JASPAR Changelog
04/12/2019
The following TFFMs have been removed.
TFFM0098.1 because of discrepancy with PFM. New TFFM version is better nowTFFM0063.1 because of discrepancy with PFM.TFFM0083.1 because of discrepancy with PFM.TFFM0057.3 because of discrepancy with PFM. TFFM0057.2 is betterTFFM0510.1 because of discrepancy with PFM.TFFM0541.1 because of discrepancy with PFM.TFFM0589.1 because of discrepancy with PFM.TFFM0602.1 because of discrepancy with PFM.TFFM0607.1 because of discrepancy with PFM.TFFM0615.1 because of discrepancy with PFM.TFFM0649.1 because of discrepancy with PFM.13/09/2019
We've introduced the following changes in the JASPAR 2020.- Profile
MA1073.1is removed because it is not a TF. - Validation 2516827 does not support http://jaspar.genereg.net/matrix/MA0835.1; this profile removed and replaced with the one coming from ReMap 2020
- MA1004.1 and MA1254.1 entries for the same TF (ERF13). Keep MA1004.1
- Rename TF Class (from *C2H2* to *C2H2 zinc finger factors*) for the following profiles: MA1158.1, MA1156.1, MA1157.1,MA1159.1
- For two profiles including MA1629.1 class: from *C2H2 zinc finger factors::C2H2 zinc finger factors* to *C2H2 zinc finger factors *
- For 17 entries (e.g. http://jaspar.genereg.net/matrix/MA0102.3/), replace TF family C/EBP-related by C/EBP-related factors
- Use validation 22284184 for profile http://jaspar.genereg.net/matrix/MA0818.1/
- Use validation 31086315 for profile http://jaspar.genereg.net/matrix/MA1100.1/
- Replaced MA1469.1 by MA1101.2
- Replaced MA1347.1 by MA0968.2
- MA1319.1 this need to added as new verison for MA0577.1
- Changed the TF family for 7 profile from "G2like" to "G2-like"
- MA0529.2 UniProt ID has to be set to Q94513
- Changed validation for MAX http://jaspar.genereg.net/matrix/MA0058.3/ to 8265351
- AT4G36780 renamed as BEH2: https://www.uniprot.org/uniprot/Q94A43
- At4g18890 renamed as BEH3: https://www.uniprot.org/uniprot/O49404
- At1g78700 renamed as BEH4: https://www.uniprot.org/uniprot/Q9ZV88
- AT2G03500 renamed as EFM: https://www.uniprot.org/uniprot/Q9ZQ85
- AT4G31060 renamed as ERF015: https://www.uniprot.org/uniprot/Q6NLD5
- AT1G19210 renamed as ERF017: https://www.uniprot.org/uniprot/Q84QC2
- AT1G71450 renamed as ERF021: https://www.uniprot.org/uniprot/Q9C9I2
- AT1G12630 renamed as ERF027: https://www.uniprot.org/uniprot/Q38Q39
- AT3G60490 renamed as ERF035: https://www.uniprot.org/uniprot/Q9M210
- AT1G77200 renamed as ERF037: https://www.uniprot.org/uniprot/O80654
- AT1G28160 renamed as ERF087: https://www.uniprot.org/uniprot/Q9FZ90
- AT3G25990 renamed as GT-4: https://www.uniprot.org/uniprot/Q9LU92
- AT1G68670 renamed as HHO2: https://www.uniprot.org/uniprot/Q8VZS3
- AT1G25550 renamed as HHO3: https://www.uniprot.org/uniprot/Q9FPE8
- AT4G37180 renamed as HHO5: https://www.uniprot.org/uniprot/F4JRB0
- AT1G49560 renamed as HHO6: https://www.uniprot.org/uniprot/Q9FX84
- At5g47390 renamed as KUA1: https://www.uniprot.org/uniprot/Q9LVS0
- AT3G04030 renamed as MYR2: https://www.uniprot.org/uniprot/Q9SQQ9
- AT5G45580 renamed as PHL11: https://www.uniprot.org/uniprot/C0SVS4
- AT3G12730 renamed as PHL12: https://www.uniprot.org/uniprot/Q8VYI2
- AT5G29000 renamed as PHL1: https://www.uniprot.org/uniprot/Q8GUN5
- AT2G01060 renamed as PHL7: https://www.uniprot.org/uniprot/Q9SJW0
- At4g01280 renamed as RVE5: https://www.uniprot.org/uniprot/C0SVG5
- At5g52660 renamed as RVE6: https://www.uniprot.org/uniprot/C0SVG5
- At5g08330 renamed as TCP21: https://www.uniprot.org/uniprot/Q9FTA2
- ATHB25 renamed as ZHD1: https://www.uniprot.org/uniprot/Q9FKP8
- ATHB21 renamed as ZHD3: https://www.uniprot.org/uniprot/O64722
- ATHB33 renamed as ZHD5: https://www.uniprot.org/uniprot/Q9FRL5
- ATHB24 renamed as ZHD6: https://www.uniprot.org/uniprot/Q9ZPW7
- Removed ID2 (MA0617.1) , ID4 (MA0824.1)
- The validation PMID for ceh-48 MA0921.1 is incorrect and changed to 22080565.
