Table 6 Related Transcription Factors (TFs) and Regulatory Genes (RG) that were found at significant (p < 0.001) differential transcription level due to HA exposition
Transcription factors | Description | UP | DOWN |
|---|---|---|---|
MYB transcription factor | DNA-binding domains | 43 | 66 |
Zinc finger family | Metal-binding, Zinc | 37 | 58 |
WRKY domain transcription factor family | DNA-binding transcription factor activity, sequence-specific DNA binding | 10 | 49 |
AP2/EREBP, APETALA2/Ethylene-responsive element-binding protein family | DNA-binding, transcription factor activity | 12 | 42 |
Basic Helix-Loop-Helix family (bHLH) | DNA-binding, protein dimerization activity | 20 | 32 |
NAC domain transcription factor family | DNA binding, regulation of transcription, DNA templated | 8 | 31 |
Homeobox transcription factor family | DNA-binding transcription factor activity, sequence-specific DNA binding, RNA polymerase II-specific, positive regulation of transcription, DNA templated | 24 | 17 |
bZIP transcription factor | DNA binding, DNA-binding transcription factor activity | 20 | 17 |
Auxin Response Factor family (ARF) | Auxin-activated signalling pathway, regulation of transcription, DNA templated | 9 | 12 |
Chromatin Remodelling Factors | Uncharacterized | 0 | 12 |
GRAS transcription factor family (Scarecrow) | DNA binding, DNA-binding transcription factor activity, transferase activity, transferring acyl groups other than amino-acyl groups | 14 | 11 |
Remorin family protein | Abscisic acid-activated signalling pathway. Negative regulation of brassinosteroid-mediated signalling pathway | 5 | 8 |
Triple-Helix transcription factor family | DNA-binding transcription factor activity, sequence-specific DNA binding | 1 | 8 |
Aux/IAA family | Auxin-activated signalling pathway, regulation of transcription, DNA-templated. Repressor | 0 | 8 |
MADS transcription factor | Protein dimerization activity, DNA-binding transcription factor activity. RNA polymerase II transcription regulatory region sequence-specific DNA binding | 0 | 8 |
Argonaute | Argonaute protein, nucleic acid binding, gene silencing by RNA | 1 | 7 |
Eukaryotic aspartyl protease family protein | Aspartic-type endopeptidase activity | 7 | 6 |
Histone-lysine N-methyltransferase | Histone binding, metal ion binding, methyltransferase activity, methylation. Negative regulation of transcription, DNA template, and positive regulation of transcription by RNA polymerase II | 6 | 6 |
B3 domain-containing protein | Plant-specific B3 DNA-binding domain, PHD finger | 3 | 6 |
G2-like transcription factor family | Transcription regulation | 2 | 6 |
Nuclear transcription factor Y subunit | DNA-binding transcription factor activity, RNA polymerase II-specific, regulation of transcription, protein heterodimerization activity, RNA polymerase II cis-regulatory region sequence-specific DNA binding | 9 | 5 |
Two-component response regulator (ARR) | DNA-binding transcription factor activity, sequence-specific DNA binding, phosphorelay signal transduction system. Transcriptional activator that binds specific DNA sequence | 6 | 5 |
Aspartic proteinase nepenthesin-1 | Aspartic-type endopeptidase activity | 0 | 5 |
Transcription factor GTE | Bromodomain, chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine | 3 | 4 |
DNA-binding bromodomain-containing protein | DNA binding | 3 | 4 |
Histone deacetylase | NAD-dependent histone deacetylase activity (H3-K14 specific) | 1 | 4 |
Putative pentatricopeptide repeat-containing protein | DNA binding, zinc ion binding, RNA modification | 9 | 3 |
S-acyltransferase | Protein-cysteine S-palmitoyltransferase activity, peptidyl-L-cysteine S-palmitoylation, protein targeting to the membrane | 9 | 3 |
Agamous-like MADS-box protein | Protein dimerization activity, DNA-binding transcription factor activity. RNA polymerase II transcription regulatory region sequence-specific DNA binding | 7 | 3 |
Lysine-specific demethylase | Histone demethylase activity, histone demethylase activity (H3-trimethyl-K4 specific), methyltransferase activity, chromatin remodelling, methylation | 2 | 3 |
PLATZ transcription factor (PLT) | Leaf development and leaf senescence | 2 | 3 |
Calmodulin-binding transcription | DNA binding, calmodulin binding | 1 | 3 |
DUF domain family protein | DNA-binding transcription factor activity, sequence-specific DNA binding | 1 | 3 |
