Transcription Factor Annotation in Apicomplexans
Explore the updated transcription factors annotation in ApicoTFdb for various species, including the number of validated and predicted TFs, total protein counts, and distribution across TF families. Discover experimentally verified databases, transcription-associated factors, and repositories used for TFBS prediction.
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Presentation Transcript
Updated transcription factors annotation in ApicoTFdb Number of validated and predcited TFs in published databases Number of validated and predcited TFs in published databases Total number of Total number of proteins proteins (PlasmoDB ver.39) (PlasmoDB ver.39) PlasmoDb TextSearch PlasmoDb TextSearch ApicoTFdb Species Species DBD CisBP TF count TF count TF family TF family TF count TF count TF family TF family TF count TF count TF family TF family P.falciparum 5635 548 18 7 44 10 107s 19 P.berghii 5089 418 19 12 46 11 99 20 P.chabaudii 5282 372 19 7 46 11 99 20 P.knowlesi 5261 386 14 8 46 10 86 18 P.vivax 5390 372 15 7 49 8 104 19 P.yoelii 7774 360 15 6 46 9 83 16 T. gondii 49 8920 443 0 0 81 14 146 18 T. gondii 89 9874 486 0 0 0 0 145 18 B. bovis 3721 126 0 0 0 0 10 6 C. parvum 4020 248 30 11 0 0 72 13 C.cayetanensis 7592 332 0 0 0 0 67 13 N. caninum 7266 361 0 0 84 11 107 15 E. maxima, 6249 241 0 0 0 0 74 18 E.tenella 8634 307 0 0 0 0 101 13
TF-family count across apicomplexans 0% 0% 1% 0% 19% 28% 1% 6% 1% 1% 2% 5% 2% AP2 BBOX BUR6 CCAAT Cupin/Jmc General TF HMG mTERF NAC SART DUF TUB ARID/BRIGHT BSD CBFD CSD FHA GO- Based HTH Myb/SANT SANT Zn-finger Winged helix bZIP 0% 1% 1% 0% 3% 4% 1% 8% 2% 12% 1%
TF proteins count across apicomplexans Species Total TF count Total TF count Total TF-Count P.falciparum 107 250 P.berghii 99 P.chabaudii 99 200 P.vivax 104 P.yoelii 83 150 P.knowlesi 86 C. parvum 77 100 E. maxima 74 T. gondiip89 145 50 Tgondii ME49 146 N. caninum 107 0 B.bovis 10 E. tenella 101 C.cayetanensis 67 Total- 1449 TFs
TF family distribution across TF family distribution across Apicomplexans Apicomplexans 80 70 60 50 40 30 20 10 0 AP2 ARID/BRIGHT BBOX BSD CBFD CCAAT CSD Cupin/Jmc FHA General TF GO- Based HMG HTH mTERF Myb/SANT NAC SANT SART Zn-finger DUF Winged helix TUB bZIP
Experimetaly verified (PBM) Database used Number of species Species Total number of predicted TF(ApicoTFdb) P.falciparum, P.vivax, P.berghii, P.chabaudii, P. yoelii & P.knowlesii 578 21 PlasmoDb 6 C.parvum 77 1 CryptoDB 1 Babesia bovis 10 0 PiroplasmaDb 1 Emaximamaxima, TgondiiME49, Tgondiip89, Eimeria tenella, Neospora caninum, Cyclospora cayetanensis 640 3 ToxoDB 5 Transcription Associated Factors in plasmodium Ortholog Groups TAFs Unique GO known GO predicted TF-regulators 504 104 408 96 RNA-regulators 1217 204 1060 157 CromatinRegulators (CR) 252 39 215 37
Repositories used for TFBS prediction Organisms DATABASE No. of Binding Sites ECK-12 Escherichia coli K-12 Regulon DB 1860 Drosophila melanogaster Drosophila 911 Arabidopsis thaliana AthaMYB 16 Mus Musculus,Homo sapiens etc 3D Footprint 1209 Arabidopsis thaliana AthaMap 83 Arabidopsis thaliana, Fundulus heteroclitus,etc EEADannot 16 Mus musculus, Drosophila melanogaster etc UniPROBE 4502 Bacillus subtilis DBTBS 1283 Homo sapiens, Mus musculus, Drosophila melanogaster, Rattus norvegius, Arabidopsis thaliana, Rattus rattus, Zea mays, Vertebrata, Petunia x hybrida, Oryctologus cuniculus JASPAR 13564
