invading': [1630], 'pathogens.': [1631, 1728, 2591, 2892], 'If': [1632, 2745], 'not': [1633, 1740, 2262, 2746, 2904, 3701, 3741, 4159], 'tightly': [1634, 2747], 'regulated,': [1635, 2748], 'however,': [1636, 2738], 'overwhelming': [1638, 2750], 'lead': [1642, 2577, 2754], 'what': [1644, 2756, 3844], 'sometimes': [1646, 2758], 'called': [1647, 2759], 'cytokine': [1649, 2761], 'storm.': [1650, 2762], 'One': [1651, 1982, 2763, 3591], 'such': [1652, 2377, 2507, 2764, 2832, 3043, 3079, 3732], 'out-of-control': [1653, 2765], 'sepsis,': [1655, 2767], 'results': [1656, 2768], '200': [1660, 2772], '000': [1661, 2219, 2773, 3367, 4222], 'deaths': [1662, 2774], 'year': [1664, 2776], 'United': [1667, 2779], 'States': [1668, 2780], 'alone': [1669, 2781], '(Angus': [1670, 2782], 'et': [1671, 1763, 1815, 1819, 1823, 1859, 1863, 1867, 1871, 1875, 1879, 1883, 2168, 2560, 2568, 2572, 2731, 2783, 2854, 2867, 2927, 2979, 2987, 2991, 3038, 3064, 3153, 3157, 3161, 3165, 3169, 3173, 3177, 3917, 4021, 4025, 4050, 4087, 4092, 4101], 'al,': [1672, 1764, 1816, 1820, 1824, 1860, 1864, 1868, 1872, 1876, 1880, 1884, 2169, 2561, 2569, 2573, 2732, 2784, 2855, 2868, 2928, 2980, 2988, 2992, 3039, 3065, 3154, 3158, 3162, 3166, 3170, 3174, 3178, 3918, 4022, 4026, 4051, 4088, 4093, 4102], '2001).': [1673, 2785], 'Over': [1674, 2786], 'course': [1676, 2788], 'last': [1679, 2791], 'decade,': [1680, 2792], 'significant': [1681, 2793, 3509], 'understanding': [1687, 2799, 3858], 'detailed': [1694, 2036, 2128, 2175, 2806, 3104, 3650, 3745, 3792, 4178], 'dissection': [1695, 2807], 'some': [1697, 2809], 'critical': [1700, 2812], '(Lang': [1704, 2816], 'Mansell,': [1706, 2818], '2007;': [1707, 1873, 1877, 1881, 2570, 2819, 3167, 3171, 3175, 3919, 3923, 4023], 'Matsukawa,': [1708, 2820], '2007).': [1709, 1769, 2733, 2873, 2933, 3927, 4027], 'Despite': [1710, 1838, 2874], 'these': [1711, 1834, 1926, 2039, 2136, 2426, 2445, 2536, 2875, 3002, 3008, 3101, 3251, 3293, 3297, 3653, 3800, 3936, 4172], 'efforts,': [1712, 2876], 'many': [1713, 2877], 'questions': [1714, 2878], 'remain': [1715, 2879], 'unanswered': [1716, 2880], 'how': [1718, 2882], 'system': [1722, 1813, 2048, 2346, 2886, 2977, 3663, 3980], 'initiates': [1723, 2887], 'distinct': [1724, 2888], 'responses': [1725, 1761, 2889, 2925, 4130], 'toward': [1726, 2890], 'particular': [1727, 2254, 2406, 2526, 2590, 2891, 3015], 'It': [1729, 2664, 2893], 'becoming': [1731, 2895, 4132], 'increasingly': [1732, 2896, 4133], 'clear': [1733, 2897], 'does': [1739, 2903], 'involve': [1741, 2905], 'but': [1745, 2268, 2909, 3523], 'rather': [1746, 2910], 'interactions,': [1752, 2057, 2303, 2916, 3281, 3407, 3675], 'positive': [1753, 2917], 'negative': [1755, 2919], 'feedback': [1756, 2920], 'loops': [1757, 2921], 'multifaceted': [1759, 2923], 'transcriptional': [1760, 2924], '(Tegner': [1762, 2926], '2006;': [1765, 1817, 1821, 2566, 2929, 2981, 2985, 2989], 'Lee': [1766, 2930, 3920], 'Kim,': [1768, 2932, 3922], 'understand': [1772, 2936], 'complexities': [1774, 2938], 'cross-talk': [1782, 2432, 2946], 