GSE43616: Time-course of wild-type Arabidopsis leaf
Gene Symbol | Gene ID | Gene Info |
---|---|---|
AT2G36010
|
AT2G36010 | E2F transcription factor 3 |
AT5G02470
|
AT5G02470 | Transcription factor DP |
Gene | Promoter | Pearson corr. coef. | P-value | Plot |
---|---|---|---|---|
DPA | arTal_v1_Chr5_-_544938_544955 | -0.51 | 5.1e-03 | Click! |
E2F3 | arTal_v1_Chr2_+_15119516_15119589 | 0.36 | 5.8e-02 | Click! |
Promoter | Log-likelihood | Transcript | Gene | Gene Info |
---|---|---|---|---|
Chr3_-_17288953 | 4.70 |
AT3G46940.1
AT3G46940.2 |
DUT1
|
DUTP-PYROPHOSPHATASE-LIKE 1 |
Chr1_+_2263037 | 4.56 |
AT1G07370.1
|
PCNA1
|
proliferating cellular nuclear antigen 1 |
Chr1_+_16970214 | 4.29 |
AT1G44900.2
AT1G44900.1 |
MCM2
|
minichromosome maintenance (MCM2/3/5) family protein |
Chr2_+_9293261 | 3.87 |
AT2G21790.1
|
RNR1
|
ribonucleotide reductase 1 |
Chr3_-_9981620 | 3.57 |
AT3G27060.1
|
TSO2
|
Ferritin/ribonucleotide reductase-like family protein |
Chr5_+_19932114 | 3.52 |
AT5G49160.1
AT5G49160.2 |
MET1
|
methyltransferase 1 |
Chr5_+_26776953 | 3.24 |
AT5G67100.2
AT5G67100.1 |
ICU2
|
DNA-directed DNA polymerase |
Chr2_+_16934621 | 3.09 |
AT2G40550.1
|
ETG1
|
E2F target protein 1 (ETG1) |
Chr2_-_7130729 | 2.92 |
AT2G16440.1
|
MCM4
|
Minichromosome maintenance (MCM2/3/5) family protein |
Chr1_-_26253687 | 2.84 |
AT1G69770.1
|
CMT3
|
chromomethylase 3 |
Chr4_-_7462447 | 2.64 |
AT4G12620.1
|
ORC1B
|
origin of replication complex 1B |
Chr1_-_25348406 | 2.36 |
AT1G67630.1
|
POLA2
|
DNA polymerase alpha 2 |
Chr1_-_24324064 | 2.33 |
AT1G65470.2
AT1G65470.1 |
FAS1
|
chromatin assembly factor-1 (FASCIATA1) (FAS1) |
Chr2_+_13328862 | 2.24 |
AT2G31270.1
|
CDT1A
|
CDT1-like protein A |
Chr3_+_3880908 | 2.18 |
AT3G12170.2
AT3G12170.1 |
AT3G12170
|
Chaperone DnaJ-domain superfamily protein |
Chr3_+_14751280 | 2.14 |
AT3G42660.1
|
AT3G42660
|
transducin family protein / WD-40 repeat family protein |
Chr2_+_19039024 | 2.05 |
AT2G46380.2
AT2G46380.1 |
AT2G46380
|
extra-large G-like protein, putative (DUF3133) |
Chr2_+_12689171 | 2.02 |
AT2G29680.2
|
CDC6
|
cell division control 6 |
Chr3_-_126876 | 1.93 |
AT3G01330.1
|
DEL3
|
DP-E2F-like protein 3 |
Chr5_+_16760846 | 1.89 |
AT5G41880.1
|
POLA3
|
DNA primase POLA3 |
Chr3_+_9143916 | 1.88 |
AT3G25100.1
|
CDC45
|
cell division cycle 45 |
Chr5_-_21463249 | 1.87 |
AT5G52910.1
AT5G52910.2 |
ATIM
|
timeless family protein |
Chr2_+_12689581 | 1.86 |
AT2G29680.1
|
CDC6
|
cell division control 6 |
Chr3_+_21997052 | 1.80 |
AT3G59550.1
|
SYN3
|
Rad21/Rec8-like family protein |
Chr1_+_13089816 | 1.74 |
AT1G35530.3
AT1G35530.5 AT1G35530.2 AT1G35530.1 AT1G35530.4 |
FANCM
|
DEAD/DEAH box RNA helicase family protein |
Chr3_+_20059671 | 1.70 |
AT3G54180.1
|
CDKB1%3B1
|
