Biological process to genes

Query process ID GO:0045941
Process name Any process that activates or increases the frequency, rate or extent of transcription.
Organism Arabidopsis thaliana

Click Gene ID to show a list of co-expressed genes.

ECC Gene ID Repr. ID Gene name Functional description O.I. H.G. Other DB
XAt1g25540839141PFT1 (PHYTOCHROME AND FLOWERING TIME 1)Encodes a nuclear protein that acts in a phyB pathway (but downstream of phyB) and induces flowering in response to suboptimal light conditions. Mutants are hypo-responsive to far-red and hyper-responsive to red light and flower late under long day conditions.O.I.H.G.
XAt1g32640840158MYC2Encodes a MYC-related transcriptional activator with a typical DNA binding domain of a basic helix-loop-helix leucine zipper motif. Binds to an extended G-Box promoter motif. Its transcription is induced by dehydration stress and ABA treatment. Negative regulator of blue light–mediated photomorphogenic growth and blue and far-red-light–regulated gene expression. Positive regulator of lateral root formation. Regulates diverse JA-dependent functions. Negatively regulates Trp metabolism and biosynthesis of Trp-derived secondary metabolites. Positively regulates flavonoid biosynthesis, resistance to insects, and response to oxidative stress. Regulates other transcription factors, and negatively regulates its own expression.O.I.H.G.
XAt1g69120843244AP1 (APETALA1)Floral homeotic gene encoding a MADS domain protein homologous to SRF transcription factors. Specifies floral meristem and sepal identity. Required for the transcriptional activation of AGAMOUS. Interacts with LEAFY.Binds to promoter and regulates the expression of flowering time genes SVP, SOC1 and AGL24.O.I.H.G.
XAt1g73500843685MKK9 (MAP KINASE KINASE 9)member of MAP Kinase Kinase family. Autophosphorylates and also phosphorylates MPK3 and MPK6. Independently involved in ethylene and calmalexin biosynthesis. Induces transcription of ACS2, ACS6, ERF1, ERF2, ERF5, ERF6, CYP79B2, CYP79B3, CYP71A13 and PAD3.O.I.H.G.
XAt2g02540814784ATHB21 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 21)Zinc finger homeobox protein. Expressed in vascular tissue. In a yeast one hybrid system was not able to transactivate a reporter gene.O.I.H.G.
XAt2g04880815035ZAP1 (ZINC-DEPENDENT ACTIVATOR PROTEIN-1)Encodes WRKY1, a member of the WRKY transcription factors in plants involved in disease resistance, abiotic stress, senescence as well as in some developmental processes. WRKY1 is involved in the salicylic acid signaling pathway. The crystal structure of the WRKY1 C-terminal domain revealed a zinc-binding site and identified the DNA-binding residues of WRKY1.O.I.H.G.
XAt2g20570816579GPRI1 (GBF'S PRO-RICH REGION-INTERACTING FACTOR 1)Encodes GLK1, Golden2-like 1, one of a pair of partially redundant nuclear transcription factors that regulate chloroplast development in a cell-autonomous manner. GLK2, Golden2-like 2, is encoded by At5g44190. GLK1 and GLK2 regulate the expression of the photosynthetic apparatus.O.I.H.G.
XAt2g22430816775ATHB6Encodes a homeodomain leucine zipper class I (HD-Zip I) protein that is a target of the protein phosphatase ABI1 and regulates hormone responses in Arabidopsis.O.I.H.G.
XAt2g36990818273SIGF (RNA POLYMERASE SIGMA-SUBUNIT F)Encodes a general sigma factor in chloroplasts and is probably responsible for the recognition of sigma 70 type standard bacteria-type multi-subunit RNA polymerase (PEP) promoters in young cotyledons.O.I.H.G.
XAt3g01470821138ATHB-1 (ARABIDOPSIS THALIANA HOMEOBOX 1)Encodes a homeodomain leucine zipper class I (HD-Zip I) transcriptional activator involved in leaf development.O.I.H.G.
XAt3g19510821485HAT3.1Encodes a member of the PHD-finger homeodomain protein family. The HAT3.1 homeodomain is highly divergent in sequence even at positions that are almost invariable among homeodomains. HAT3.1 shows a preference for the sequence T(A/G)(A/C)ACCA, different from those bound by other homeodomains.O.I.H.G.
XAt3g24140822000FMA (FAMA)Encodes a basic helix-loop-helix transcription factor whose activity is required to promote differentiation of stomatal guard cells and to halt proliferative divisions in their immediate precursors. Both transcript and protein are expressed in and are required for halting divisions at the end of the stomatal lineage. It also has a role in the promotion of guard cell fate and in controlling the transition from guard mother cell to guard cell.O.I.H.G.