'between': [1783, 2433, 2947, 3259, 3872, 3935, 4124], 'its': [1784, 2948, 3222], 'components,': [1785, 2949], 'complementary': [1786, 2950], 'focused': [1791, 2955, 3695], 'follow-up': [1792, 2956], 'experimental': [1793, 2078, 2957, 3415, 3715], 'approaches': [1794, 1806, 2958, 2970], 'needed.': [1797, 2961], 'Recently,': [1798, 2962], 'researchers': [1799, 2963, 3088, 3575], 'started': [1801, 2965], 'apply': [1803, 2967], 'systems': [1804, 2968], 'study': [1809, 2973], '(Gilchrist': [1814, 2978], 'Tegner': [1818, 2986], 'Andersen': [1822, 2990], '2008)': [1825, 2993], 'resources': [1828, 1896, 2551, 2996, 3009, 3102, 3190], 'emerging': [1831, 2550, 2999], 'aid': [1833, 3001], 'types': [1835, 3003, 3120, 3729, 3838], 'analyses.': [1837, 3005], 'enormous': [1840, 3134], 'efforts': [1841, 3135], 'major': [1844, 2230, 2279, 3138, 3244, 3375, 4233], 'available': [1846, 1894, 1959, 2232, 2281, 3140, 3188, 3246, 3330, 3540, 3751], 'databases': [1850, 2124, 2234, 2283, 3144, 3253, 3377, 3788], 'as': [1853, 1856, 2097, 2361, 2397, 2538, 2717, 2719, 2833, 3044, 3080, 3147, 3150, 3224, 3578, 3580, 3733, 3761, 4157], 'wide-ranging': [1854, 3148], 'cover': [1855, 3149], 'possible': [1857, 2512, 3151], '(Salwinski': [1858, 3152], '2004;': [1861, 2869, 3155], 'Alfarano': [1862, 3156], '2005;': [1865, 1869, 2562, 3159, 3163], 'Joshi-Tope': [1866, 3160], 'Breitkreutz': [1870, 3164], 'Chatr-aryamontri': [1874, 3168], 'Kanehisa': [1878, 3172], 'Kerrien': [1882, 3176], '2007),': [1885, 2716, 2856, 3040, 3179, 4089, 4103], 'was': [1887, 2224, 3181, 3521, 4227], 'quickly': [1888, 3182, 3959], 'us': [1891, 2132, 3185, 3796], 'currently': [1893, 2118, 3187, 3782], 'provided': [1897, 3191, 3283, 3437, 3526], 'poor': [1898, 3192], 'coverage': [1899, 3193, 3356], 'detail': [1901, 3195], 'relevant': [1908, 2030, 2144, 2252, 3202, 3644, 3808], 'information': [1912, 3109, 3206, 4010], 'essential': [1915, 3209], 'systems-orientated': [1918, 3212], 'interpretation': [1919, 3213], 'large-scale': [1921, 3215], 'genomics': [1922, 3018, 3216], 'data.': [1923, 3217], 'overcome': [1925, 3296], 'problems': [1927, 3298], 'resource': [1932, 1996, 3303, 3573, 3605, 4059], 'manner,': [1949, 3320], 'we': [1950, 2098, 2673, 3272, 3321, 3487, 3762], 'InnateDB.': [1953, 2089, 3324, 3727], 'analysis': [1962, 2351, 2482, 2556, 3333, 3453, 3565], 'platform': [1963, 3334], 'genes,': [1966, 2061, 2180, 2244, 2494, 3337, 3679, 4183], 'proteins,': [1967, 3338], 'murine': [1978, 3349], 'responses.': [1981, 3352], 'primary': [1985, 3594], 'goals': [1986, 3595], 'curated': [1994, 2065, 3382, 3401, 3603, 3683, 3931], 'protein,': [2003, 3612], 'RNA': [2006, 3615], 'system.': [2014, 2628, 3623], 'do': [2016, 2212, 3112, 3625, 4215], 'this,': [2017, 2213, 3626, 4216], 'dedicated': [2019, 3628], 'full-time': [2020, 3629], 'team': [2021, 3393, 3630, 3693], 'curators': [2023, 3632, 3637], 'assembled': [2026, 3640], 'biomedical': [2031, 3583, 3645], 'literature': [2032, 3271, 3646], 'submit': [2035, 3649], 'customized': [2046, 3661], 'submission': [2047, 3662, 