Exocyst family protein | Exocytosis, protein transport | 1 | 3 |
Charged multivesicular body protein | Late endosome to vacuole transport via multivesicular body sorting pathway, vesicle budding from the membrane | 1 | 3 |
RING-type E3 ubiquitin transferase | This protein is involved in the pathway protein ubiquitination, which is part of Protein modification | 0 | 3 |
GTPase activating protein | GTPase activator activity | 0 | 3 |
WD-40 repeat family protein | Regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly | 0 | 3 |
Dehydration-responsive element-binding protein (DREB) | DNA-binding transcription factor activity. DNA-binding | 0 | 3 |
AT-hook motif nuclear-localized protein | DNA-binding transcription factor activity, the minor groove of adenine–thymine-rich DNA binding | 5 | 2 |
Nucleic acid-binding protein | DNA binding, RNA binding, metal ion binding | 4 | 2 |
PHD finger protein | Metal ion binding | 3 | 2 |
Putative mediator of RNA polymerase II transcription subunit 26b | DNA binding | 2 | 2 |
Mitochondrial transcription termination factor family protein | Double-stranded DNA binding, DNA-templated transcription, regulation of transcription, DNA templated | 2 | 2 |
G-box binding factor | DNA-binding transcription factor activity, sequence-specific DNA binding, regulation of transcription | 1 | 2 |
EIN3-like (EIL) transcription factor family | DNA binding, DNA-binding transcription factor activity, ethylene-activated signalling pathway | 0 | 2 |
Hydroxyproline-rich glycoprotein family protein | Structural constituent of the cell wall | 0 | 2 |
MOB kinase activator-like | Kinase activity | 0 | 2 |
UBX domain-containing protein 2 | Defence response to fungus | 0 | 2 |
SWI/SNF complex | Endosome transport via multivesicular body sorting pathway, late endosome to vacuole transport, protein transport | 0 | 2 |
Protein FREE1 | Metal ion binding | 0 | 2 |
TCP transcription factor family | DNA-binding transcription factor activity, sequence-specific DNA binding | 6 | 1 |
LOB domain-containing protein | Multicellular organism development, regulation of gene expression | 4 | 1 |
Polyadenylate-binding protein | RNA binding, regulation of mRNA splicing, via spliceosome | 3 | 1 |
NIN-like bZIP-related family | DNA binding, DNA-binding transcription factor activity | 2 | 1 |
BTB domain-containing protein | May act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins | 2 | 1 |
Transcription elongation factor | Structural constituent of ribosome, translation elongation factor activity, regulation of DNA-templated transcription, elongation, regulation of transcription by RNA polymerase II | 2 | 1 |
Alba DNA/RNA-binding protein | RNA binding | 2 | 1 |
Transcriptional corepressor SEUSS | Negative regulation of transcription, DNA-templated, negative regulation of transcription by RNA polymerase II, positive regulation of transcription by RNA polymerase II, RNA polymerase II activating transcription factor binding | 2 | 1 |
Transcription initiation factor | Initiation factor, translation initiation factor activity | 2 | 1 |
Forkhead-associated (FHA) domain-containing protein | G-quadruplex RNA binding | 2 | 1 |
JUMONJI family/Lysine-specific demethylase | Methyltransferase activity | 1 | 1 |
C3H-type transcription factor | DNA binding, metal ion binding | 1 | 1 |
GRF transcription factor | ATP binding, developmental process, regulation of transcription, DNA-templated transcription, DNA-templated | 1 | 1 |
Rubisco methyltransferase family protein | Rubisco LSMT substrate-binding | 1 | 1 |
Histone acetyltransferase | Chromatin DNA binding, histone acetyltransferase activity, RNA polymerase II transcription factor binding, transcription coactivator activity, zinc ion binding, histone acetylation, positive regulation of transcription by RNA polymerase II | 1 | 1 |
AtSR Transcription Factor family | Hydrolase activity | 0 | 1 |
C-terminal-binding protein | NAD binding, oxidation–reduction process | 0 | 1 |
MYC transcription factor | DNA-binding transcription factor activity, sequence-specific DNA binding, protein dimerization activity | 0 | 1 |
Alfin-like transcription factor (ALF2) | Histone binding, metal ion binding, regulation of transcription, DNA templated | 2 | 0 |
F-box protein | DNA binding | 2 | 0 |
Total | Â | 330 | 518 |