XAt3g26744822287ICE1 (INDUCER OF CBF EXPRESSION 1)Encodes a MYC-like bHLH transcriptional activator that binds specifically to the MYC recognition sequences in the CBF3 promoter. Mutants are defective in cold-regulated gene expression. Cold stress triggers protein degradation of nuclear GFPICE1 protein, and the RING finger protein HOS1 is required. Sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance.O.I.H.G.
XAt3g55370824703OBP3 (OBF-BINDING PROTEIN 3)Encodes a nuclear localized Dof domain containing transcription factor expressed primarily in roots. Responsive to salicylic acid. Transgenic overexpressors have yellow leaves and short, defective roots.O.I.H.G.
XAt3g55990824765ESK1 (ESKIMO 1)Encodes ESK1 (Eskimo1). A member of a large gene family of DUF231 domain proteins whose members encode a total of 45 proteins of unknown function. ESK1 functions as a negative regulator of cold acclimation. Mutations in the ESK1 gene provides strong freezing tolerance.O.I.H.G.
XAt3g61890825362ATHB-12 (ARABIDOPSIS THALIANA HOMEOBOX 12)Encodes a homeodomain leucine zipper class I (HD-Zip I) protein. Loss of function mutant has abnormally shaped leaves and stems.O.I.H.G.
XAt4g23810828481WRKY53member of WRKY Transcription Factor; Group IIIO.I.H.G.
XAt4g29940829117PRHA (PATHOGENESIS RELATED HOMEODOMAIN PROTEIN A)Homeodomain protein (PRHA). Expression of the gene differs in various vegetative and floral plant tissues and is positively influenced by the phytohormone auxin. It is often associated with regions of developing vascular tissue. The prha promoter is highly responsive to the synthetic auxin, naphthalene acetic acid, in transient assays using tobacco protoplasts. The PRHA protein has the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding.O.I.H.G.
XAt4g40060830169ATHB16 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 16)Encodes a homeodomain leucine zipper class I (HD-Zip I) protein.O.I.H.G.
XAt5g01270831743CPL2Encodes CPL2, a carboxyl-terminal domain (CTD) phosphatase that dephosphorylates CTD Ser5-PO4 of the RNA polymerase II complex. Regulates plant growth, stress and auxin responses.O.I.H.G.
XAt5g03790831723HB51Encodes a homeodomain leucine zipper class I (HD-Zip I) meristem identity regulator that acts together with LFY to induce CAL expression. It binds to the CAL promoter proximal CAATNATTG element. LMI1 acts primarily downstream of LFY in meristem identity regulation. The interaction between LFY, LMI1 and CAL resembles a feed-forward loop transcriptional network motif. The gene also had additional LFY-independent roles in leaf morphogenesis and bract formation.O.I.H.G.
XAt5g47220834768ERF2 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 2)Encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family (ATERF-2). The protein contains one AP2 domain. Functions as activator of GCC box–dependent transcription. Positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation.O.I.H.G.
XAt5g65310836656ATHB5 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 5)Encodes a class I HDZip (homeodomain-leucine zipper) protein that is a positive regulator of ABA-responsiveness, mediating the inhibitory effect of ABA on growth during seedling establishment.O.I.H.G.
SAt2g41460818744ARPapurinic endonuclease-redox protein. It functions as an apurinic/apyrimidinic class II endonuclease, and is involved in DNA repair.O.I.H.G.
SAt2g42680818868MBF1A (MULTIPROTEIN BRIDGING FACTOR 1A)One of three genes in A. thaliana encoding multiprotein bridging factor 1, a highly conserved transcriptional coactivator. May serve as a bridging factor between a bZIP factor and TBP. Its expression is developmentally regulated.O.I.H.G.
SAt3g24500822041MBF1C (MULTIPROTEIN BRIDGING FACTOR 1C)One of three genes in A. thaliana encoding multiprotein bridging factor 1, a highly conserved transcriptional coactivator. May serve as a bridging factor between a bZIP factor and TBP. Its expression is specifically elevated in response to pathogen infection, salinity, drought, heat, hydrogen peroxide, and application of abscisic acid or salicylic acid. Constitutive expression enhances the tolerance of transgenic plants to various biotic and abiotic stresses.O.I.H.G.
SAt3g50410824205OBP1 (OBF BINDING PROTEIN 1)Arabidopsis Dof protein containing a single 51-amino acid zinc finger DNA-binding domain, which may play an important roles in plant growth and development.O.I.H.G.
SAt3g54610824626GCN5Encodes a histone acetyltransferase that is plays a role in the determination of the embryonic root-shoot axis. It is also required to regulate the floral meristem activity by modulating the extent of expression of WUS and AG. In other eukaryotes, this protein is recruited to specific promoters by DNA binding transcription factors and is thought to promote transcription by acetylating the N-terminal tail of histone H3. The enzyme has indeed been shown to catalyse primarily the acetylation of H3 histone with only traces of H4 and H2A/B being acetylated. Non-acetylated H3 peptide or an H3 peptide that had been previously acetylated on K9 both serve as excellent substrates for HAG1-catalyzed acetylation. However, prior acetylation of H3 lysine 14 blocks radioactive acetylation of the peptide by HAG1. HAG1 is specific for histone H3 lysine 14.O.I.H.G.