3979, 3987], 'software.': [2049], 'involving': [2058, 3676], 'around': [2059, 3677], 'approximately': [2070, 3371, 3688], 'Only': [2073], 'published': [2076, 3714], 'direct': [2077, 3719], 'evidence': [2079, 3291, 3416, 3716, 3731], 'physical': [2082, 3720], 'biochemical': [2084, 3722], 'submitted': [2087, 3725], 'manual': [2093, 2129, 2176, 3551, 3757, 3793, 3880, 4179], 'curation': [2094, 2130, 2177, 3392, 3552, 3692, 3748, 3758, 3794, 3881, 4180], 'clear,': [2096, 3760], 'often': [2100, 3764], 'able': [2101, 2415, 3765], 'double': [2103, 3767], 'number': [2105, 2117, 3769, 3781], 'given': [2110, 3774], 'protein': [2113, 2289, 3777], 'compared': [2114, 3778], 'present': [2119, 3783], 'other': [2122, 2299, 2549, 2595, 3264, 3635, 3704, 3738, 3786, 3841, 3940, 4076], 'combined.': [2125, 3789], 'Furthermore,': [2126, 2691, 3131, 3790, 4135], 'permitted': [2131, 3795], 'richly': [2134, 3408, 3798], 'annotate': [2135, 3799], 'place': [2140, 3804], 'them': [2141, 3410, 3805], 'context.': [2145, 3809], 'Interaction': [2146, 2162, 4028, 4044], 'also': [2151, 2201, 2257, 2269, 2292, 2740, 3525, 4033, 4204], 'stored': [2153, 4035], 'downloadable': [2155, 4037], 'Proteomics': [2158, 4040], 'Standards': [2159, 4041], 'Initiative': [2160, 4042], '(PSI-MI)': [2163, 4045], '2.5-compliant': [2164, 4046], 'XML': [2165, 4047], 'format': [2166, 4048], '(Hermjakob': [2167, 4049], '2004).': [2170, 4052], 'In': [2171, 2649, 3447, 3955], 'addition': [2172, 4175], 'proteins': [2181, 2245, 2308, 4154, 4184], 'specifically': [2189, 4192], 'known': [2190, 3368, 3950, 4160, 4193], 'role': [2194, 3951, 4197], 'incorporates': [2202, 4205], 'entire': [2206, 4209], '100': [2218, 3366, 4221], 'integrated': [2225, 3429, 4228], 'from': [2226, 2275, 2295, 2347, 3034, 3374, 3752, 4065, 4229], 'several': [2227, 2276, 2826, 3428, 3502, 3634, 3840, 4230], '(Figure': [2237, 2284, 2544], '1).': [2238, 2285], 'investigation': [2242, 3126], 'pathways,': [2255, 2435, 3558, 3894, 3898], 'includes': [2258, 3813], 'cross-references': [2259], 'genes': [2261, 2306, 3062, 4152], 'only': [2263, 3711], '2500': [2273, 3372], 'Detailed': [2286], 'extracted': [2294], 'variety': [2297], 'sources.': [2301], 'Specific': [2302], 'interest': [2310, 2658], 'interactively': [2313, 3480], 'searched': [2314], 'flexible': [2320], 'web-based': [2321], 'search': [2322], 'interface': [2323], 'database,': [2326], 'providing': [2327, 3561], 'knowledge': [2329], 'base': [2330], 'community,': [2333], 'whereas': [2334, 3041], 'tools': [2340, 3435], 'incorporated': [2341], 'elevate': [2344], 'robust': [2350], 'platform.': [2352], 'allows': [2354, 2450], 'one': [2355, 2451, 3225, 4137], 'integrate': [2357, 3118, 3472], 'quantitative': [2358, 2459], '(such': [2360], 'differential': [2362], 'expression)': [2364], 'enabling': [2373], 'interrogation': [2375], 'insightful': [2382], 'ways.': [2383], 'Investigating': [2384], 'differentially': [2385, 2492], 'expressed': [2386], 'may': [2390], 'identify': [2391, 2484, 2514, 2530, 4140], 'subnetworks': [2392], 'as-yet': [2394], 