Functional clusters

Information

  • Type MapMan
  • Description RNA biosynthesis.RNA polymerase II-dependent transcription

Cluster overview

Species Chromosome Experiment Cluster id Cluster size Number of genes E-value
Nelumbo nucifera chr2 1 CH_nnu_447 7 73 0.000680746
Sequoiadendron giganteum chr10 1 CH_sgi_612 5 7 0.00000158993
Solanum lycopersicum SL4.0ch02 1 CH_sly_446 6 29 0.000292176
Nelumbo nucifera chr2 2 CH_nnu_447 7 73 0.000680746
Sequoiadendron giganteum chr10 2 CH_sgi_612 5 7 0.00000158993
Solanum lycopersicum SL4.0ch02 2 CH_sly_446 6 29 0.000292176

Available child term results

Ontology identifier Description Number of clusters
15.3.1 RNA biosynthesis.RNA polymerase II-dependent transcription.RNA polymerase-II assembly and nuclear import 2
15.3.1.1 RNA biosynthesis.RNA polymerase II-dependent transcription.RNA polymerase-II assembly and nuclear import.assembly factor (RPAP3) 11
15.3.1.2 RNA biosynthesis.RNA polymerase II-dependent transcription.RNA polymerase-II assembly and nuclear import.nuclear import factor (RIMA) 4
15.3.1.4 RNA biosynthesis.RNA polymerase II-dependent transcription.RNA polymerase-II assembly and nuclear import.nuclear import factor (GPN2/QQT1) 1
15.3.1.5 RNA biosynthesis.RNA polymerase II-dependent transcription.RNA polymerase-II assembly and nuclear import.nuclear import factor (GPN3) 2
15.3.2.1.2 RNA biosynthesis.RNA polymerase II-dependent transcription.RNA polymerase-II phosphorylation/dephosphorylation.CTDK-I protein kinase complex.T-class cyclin regulatory component 15
15.3.2.2 RNA biosynthesis.RNA polymerase II-dependent transcription.RNA polymerase-II phosphorylation/dephosphorylation.group-I phosphatase 15
15.3.2.3 RNA biosynthesis.RNA polymerase II-dependent transcription.RNA polymerase-II phosphorylation/dephosphorylation.group-II phosphatase 7
15.3.3.1.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIa basal transcription factor heterodimer.large subunit 26
15.3.3.1.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIa basal transcription factor heterodimer.small subunit 2
15.3.3.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.basal transcription factor (TFIIb) 20
15.3.3.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIe basal transcription factor heterodimer 14
15.3.3.3.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIe basal transcription factor heterodimer.subunit alpha 13
15.3.3.3.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIe basal transcription factor heterodimer.subunit beta 4
15.3.3.4.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIf basal transcription factor heterodimer.subunit alpha 5
15.3.3.4.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIf basal transcription factor heterodimer.subunit beta 10
15.3.3.5.1.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIh basal transcription factor complex.core module.component SSL1 2
15.3.3.5.1.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIh basal transcription factor complex.core module.component SSL2/XPB 16
15.3.3.5.1.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIh basal transcription factor complex.core module.component TFB1 8
15.3.3.5.1.5 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIh basal transcription factor complex.core module.component TFB2 4
15.3.3.5.1.6 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIh basal transcription factor complex.core module.component TFB4 8
15.3.3.5.1.7 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIh basal transcription factor complex.core module.component TFB5 5
15.3.3.5.2.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIh basal transcription factor complex.CAK kinase module.cyclin component 2
15.3.3.5.2.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIh basal transcription factor complex.CAK kinase module.cyclin-dependent kinase component 4
15.3.3.5.2.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TFIIh basal transcription factor complex.CAK kinase module.scaffolding component TFB3 6
15.3.3.6.1.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TATA box-binding protein (TBP) regulation.NC2 regulator heterodimer.component alpha 8
15.3.3.6.1.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.TATA box-binding protein (TBP) regulation.NC2 regulator heterodimer.component beta 8
15.3.3.7.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.SNAP snRNA transcription factor complex.component SNAPC1 9
15.3.3.7.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.SNAP snRNA transcription factor complex.component SNAPC3/SRD2 4
15.3.3.7.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription initiation.SNAP snRNA transcription factor complex.component SNAPC4 4
15.3.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation 4
15.3.4.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TAF module shared with SAGA/TFIId complexes 2
15.3.4.1.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TAF module shared with SAGA/TFIId complexes.component TAF5 12
15.3.4.1.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TAF module shared with SAGA/TFIId complexes.component TAF6 15
15.3.4.1.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TAF module shared with SAGA/TFIId complexes.component TAF10 11
15.3.4.1.5 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TAF module shared with SAGA/TFIId complexes.component TAF12 3
15.3.4.2.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TFIId complex.TATA-box-binding component 14
15.3.4.2.10 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TFIId complex.component TAF15 2
15.3.4.2.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TFIId complex.component HAF/TAF1 4
15.3.4.2.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TFIId complex.component TAF2 17
15.3.4.2.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TFIId complex.component TAF4 25
15.3.4.2.5 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TFIId complex.component TAF7 6
15.3.4.2.6 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TFIId complex.component TAF8 4
15.3.4.2.7 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.TFIId complex.component TAF11 4
15.3.4.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.SAGA complex 2
15.3.4.3.1.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.SAGA complex.HAT histone acetyltransferase module.component GCN5/ADA4 7
15.3.4.3.1.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.SAGA complex.HAT histone acetyltransferase module.component ADA2 13
15.3.4.3.1.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.SAGA complex.HAT histone acetyltransferase module.component ADA3 12
15.3.4.3.1.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.SAGA complex.HAT histone acetyltransferase module.component SGF29 14