SAt3g58680825037MBF1B (MULTIPROTEIN BRIDGING FACTOR 1B)One of three genes in A. thaliana encoding multiprotein bridging factor 1, a highly conserved transcriptional coactivator. May serve as a bridging factor between a bZIP factor and TBP. Its expression is developmentally regulated.O.I.H.G.
CAt3g04740819634SWP (STRUWWELPETER)encodes a protein with similarities to subunits of the Mediator complex, required for RNA polymerase II recruitment at target promoters in response to specific activators. Lines carrying loss of function mutations in the gene have reduced cell numbers in aerial organs. On the other hand, lines overexpressing the gene have increased number of small cells in clusters, suggesting cell division is more unsynchronized in the overexpressors.O.I.H.G.
LAt1g304556240845protein binding / transcription activator/ transcription regulator/ translation initiation factor/ zinc ion bindingF:protein binding, transcription regulator activity, transcription activator activity, zinc ion binding, translation initiation factor activity;P:translational initiation, positive regulation of transcription, regulation of transcription, DNA-dependent, transcription initiation;C:transcription factor complex, nucleus;MFOPO.I.H.G.
LAt2g45100819117RNA polymerase II transcription factor/ protein binding / transcription activator/ transcription regulator/ translation initiation factor/ zinc ion bindingF:in 6 functions;P:translational initiation, positive regulation of transcription, regulation of transcription, DNA-dependent, transcription initiation;C:transcription factor complex, nucleus;OMAFPVBO.I.H.G.
LAt3g09360820092RNA polymerase II transcription factor/ protein binding / transcription activator/ transcription regulator/ translation initiation factor/ zinc ion bindingF:in 6 functions;P:translational initiation, positive regulation of transcription, regulation of transcription, DNA-dependent, transcription initiation;C:transcription factor complex, nucleus;MOFBPAVO.I.H.G.
LAt4g12610826874transcription initiation factor IIF alpha subunit (TFIIF-alpha) family proteinF:RNA polymerase II transcription factor activity, transcription initiation factor activity, transcription activator activity, DNA binding, catalytic activity;P:transcription initiation from RNA polymerase II promoter, positive regulation of transcription;C:nucleus, chloroplast;MOFBPVAO.I.H.G.
LAt5g03220831902transcriptional co-activator-relatedF:transcription coactivator activity;P:positive regulation of transcription;C:nucleus;MFOPO.I.H.G.
LAt5g03500831822transcription coactivatorF:transcription coactivator activity;P:positive regulation of transcription;C:nucleus;MFOPO.I.H.G.
LAt5g08565830757positive transcription elongation factor/ zinc ion bindingF:positive transcription elongation factor activity, zinc ion binding;P:positive regulation of transcription;C:nucleus;MFOPO.I.H.G.
LAt5g63670836487SPT42 (SPT4 HOMOLOG 2)F:positive transcription elongation factor activity, zinc ion binding;P:positive regulation of transcription, N-terminal protein myristoylation;C:nucleus;MFOPO.I.H.G.



The upper GO terms

Process ID Gene number Process name
GO:00105570Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
GO:00106281Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
GO:00313280Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
GO:00454490Any process that modulates the frequency, rate or extent of the synthesis of either RNA on a template of DNA or DNA on a template of RNA.
GO:00459350Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.



The lower GO terms

Process ID Gene number Process name
GO:00070720Any process that increases the frequency, rate or extent of transcription as the cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
GO:00458937Any process that activates or increases the frequency, rate or extent of DNA-dependent transcription.
GO:00604690Any process that increases the rate, frequency or extent of transcription as a part of the process of egg activation.
GO:00751810Any process by which an organism activates, maintains or increases the frequency, rate or extent of its transcription as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.





Comparison with co-expressed genes



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