'unidentified': [2395], 'being': [2398, 2700], 'significantly': [2399, 2489, 2500], 'stimulus.': [2407], 'By': [2408, 3536], 'incorporating': [2409], 'Cytoscape': [2410], 'InnateDB,': [2412, 2546, 3506], 'investigators': [2413], 'take': [2417], 'closer': [2419], 'look': [2420], 'at': [2421, 3501], 'subnetworks,': [2429], 'potentially': [2430], 'identifying': [2431], 'key': [2434, 3890], 'highlighting': [2437, 2495], 'molecules': [2439, 3230, 3884, 3937], 'hubs': [2443], 'networks.': [2446], 'Our': [2447], 'Cerebral': [2448], 'plugin': [2449], 'further': [2453, 3278], 'extend': [2454], 'experience,': [2456], 'visually': [2457], 'interrogating': [2458], 'across': [2461], 'multiple': [2462], 'conditions': [2463], 'biologically': [2466], 'intuitive': [2467], 'pathway-like': [2468], 'layouts': [2469], 'networks,': [2471], 'generated': [2474], 'using': [2475, 3991], 'subcellular': [2476], 'localization': [2477], 'information.': [2478], 'over-representation': [2481], 'those': [2485, 2496], 'associated': [2490], 'regulated': [2493], 'altered': [2501], 'expression.': [2505], 'Through': [2506, 3266], 'common': [2515, 2532], 'infections,': [2527], 'central': [2533], 'regulators': [2534], 'attractive': [2539], 'targets': [2540], 'modulation.': [2543], '4).': [2545], 'immunology': [2558, 3577], '(Kelley': [2559], 'Ortutay': [2563], 'Vihinen,': [2565], 'Hijikata': [2567], 'Korb': [2571], '2008),': [2574], 'undoubtedly': [2576], 'much': [2581], 'deeper': [2582, 3527], 'insights': [2583], 'Introduction': [2592], 'Humans': [2593], 'mammals': [2596], 'constantly': [2598], 'exposed': [2599, 2675], 'deluge': [2602], 'microorganisms,': [2604], 'although': [2605], 'they': [2606, 3113, 3422], 'usually': [2607], 'suffer': [2608], 'little': [2609], 'detrimental': [2612], 'effects': [2613], 'largely': [2614], 'because': [2615], 'microbes': [2616], 'efficiently': [2618], 'dealt': [2619], 'most': [2622, 2669, 3228], 'cases': [2623], "host's": [2626], 'Traditionally,': [2629], 'divided': [2635], 'two': [2637], 'different': [2638, 3288], 'branches,': [2639], 'adaptive': [2641, 2689, 2710, 3875, 4128], 'recent': [2650], 'years,': [2651], 'there': [2652], 'explosion': [2656], 'appreciated': [2667], 'pathogens': [2670], 'eliminated': [2677], 'necessarily': [2684], 'requiring': [2685], 'activation': [2687, 4097], 'immunity.': [2690, 3876, 3954], 'initiation': [2704], 'interplay': [2707], '(MacLeod': [2713], 'Wetzler,': [2715], 'well': [2718, 3579], 'mechanism': [2721], 'vaccine': [2724], 'adjuvants': [2725], 'operate': [2726], 'boosting': [2728], 'immunity': [2729, 3360, 3892, 3968], '(Kwissa': [2730], 'double-edged': [2743], 'sword.': [2744], '2007)': [2821, 4094], 'discovery': [2824], 'important': [2827, 3229], 'pathogen': [2828], 'recognition': [2829], 'receptor': [2830, 3909], 'families,': [2831], 'Toll-like': [2835], 'receptors': [2836, 2847, 2864], '(TLRs)': [2837], '(Akira,': [2838], '2006),': [2839], 'nucleotide': [2841], 'binding': [2842], 'oligomerization': [2844], 'domain': [2845], '(NOD)-like': [2846], '(NLRs)': [2848], '(Inohara': [2849], 