JASPAR Changelog

JASPAR Changelog

13/09/2019

We've introduced the following changes in the JASPAR 2020.
  • Profile MA1073.1 is 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 profiles MA0173.1 (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 profiles MA1352.1, 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