### JASPAR Changelog

### 22/01/2021

We have updated the .sites and .bed files for the following profile matrices:

`MA0110.3, MA0529.2, MA0565.2, MA0570.2, MA0974.2, MA0976.2, MA0992.2, MA0995.2, MA1001.2, MA1005.2, MA1227.2, MA1233.2, MA1238.2, MA1245.2, MA1265.2, MA1327.2, MA1365.2, MA1444.1, MA1445.1, MA1446.1, MA1456.1, MA1457.1, MA1603.1, MA1604.1, MA1606.1, MA1607.1, MA1659.1, MA1660.1, MA1661.1, MA1662.1, MA1668.1, MA1669.1, MA1670.1, MA1671.1, MA1672.1, MA1685.1, MA1686.1, MA1687.1, MA1688.1, MA1689.1, MA1690.1, MA1691.1, MA1692.1, MA1693.1, MA1694.1, MA1695.1, MA1696.1, MA1697.1, MA1698.1, UN0107.1, UN0108.1, UN0251.1, UN0252.1, UN0342.1, UN0343.1, UN0344.1, UN0345.1, UN0346.1, UN0347.1, UN0348.1, UN0349.1, UN0350.1, UN0351.1, UN0352.1, UN0353.1, UN0354.1, UN0355.1, UN0356.1, UN0357.1, UN0358.1, UN0359.1, UN0360.1, UN0361.1, UN0362.1, UN0363.1, UN0364.1`

### 04/12/2019

The following TFFMs have been removed.

- Remove
`TFFM0098.1`

because of discrepancy with PFM. New TFFM version is better now - Remove
`TFFM0063.1`

because of discrepancy with PFM. - Remove
`TFFM0083.1`

because of discrepancy with PFM. - Remove
`TFFM0057.3`

because of discrepancy with PFM.`TFFM0057.2`

is better - Remove
`TFFM0510.1`

because of discrepancy with PFM. - Remove
`TFFM0541.1`

because of discrepancy with PFM. - Remove
`TFFM0589.1`

because of discrepancy with PFM. - Remove
`TFFM0602.1`

because of discrepancy with PFM. - Remove
`TFFM0607.1`

because of discrepancy with PFM. - Remove
`TFFM0615.1`

because of discrepancy with PFM. - Remove
`TFFM0649.1`

because of discrepancy with PFM.

### 13/09/2019

We've introduced the following changes in 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