'Nunez,': [2851], '2001;': [2852], 'Kanneganti': [2853], 'retinoic': [2859], 'acid-inducible': [2860], '(RIG-1)-like': [2863], '(RLRs)': [2865], '(Yoneyama': [2866], 'Thompson': [2870, 3924], 'Locarnini,': [2872, 3926], 'Oda': [2982], 'Kitano,': [2984], 'So': [3006], 'far,': [3007], 'tended': [3011], 'focus': [3013], 'aspects': [3016], 'research;': [3019], 'Reference': [3021], 'Database': [3022], 'Immune': [3024], 'Cells': [3025], '(RefDIC),': [3026], 'example,': [3028, 3219], 'provides': [3029, 3568], 'transcriptomic': [3030], 'proteomic': [3032], 'immune-relevant': [3035, 3555], 'cells': [3036, 3500], '(Hijikata': [3037], 'others,': [3042], 'Innate': [3046], 'Database,': [3048], 'contain': [3049], 'transcription': [3050, 3055], 'profiles': [3051, 3493], 'computationally': [3053], 'predicted': [3054], 'factor-binding': [3056], 'sites': [3057], '2000': [3059], '(Korb': [3063], '2008).': [3066], 'Others': [3067], 'still': [3068], 'established': [3071], 'primarily': [3072], 'specific': [3075, 4163], 'group': [3076], 'researchers,': [3078], 'ImmPort': [3081], '(http://www.immport.org),': [3082], 'created': [3086], 'funded': [3089], 'National': [3092], 'Allergy': [3095], 'Infectious': [3097], 'Diseases.': [3098], 'None': [3099], 'nor': [3111], 'capability': [3116], 'disparate': [3119, 4077], 'despite': [3132, 3221], 'For': [3218], 'TLR4,': [3220], 'status': [3223], 'relatively': [3237], 'few': [3238], 'databases.': [3248], 'Five': [3249], 'combined': [3254], 'contained': [3255], 'TLR4': [3260], 'just': [3262], '11': [3263], 'proteins.': [3265], 'detail,': [3276], '16': [3279], 'unique': [3280], 'nearly': [3286], '60': [3287], 'lines': [3289], 'supporting': [3292, 3817], 'interactions.': [3294], 'captures': [3354], 'improved': [3355], 'interactome': [3361], 'integrating': [3363], 'public': [3376], 'together': [3378], 'in-house': [3380], 'resource.': [3387], 'reviewed': [3395], 'publications': [3399], 'annotating': [3409], 'context': [3419], 'occur.': [3423], 'Building': [3424], 'data,': [3427], 'investigations': [3441], 'particular,': [3448], 'facilitates': [3450], 'efficient': [3452], 'large': [3455], 'sets': [3459], 'allowing': [3467], 'users': [3468], 'upload': [3470], 'own': [3474], 'then': [3478, 3930], 'investigated.': [3481], 'As': [3482], 'proof': [3484], 'concept,': [3486], 'investigated': [3489], 'lipopolysaccharide': [3495], '(LPS)-stimulated': [3496], 'THP-1': [3497], 'monocytic': [3499], 'time': [3503], 'points.': [3504], 'Using': [3505], 'expected': [3508], 'involvement': [3510], 'TNF-α': [3513], 'NF-κB': [3515, 3900], 'LPS': [3519], 'identified,': [3522], 'probing': [3530], 'component': [3532], 'involved.': [3535], 'combining': [3537], 'existing': [3538], 'general': [3544], 'interactomes': [3548], 'biomolecules': [3556], 'user-friendly,': [3563], 'accessible': [3564], 'environment,': [3566], 'community.': [3584], 'Results': [3585], 'Contextually': [3586], 'curating': [3587], 'part-time': [3636], 'software': [3664, 3981], 'database.': [3667], 'reviewing': [3697], 