- http://jaspar2018.genereg.net/matrix/MA0069.1/ Pax6 => PAX6
- The profile name NR1A4::RXRA has changed to NR1H4::RXRA
- Striped UniProt Accession for profiles MA0037.3 and MA0831.2
- Changed the TF family for profile [MA0610.1] from "DMRT" to "DMRT factors"
- For profile MA1186.1, Class and Family set to Tryptophan cluster factors and Myb/SANT domain factors, respectively.
- For profile MA0637.1, Class set to CENP-B. For this family of TFs, there is no TF Class, so we used the assigned Pfam family instead.
- For profile MA0610.1, we change the family form DMRT to DMRT factors.
- For profile MA1160.1, could you replace the class from C2H2 to C2H2 zinc finger factors
- For MA1368.1, Class has to be set to Tryptophan cluster factors
- For the profile MA1366.1 Class has to be set to Tryptophan cluster factors and added Uniprot ID: Q9C6K3
- MA1365.1 class is also Tryptophan cluster factors. The Name replaced to MNJ7.25 and the Uniprot ID to Q9FGJ1.
- For MA1208.1, the name changed to GT-2, and the class to Tryptophan cluster factors
- For MA1207.1, the Name GT-3A and the Class Tryptophan cluster factors
- The TF name “T” for matrices MA0009.1 and MA0009.2 were changed to Tbxt and TBXT, respectively.
- The Class for MA1020.1 and MA1367.1 replaced with Tryptophan cluster factors
- Added Uniprot ID Q9M9A3 for profile MA1186.1
- Changed Uniprot IDs for the following profiles:
MA0328.1=P0CY08; MA0110.1=P46667; MA0058.1=P61244; MA0046.1=P20823; MA0098.1=P14921; MA0052.1=Q02078; MA0024.1=Q01094; MA0138.1=Q13127 - Removed all the TFencyclopedia IDs for 526 profiles
- Removed all the Pazar IDs for 793 profiles
31/10/2017
The plant profilesMA0173.1 (CG11617) was incorrect in JASPAR due to a manual annotation problem.
The updated matrix PFM is:
>MA0173.1 CG11617 A [ 1 0 10 17 0 17 0 ] C [ 0 0 0 0 17 0 0 ] G [ 0 0 3 0 0 0 0 ] T [ 16 17 4 0 0 0 17 ]
31/10/2017
The plant profilesMA1352.1, MA1353.1, MA1355.1 and MA1356.1 were incorrect in JASPAR 2018 release due to a manual annotation problem.
