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DNA binding transcription factors (check after V 43 goes live) #258

Closed pombase-admin closed 9 years ago

pombase-admin commented 11 years ago

All of the 95 DNA binding transcription factors used to be annotated to 000978/ 0000982 (the DNA binding and the transcription factor term)

or one of their children.

However, probably because of reannotation, mapping removal etc the numbers have changed

It should be possible to make annotations to the relevant DNA binding term to sak1

and the transcription factor term to: SPBC1289.10c, adn2, II, transcription factor (predicted) SPBC725.16, res1, II, MBF transcription factor complex subunit Res1 SPAC56F8.16, esc1, I, transcription factor Esc1 (predicted) SPBC2F12.11c, rep2, II, transcriptional activator, MBF subunit Rep2 SPAC105.03c, SPAC105.03c, I, transcription factor (predicted) SPBC1778.02, rap1, II, telomere binding protein Rap1 SPAC2E12.02, hsf1, I, transcription factor Hsf1 SPBC19G7.04, SPBC19G7.04, II, HMG box protein SPBC1105.14, rsv2, II, transcription factor Rsv2 SPCC1494.10, adn3, III, transcription factor (predicted) SPAC16.05c, sfp1, I, transcription factor Sfp1 (predicted) SPAC3F10.12c, SPAC3F10.12c, I, transcription factor (predicted) SPAC25B8.19c, loz1, I, transcription factor zf-C2H2 type (predicted) SPAC22F3.09c, res2, I, MBF transcription factor complex subunit Res2 SPBC1198.04c, zas1, II, zinc finger protein, transcription factor Zas1 (predicted) SPBC354.05c, sre2, II, membrane-tethered transcription factor (predicted) SPBC1711.02, mat3-Mc, II, mating-type m-specific HMG-box transcription factor Mc at silenced MAT3 locus SPBC336.12c, cdc10, II, MBF transcription factor complex subunit Cdc10 SPBC29A10.12, SPBC29A10.12, II, DUF1014 family protein, HMG-box clan member SPBC16A3.07c, nrm1, II, negative regulator of MBF SPBC530.11c, SPBC530.11c, II, transcription factor, zf-fungal binuclear cluster type (predicted) SPBC1D7.02c, scr1, II, transcription factor Scr1 SPAC4G8.13c, prz1, I, calcineurin responsive transcription factor Prz1 SPAC3H1.11, hsr1, I, transcription factor Hsr1 SPAC1327.01c, SPAC1327.01c, I, transcription factor, zf-fungal binuclear cluster type (predicted)

(ISO can be use if there is a cerevisiae ortholog, and no exp data or ISM if there is a TF specific sequence model (PFAM)

Original comment by: ValWood

pombase-admin commented 11 years ago

Original comment by: ValWood

pombase-admin commented 10 years ago

fixed more, down to

SPBC725.16 res1 MBF transcription factor complex subunit Res1 SPBC2F12.11c rep2 MBF transcription factor activator Rep2 SPBC19G7.04 HMG box protein SPAC22F3.09c res2 MBF transcription factor complex subunit Res2 SPBC336.12c cdc10 MBF transcription factor complex subunit Cdc10 SPBC29A10.12 DUF1014 family protein, HMG-box clan member SPBC16A3.07c nrm1 MBF complex corepressor nrm1

Original comment by: ValWood

pombase-admin commented 10 years ago

Original comment by: ValWood

pombase-admin commented 10 years ago

closer: GO:0000978 - RNA polymerase II core promoter proximal region sequence-specific DNA binding) ) NOT ( ( GO_ID(GO:0000982 - RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity

SPBC1348.12 SPBC1348.12 transcription factor (predicted) SPBC19G7.04 SPBC19G7.04 HMG box protein protein_coding II SPBC16A3.07c nrm1 MBF complex corepressor Nrm1
SPBC2F12.11c rep2 MBF transcription factor activator Rep2 protein_coding

and

SPBC1198.11c reb1 RNA polymerase I transcription termination factor Reb1 t'other way around

Original comment by: ValWood

pombase-admin commented 10 years ago

Original comment by: ValWood

pombase-admin commented 10 years ago

all done numbers should be equivalent for V47

Original comment by: ValWood