'databases,': [3706], 'ensured': [3709], 'Other': [3728], 'colocalization,': [3734], 'overexpression,': [3735], 'microarray': [3736], 'inferences,': [3739], 'deemed': [3742], 'acceptable.': [3743], 'A': [3744], 'guide': [3746], 'process': [3749], 'www.innatedb.ca/help.': [3753], 'This': [3810], 'contextual': [3811], 'details': [3814], 'publication;': [3818], 'participant': [3819], 'molecules;': [3820], 'species;': [3822], 'detection': [3825], 'method;': [3826], 'host': [3828], 'system;': [3829], 'type;': [3832], 'cell,': [3834], 'cell-line': [3835], 'tissue': [3837], 'fields.': [3842], 'Defining': [3843], 'difficult': [3852], 'task': [3853], 'due': [3854], 'increasing': [3857], 'complexity': [3861, 4117], 'difficulty': [3867], 'drawing': [3869], 'prioritized': [3883], 'well-described': [3887], 'members': [3888], 'TLR': [3897, 4071], 'pathway,': [3901, 3904, 3907], 'MAPK': [3902], 'JNK': [3905], 'NOD-like': [3908], 'RIG-I': [3913], 'antiviral': [3914], '(Kanneganti': [3916], 'We': [3928], 'any': [3939, 3949], 'molecule,': [3941], 'regardless': [3942], 'whether': [3944], 'interacting': [3946], 'molecule': [3947], 'way,': [3957], 'expands': [3960], 'upon': [3961], 'view': [3965], 'comprehensive': [3973], 'perspective.': [3976], 'designed': [3984], 'allow': [3986], 'Open': [3992], 'Biomedical': [3993], 'Ontology': [3994], '(OBO)': [3995], 'controlled': [3996], 'manner': [4001], 'compliant': [4004], 'recently': [4007], 'proposed': [4008], "'minimum": [4009], 'required': [4011, 4106], 'reporting': [4013], "experiment'": [4017], '(MIMIx)': [4018], 'guidelines': [4019], '(Orchard': [4020], 'Smith': [4024], 'Going': [4053], 'beyond': [4054], 'immunity:': [4056], 'Aside': [4064], 'well-known': [4067], '(e.g.': [4070], 'signaling),': [4072], 'range': [4074], 'processes,': [4078], 'apoptosis': [4080], '(Mayadas': [4081], 'Cullere,': [4083], '2005),': [4084], 'ubiquitination': [4085], '(Carmody': [4086], 'endocytosis': [4090], '(Tateno': [4091], 'cell': [4096], 'recruitment': [4099], '(Coelho': [4100], 'all': [4105], 'mount': [4108], 'effective': [4110], 'Adding': [4114], 'fact': [4120], 'borders': [4123], 'blurred.': [4134], 'if': [4136], 'hopes': [4138], 'new': [4141], 'must': [4150], 'include': [4151], 'are,': [4156], 'yet,': [4158], 'play': [4162], 'roles': [4164], 'address': [4171], 'issues,': [4173], 'ava': [4235]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2163783674', 'counts_by_year': [{'year': 2024, 'cited_by_count': 11}, {'year': 2023, 'cited_by_count': 9}, {'year': 2022, 'cited_by_count': 14}, {'year': 2021, 'cited_by_count': 14}, {'year': 2020, 'cited_by_count': 12}, {'year': 2019, 'cited_by_count': 11}, {'year': 2018, 'cited_by_count': 20}, {'year': 2017, 'cited_by_count': 35}, {'year': 2016, 'cited_by_count': 22}, {'year': 2015, 'cited_by_count': 30}, {'year': 2014, 'cited_by_count': 38}, {'year': 2013, 'cited_by_count': 38}, {'year': 2012, 'cited_by_count': 44}], 'updated_date': '2024-12-14T02:21:43.150587', 'created_date': '2016-06-24'}
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