The updated matrix PFMs are:
>MA1352.1 TRP1 A [ 253 19 17 30 29 302 304 307 4 13 1 3 296 295 306 3 6 24 13 290 263 ] C [ 4 250 263 218 0 0 0 0 302 290 296 2 2 9 0 288 292 272 8 4 8 ] G [ 8 11 14 11 3 2 1 0 0 0 6 2 2 2 0 1 4 0 1 6 28 ] T [ 42 27 13 48 275 3 2 0 1 4 4 300 7 1 1 15 5 11 285 7 8 ] >MA1353.1 AT1G72740 A [ 187 187 278 254 2 3 595 0 0 0 1 22 77 229 76 ] C [ 94 71 23 10 107 1 0 1 0 3 28 1 33 120 82 ] G [ 223 242 230 77 1 0 4 599 597 566 0 0 19 73 281 ] T [ 96 100 69 259 490 596 1 0 3 31 571 577 471 178 161 ] >MA1353.1 AT1G72740 A [ 187 187 278 254 2 3 595 0 0 0 1 22 77 229 76 ] C [ 94 71 23 10 107 1 0 1 0 3 28 1 33 120 82 ] G [ 223 242 230 77 1 0 4 599 597 566 0 0 19 73 281 ] T [ 96 100 69 259 490 596 1 0 3 31 571 577 471 178 161 ] >MA1356.1 TRP2 A [ 335 317 44 23 47 72 423 419 422 7 6 0 4 407 422 409 27 18 54 37 337 ] C [ 34 24 303 344 272 0 0 1 2 416 414 416 3 2 1 4 350 383 303 43 28 ] G [ 21 18 22 28 15 4 1 2 0 0 2 0 0 13 2 2 1 0 7 7 15 ] T [ 35 66 56 30 91 349 1 3 1 2 3 9 418 3 0 10 47 24 61 338 45 ]
31/10/2017
We have added the .sites and .bed files for the following profile matrices in plants:
MA0110.2, MA0548.2, MA0555.1, MA0565.1, MA0573.1, MA0582.1, MA0586.2, MA0588.1, MA0931.1, MA0937.1, MA0938.1, MA0941.1, MA0943.1, MA0952.1, MA0953.1, MA0954.2, MA0964.1, MA0965.1, MA0971.1, MA0974.1, MA0981.1, MA0982.1, MA0983.1, MA0992.1, MA0993.1, MA0994.1, MA1000.2, MA1001.1, MA1005.1, MA1014.1, MA1020.1, MA1026.2, MA1043.1, MA1045.1, MA1047.1, MA1055.1, MA1059.2, MA1062.1, MA1065.1, MA1068.1, MA1069.1, MA1076.1, MA1077.1, MA1079.1, MA1081.1, MA1085.2, MA1087.1, MA1093.1, MA1156.1, MA1159.1, MA1162.1, MA1163.1, MA1164.1, MA1165.1, MA1167.1, MA1168.1, MA1172.1, MA1173.1, MA1174.1, MA1175.1, MA1176.1, MA1177.1, MA1178.1, MA1180.1, MA1182.1, MA1183.1, MA1184.1, MA1185.1, MA1186.1, MA1187.1, MA1188.1, MA1189.1, MA1190.1, MA1191.1, MA1195.1, MA1196.1, MA1197.1, MA1198.1, MA1203.1, MA1206.1, MA1207.1, MA1208.1, MA1211.1, MA1212.1, MA1213.1, MA1214.1, MA1215.1, MA1216.1, MA1217.1, MA1218.1, MA1219.1, MA1220.1, MA1221.1, MA1222.1, MA1224.1, MA1225.1, MA1226.1, MA1227.1, MA1228.1, MA1230.1, MA1231.1, MA1233.1, MA1234.1, MA1235.1, MA1236.1, MA1237.1, MA1238.1, MA1240.1, MA1241.1, MA1243.1, MA1244.1, MA1245.1, MA1246.1, MA1247.1, MA1249.1, MA1251.1, MA1255.1, MA1256.1, MA1259.1, MA1262.1, MA1263.1, MA1264.1, MA1265.1, MA1266.1, MA1267.1, MA1268.1, MA1269.1, MA1270.1, MA1271.1, MA1272.1, MA1273.1, MA1274.1, MA1275.1, MA1276.1, MA1277.1, MA1278.1, MA1279.1, MA1280.1, MA1281.1, MA1285.1, MA1286.1, MA1287.1, MA1288.1, MA1289.1, MA1291.1, MA1292.1, MA1293.1, MA1295.1, MA1298.1, MA1301.1, MA1302.1, MA1303.1, MA1305.1, MA1308.1, MA1309.1, MA1311.1, MA1313.1, MA