15.3.4.3.2.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.SAGA complex.DUB histone deubiquitinating module.component SGF11 4
15.3.4.3.3.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.SAGA complex.SPT recruitment module.component ADA1 20
15.3.4.3.3.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.SAGA complex.SPT recruitment module.component SPT20/ADA5 22
15.3.4.3.3.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.SAGA complex.SPT recruitment module.component HAF/TAF1 18
15.3.4.3.3.5 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.SAGA complex.SPT recruitment module.component SPT3/TAF13 4
15.3.4.4.1.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.head module.component MED6 13
15.3.4.4.1.10 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.head module.component MED30 2
15.3.4.4.1.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.head module.component MED8 10
15.3.4.4.1.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.head module.component MED11 8
15.3.4.4.1.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.head module.component MED17 6
15.3.4.4.1.5 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.head module.component MED18 6
15.3.4.4.1.6 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.head module.component MED19 2
15.3.4.4.1.7 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.head module.component MED20 12
15.3.4.4.1.8 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.head module.component MED22 7
15.3.4.4.2.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.middle module.component MED4 1
15.3.4.4.2.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.middle module.component MED7 10
15.3.4.4.2.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.middle module.component MED9 4
15.3.4.4.2.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.middle module.component MED10 4
15.3.4.4.2.5 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.middle module.component MED21 12
15.3.4.4.2.6 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.middle module.component MED31 6
15.3.4.4.3.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.tail module.component MED2/MED29/MED32 15
15.3.4.4.3.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.tail module.component MED3/MED27 8
15.3.4.4.3.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.tail module.component MED5/MED24/MED33 45
15.3.4.4.3.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.tail module.component MED14 22
15.3.4.4.3.5 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.tail module.component MED15 45
15.3.4.4.3.6 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.tail module.component MED16 15
15.3.4.4.3.7 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.tail module.component MED23 18
15.3.4.4.4.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.regulatory kinase module.component MED12 14
15.3.4.4.4.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.regulatory kinase module.component MED13 28
15.3.4.4.4.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.regulatory kinase module.component CDK8 2
15.3.4.4.4.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.regulatory kinase module.component CycC 26
15.3.4.4.5.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.other components.component MED25 32
15.3.4.4.5.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription co-activation.MEDIATOR complex.other components.component MED26 6
15.3.5 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation 2
15.3.5.1.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.PAF1C transcription initiation and elongation complex.component ELF7/PAF1 8
15.3.5.1.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.PAF1C transcription initiation and elongation complex.component VIP4/LEO1 14
15.3.5.1.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.PAF1C transcription initiation and elongation complex.component VIP5/RTF1 6
15.3.5.1.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.PAF1C transcription initiation and elongation complex.component VIP6/CTR9 14
15.3.5.1.5 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.PAF1C transcription initiation and elongation complex.component CDC73/PHP 6
15.3.5.2.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.ELONGATOR transcription elongation complex.component ELP1 8
15.3.5.2.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.ELONGATOR transcription elongation complex.component ELP2 4
15.3.5.2.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.ELONGATOR transcription elongation complex.component ELP3 11
15.3.5.2.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.ELONGATOR transcription elongation complex.component ELP4 16
15.3.5.2.5 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.ELONGATOR transcription elongation complex.component ELP5 10
15.3.5.2.6 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.ELONGATOR transcription elongation complex.component ELP6 12
15.3.5.2.7 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.ELONGATOR transcription elongation complex.associated regulatory component DRL1 4
15.3.5.3.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.SPT4-SPT5 transcription elongation complex.component SPT4 11
15.3.5.3.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.SPT4-SPT5 transcription elongation complex.component SPT5 6
15.3.5.4.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.SPT6-IWS1 transcription elongation complex.component SPT6 11
15.3.5.4.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.SPT6-IWS1 transcription elongation complex.component IWS1 29
15.3.5.5 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription elongation.regulatory protein (MINIYO) 6
15.3.6.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription termination.helicase (SEN1) 14
15.3.6.2.1 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription termination.R-loop removal.R-loop reader protein (ALBA1/2) 10
15.3.6.2.2 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription termination.R-loop removal.ribonuclease (RNH1) 14
15.3.6.2.3 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription termination.R-loop removal.type-1A topoisomerase (TOP3b) 2
15.3.6.2.4 RNA biosynthesis.RNA polymerase II-dependent transcription.transcription termination.R-loop removal.plastidial DNA:RNA hybrid helicase (RHON1) 2

Functional Clusters Experiments

Exp id Data type Data filter Min genes cluster Max genes cluster Max cluster size E-value Tandems removal
1 MapMan No filter applied. 2 30 80 0.001
2 MapMan No filter applied. 2 30 80 0.001
3 GO All GO data. 2 30 80 0.001
4 GO All GO data. 2 30 80 0.001
5 InterPro No filter applied. 2 30 80 0.001
6 InterPro No filter applied. 2 30 80 0.001