Functional clusters

Information

  • Type Gene Ontology
  • Description cellular nitrogen compound biosynthetic process

Cluster overview

Species Chromosome Experiment Cluster id Cluster size Number of genes E-value
Rhododendron simsii chr08 3 CH_rsi_391 23 68 0.000174958
Vanilla planifolia CM028158.1 3 CH_vpl_284 10 13 0.000307686
Rhododendron simsii chr08 4 CH_rsi_391 23 68 0.000174958
Vanilla planifolia CM028158.1 4 CH_vpl_284 10 13 0.000307686

Available child term results

Ontology identifier Description Number of clusters
GO:0000122 negative regulation of transcription by RNA polymerase II 14
GO:0000162 tryptophan biosynthetic process 2
GO:0000183 rDNA heterochromatin assembly 16
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay 2
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening 8
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA 10
GO:0000731 DNA synthesis involved in DNA repair 4
GO:0001172 transcription, RNA-templated 12
GO:0001188 RNA polymerase I preinitiation complex assembly 8
GO:0001731 formation of translation preinitiation complex 14
GO:0002182 cytoplasmic translational elongation 20
GO:0006065 UDP-glucuronate biosynthetic process 2
GO:0006085 acetyl-CoA biosynthetic process 2
GO:0006167 AMP biosynthetic process 8
GO:0006169 adenosine salvage 10
GO:0006176 dATP biosynthetic process from ADP 4
GO:0006182 cGMP biosynthetic process 6
GO:0006183 GTP biosynthetic process 4
GO:0006189 'de novo' IMP biosynthetic process 4
GO:0006223 uracil salvage 2
GO:0006226 dUMP biosynthetic process 6
GO:0006228 UTP biosynthetic process 2
GO:0006231 dTMP biosynthetic process 2
GO:0006233 dTDP biosynthetic process 4
GO:0006269 DNA replication, synthesis of RNA primer 14
GO:0006342 chromatin silencing 16
GO:0006346 DNA methylation-dependent heterochromatin assembly 6
GO:0006348 chromatin silencing at telomere 6
GO:0006351 transcription, DNA-templated 10
GO:0006352 DNA-templated transcription, initiation 14
GO:0006353 DNA-templated transcription, termination 36
GO:0006355 regulation of transcription, DNA-templated 42
GO:0006357 regulation of transcription by RNA polymerase II 62
GO:0006360 transcription by RNA polymerase I 14
GO:0006367 transcription initiation from RNA polymerase II promoter 6
GO:0006368 transcription elongation from RNA polymerase II promoter 4
GO:0006369 termination of RNA polymerase II transcription 42
GO:0006383 transcription by RNA polymerase III 10
GO:0006384 transcription initiation from RNA polymerase III promoter 2
GO:0006393 termination of mitochondrial transcription 2
GO:0006412 translation 8
GO:0006413 translational initiation 8
GO:0006414 translational elongation 2
GO:0006415 translational termination 12
GO:0006417 regulation of translation 8
GO:0006418 tRNA aminoacylation for protein translation 14
GO:0006419 alanyl-tRNA aminoacylation 26
GO:0006420 arginyl-tRNA aminoacylation 24
GO:0006421 asparaginyl-tRNA aminoacylation 2
GO:0006422 aspartyl-tRNA aminoacylation 22
GO:0006423 cysteinyl-tRNA aminoacylation 2
GO:0006424 glutamyl-tRNA aminoacylation 8
GO:0006425 glutaminyl-tRNA aminoacylation 2
GO:0006426 glycyl-tRNA aminoacylation 24
GO:0006427 histidyl-tRNA aminoacylation 2
GO:0006428 isoleucyl-tRNA aminoacylation 6
GO:0006429 leucyl-tRNA aminoacylation 44
GO:0006430 lysyl-tRNA aminoacylation 16
GO:0006431 methionyl-tRNA aminoacylation 12
GO:0006432 phenylalanyl-tRNA aminoacylation 16
GO:0006433 prolyl-tRNA aminoacylation 28
GO:0006434 seryl-tRNA aminoacylation 24
GO:0006435 threonyl-tRNA aminoacylation 32
GO:0006436 tryptophanyl-tRNA aminoacylation 10
GO:0006437 tyrosyl-tRNA aminoacylation 4
GO:0006438 valyl-tRNA aminoacylation 54
GO:0006557 S-adenosylmethioninamine biosynthetic process 2
GO:0006596 polyamine biosynthetic process 6
GO:0006679 glucosylceramide biosynthetic process 2
GO:0006729 tetrahydrobiopterin biosynthetic process 4
GO:0006741 NADP biosynthetic process 16
GO:0006747 FAD biosynthetic process 2
GO:0006780 uroporphyrinogen III biosynthetic process 4
GO:0006784 heme A biosynthetic process 22
GO:0006809 nitric oxide biosynthetic process 4
GO:0006990 positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response 6
GO:0007004 telomere maintenance via telomerase 2
GO:0009127 purine nucleoside monophosphate biosynthetic process 2
GO:0009152 purine ribonucleotide biosynthetic process 2
GO:0009190 cyclic nucleotide biosynthetic process 2
GO:0009202 deoxyribonucleoside triphosphate biosynthetic process 2
GO:0009221 pyrimidine deoxyribonucleotide biosynthetic process 2
GO:0009228 thiamine biosynthetic process 4
GO:0009229 thiamine diphosphate biosynthetic process 2
GO:0009231 riboflavin biosynthetic process 2
GO:0009263 deoxyribonucleotide biosynthetic process 4
GO:0009299 mRNA transcription 4
GO:0009303 rRNA transcription 2
GO:0009309 amine biosynthetic process 2
GO:0009684 indoleacetic acid biosynthetic process 2
GO:0009759 indole glucosinolate biosynthetic process 20
GO:0010024 phytochromobilin biosynthetic process 6
GO:0010767 regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage 4
GO:0010964 regulation of heterochromatin assembly by small RNA 4