1314.1, MA1315.1, MA1316.1, MA1317.1, MA1318.1, MA1321.1, MA1322.1, MA1323.1, MA1326.1, MA1327.1, MA1328.1, MA1329.1, MA1330.1, MA1331.1, MA1332.1, MA1333.1, MA1334.1, MA1335.1, MA1336.1, MA1337.1, MA1338.1, MA1340.1, MA1341.1, MA1342.1, MA1343.1, MA1344.1, MA1345.1, MA1346.1, MA1347.1, MA1348.1, MA1349.1, MA1351.1, MA1352.1, MA1353.1, MA1355.1, MA1356.1, MA1357.1, MA1359.1, MA1366.1, MA1369.1, MA1371.1, MA1372.1, MA1374.1, MA1375.1, MA1376.1, MA1378.1, MA1379.1, MA1380.1, MA1382.1, MA1384.1, MA1385.1, MA1386.1, MA1388.1, MA1389.1, MA1390.1, MA1391.1, MA1392.1, MA1393.1, MA1394.1, MA1395.1, MA1397.1, MA1398.1, MA1399.1, MA1400.1, MA1401.1, MA1404.1
20/10/2016
We have updated the .sites files for the following profile matrices:
MA0529.1, MA0535.1, MA0530.1, MA0452.2, MA0216.2, MA0534.1, MA0533.1, MA0531.1, MA0536.1, MA0247.2, MA0237.2, MA0532.1, MA0149.1, MA0166.1, MA0167.1, MA0169.1, MA0170.1, MA0171.1, MA0172.1, MA0175.1, MA0176.1, MA0177.1, MA0183.1, MA0189.1, MA0191.1, MA0192.1, MA0194.1, MA0195.1, MA0196.1, MA0199.1, MA0201.1, MA0203.1, MA0204.1, MA0206.1, MA0208.1, MA0209.1, MA0210.1, MA0211.1, MA0214.1, MA0217.1, MA0219.1, MA0221.1, MA0222.1, MA0225.1, MA0228.1, MA0229.1, MA0230.1, MA0233.1, MA0234.1, MA0235.1, MA0238.1, MA0240.1, MA0245.1, MA0247.1, MA0250.1, MA0253.1, MA0256.1, MA0257.1, MA0444.1
The corrected .sites files have not been retrieved for the following profile matrices:
MA0029.1, MA0030.1, MA0139.1, MA0141.1, MA0144.1, MA0145.1, MA0146.1, MA0147.1, MA0138.2, MA0104.2, MA0168.1, MA0173.1, MA0174.1, MA0178.1, MA0180.1, MA0181.1, MA0184.1, MA0193.1, MA0200.1, MA0202.1, MA0207.1, MA0216.1, MA0218.1, MA0227.1, MA0239.1, MA0246.1, MA0248.1, MA0252.1, MA0260.1, MA0443.1, MA0445.1, MA0446.1, MA0447.1, MA0448.1, MA0449.1, MA0454.1, MA0456.1, MA0457.1, MA0459.1
10/12/2014
The plant SOC1 TF (MA0554) is incorrect in JASPAR due to a manual annotation problem. The old incorrect matrix is:
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
## A 0 0 33 0 139 78 0 78 64 0 59 0 0
## C 209 210 168 326 125 223 206 153 0 263 90 258 180
## G 115 135 0 44 119 95 23 123 6 99 57 134 10
## T 482 461 605 436 423 410 577 452 736 444 600 414 616
## [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21]
## A 0 49 117 0 33 14 79 126
## C 343 0 286 121 208 190 240 136
## G 78 115 0 0 64 0 98 147
## T 385 642 403 685 501 602 389 397
The updated matrix is:
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] ## A 288 172 65 62 117 20 0 459 137 130 22 98 90 ## C 123 264 27 0 47 855 617 37 78 6 8 24 71 ## G 99 113 34 51 89 13 9 56 0 0 0 0 86 ## T 378 339 762 775 635 0 262 336 673 752 858 766 641 ## [,14] [,15] ## A 181 17 ## C 10 23 ## G 683 665 ## T 14 183