GO:0015966 diadenosine tetraphosphate biosynthetic process 2
GO:0015986 ATP synthesis coupled proton transport 22
GO:0015995 chlorophyll biosynthetic process 4
GO:0017183 peptidyl-diphthamide biosynthetic process from peptidyl-histidine 18
GO:0019277 UDP-N-acetylgalactosamine biosynthetic process 2
GO:0019305 dTDP-rhamnose biosynthetic process 6
GO:0019354 siroheme biosynthetic process 2
GO:0019365 pyridine nucleotide salvage 6
GO:0019427 acetyl-CoA biosynthetic process from acetate 2
GO:0030187 melatonin biosynthetic process 4
GO:0030418 nicotianamine biosynthetic process 38
GO:0031508 pericentric heterochromatin assembly 18
GO:0031935 regulation of chromatin silencing 8
GO:0031937 positive regulation of chromatin silencing 14
GO:0032055 negative regulation of translation in response to stress 2
GO:0032212 positive regulation of telomere maintenance via telomerase 2
GO:0032264 IMP salvage 18
GO:0032543 mitochondrial translation 8
GO:0032774 RNA biosynthetic process 2
GO:0032784 regulation of DNA-templated transcription, elongation 14
GO:0032786 positive regulation of DNA-templated transcription, elongation 8
GO:0032968 positive regulation of transcription elongation from RNA polymerase II promoter 32
GO:0033014 tetrapyrrole biosynthetic process 2
GO:0033320 UDP-D-xylose biosynthetic process 4
GO:0033387 putrescine biosynthetic process from ornithine 34
GO:0033389 putrescine biosynthetic process from arginine, using agmatinase 18
GO:0033466 trans-zeatin biosynthetic process 2
GO:0033866 nucleoside bisphosphate biosynthetic process 2
GO:0034243 regulation of transcription elongation from RNA polymerase II promoter 2
GO:0034355 NAD salvage 2
GO:0034654 nucleobase-containing compound biosynthetic process 14
GO:0035278 miRNA mediated inhibition of translation 56
GO:0042276 error-prone translesion synthesis 36
GO:0042351 'de novo' GDP-L-fucose biosynthetic process 8
GO:0042793 plastid transcription 2
GO:0042794 plastid rRNA transcription 2
GO:0042819 vitamin B6 biosynthetic process 12
GO:0043043 peptide biosynthetic process 2
GO:0043100 pyrimidine nucleobase salvage 10
GO:0043433 negative regulation of DNA-binding transcription factor activity 4
GO:0043619 regulation of transcription from RNA polymerase II promoter in response to oxidative stress 6
GO:0044205 'de novo' UMP biosynthetic process 2
GO:0044209 AMP salvage 8
GO:0045014 carbon catabolite repression of transcription by glucose 2
GO:0045727 positive regulation of translation 18
GO:0045892 negative regulation of transcription, DNA-templated 8
GO:0045893 positive regulation of transcription, DNA-templated 4
GO:0045901 positive regulation of translational elongation 18
GO:0045905 positive regulation of translational termination 2
GO:0045943 positive regulation of transcription by RNA polymerase I 2
GO:0045944 positive regulation of transcription by RNA polymerase II 34
GO:0046109 uridine biosynthetic process 2
GO:0046202 cyanide biosynthetic process 2
GO:0046512 sphingosine biosynthetic process 16
GO:0046656 folic acid biosynthetic process 2
GO:0046901 tetrahydrofolylpolyglutamate biosynthetic process 6
GO:0046938 phytochelatin biosynthetic process 52
GO:0046949 fatty-acyl-CoA biosynthetic process 4
GO:0051091 positive regulation of DNA-binding transcription factor activity 6
GO:0051123 RNA polymerase II preinitiation complex assembly 12
GO:0051973 positive regulation of telomerase activity 14
GO:0060195 negative regulation of antisense RNA transcription 2
GO:0060261 positive regulation of transcription initiation from RNA polymerase II promoter 16
GO:0060567 negative regulation of DNA-templated transcription, termination 2
GO:0061158 3'-UTR-mediated mRNA destabilization 4
GO:0070158 mitochondrial seryl-tRNA aminoacylation 2
GO:0070455 positive regulation of heme biosynthetic process 4
GO:0070829 heterochromatin maintenance 4
GO:0070897 transcription preinitiation complex assembly 4
GO:0070919 production of siRNA involved in chromatin silencing by small RNA 8
GO:0070940 dephosphorylation of RNA polymerase II C-terminal domain 50
GO:0072344 rescue of stalled ribosome 12
GO:0080020 regulation of coenzyme A biosynthetic process 4
GO:0080028 nitrile biosynthetic process 2
GO:0080149 sucrose induced translational repression 2
GO:0090309 positive regulation of DNA methylation-dependent heterochromatin assembly 2
GO:0097167 circadian regulation of translation 4
GO:0097659 nucleic acid-templated transcription 10
GO:1900151 regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay 2
GO:1900706 positive regulation of siderophore biosynthetic process 96
GO:1901293 nucleoside phosphate biosynthetic process 2
GO:1901407 regulation of phosphorylation of RNA polymerase II C-terminal domain 2
GO:1901997 negative regulation of indoleacetic acid biosynthetic process via tryptophan 4
GO:1903506 regulation of nucleic acid-templated transcription 4
GO:2000143 negative regulation of DNA-templated transcription, initiation 48
GO:2001141 regulation of RNA biosynthetic process 10

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