cyclin-dependent kinase B1;1 |
Chr1_-_1331163 | 1.69 |
AT1G04730.2
AT1G04730.1 AT1G04730.4 |
CTF18
|
P-loop containing nucleoside triphosphate hydrolases superfamily protein |
Chr3_+_1698079 | 1.56 |
AT3G05740.1
|
RECQI1
|
RECQ helicase l1 |
Chr1_-_25208972 | 1.53 |
AT1G67320.1
AT1G67320.3 AT1G67320.2 |
EMB2813
|
DNA primase, large subunit family |
Chr5_+_25574419 | 1.48 |
AT5G63920.1
|
TOP3A
|
topoisomerase 3alpha |
Chr5_-_7890180 | 1.46 |
AT5G23420.2
|
HMGB6
|
high-mobility group box 6 |
Chr3_+_10232242 | 1.43 |
AT3G27640.1
AT3G27640.2 |
AT3G27640
|
Transducin/WD40 repeat-like superfamily protein |
Chr3_+_1698297 | 1.43 |
AT3G05740.2
|
RECQI1
|
RECQ helicase l1 |
Chr3_+_5008676 | 1.42 |
AT3G14890.1
AT3G14890.2 |
AT3G14890
|
phosphoesterase |
Chr1_-_2232897 | 1.41 |
AT1G07270.2
AT1G07270.1 |
AT1G07270
|
Cell division control, Cdc6 |
Chr3_+_611490 | 1.40 |
AT3G02820.2
AT3G02820.1 |
AT3G02820
|
zinc knuckle (CCHC-type) family protein |
Chr4_-_8484330 | 1.33 |
AT4G14770.3
|
TCX2
|
TESMIN/TSO1-like CXC 2 |
Chr2_-_10400802 | 1.33 |
AT2G24490.1
|
RPA2
|
replicon protein A2 |
Chr5_-_7890355 | 1.32 |
AT5G23420.1
|
HMGB6
|
high-mobility group box 6 |
Chr4_-_8484976 | 1.29 |
AT4G14770.1
|
TCX2
|
TESMIN/TSO1-like CXC 2 |
Chr4_-_8484582 | 1.29 |
AT4G14770.2
|
TCX2
|
TESMIN/TSO1-like CXC 2 |
Chr5_+_25056025 | 1.25 |
AT5G62410.1
|
SMC2
|
structural maintenance of chromosomes 2 |
Chr2_-_10400498 | 1.20 |
AT2G24490.2
|
RPA2
|
replicon protein A2 |
Chr1_-_2547946 | 1.19 |
AT1G08130.1
|
LIG1
|
DNA ligase 1 |
Chr3_-_6413196 | 1.16 |
AT3G18630.1
|
UNG
|
uracil dna glycosylase |
Chr2_-_19551171 | 1.16 |
AT2G47680.1
|
AT2G47680
|
zinc finger (CCCH type) helicase family protein |
Chr5_-_7571109 | 1.11 |
AT5G22750.1
|
RAD5
|
DNA/RNA helicase protein |
Chr5_+_2422783 | 1.11 |
AT5G07660.1
|
SMC6A
|
structural maintenance of chromosomes 6A |
Chr1_+_9298670 | 1.09 |
AT1G26840.1
|
ORC6
|
origin recognition complex protein 6 |
Chr4_-_13048262 | 1.04 |
AT4G25540.1
|
MSH3
|
homolog of DNA mismatch repair protein MSH3 |
Chr1_+_29582907 | 1.00 |
AT1G78650.1
|
POLD3
|
DNA-directed DNA polymerase |
Chr4_+_9871761 | 0.98 |
AT4G17760.2
AT4G17760.1 |
AT4G17760
|
PCNA domain-containing protein |
Chr5_+_5474366 | 0.94 |
AT5G16690.2
AT5G16690.1 |
ORC3
|
origin recognition complex subunit 3 |
Chr5_+_15208358 | 0.93 |
AT5G38110.1
|
ASF1B
|
anti- silencing function 1b |
Chr1_-_7192794 | 0.91 |
AT1G20720.1
AT1G20720.2 |
AT1G20720
|
RAD3-like DNA-binding helicase protein |
Chr5_-_6202166 | 0.88 |
AT5G18620.2
AT5G18620.1 |
CHR17
|
chromatin remodeling factor17 |
Chr5_+_17114329 | 0.85 |
AT5G42680.1
|
AT5G42680
|
MIZU-KUSSEI-like protein (Protein of unknown function, DUF617) |
Chr5_+_17114098 | 0.82 |
AT5G42680.2
|
AT5G42680
|
MIZU-KUSSEI-like protein (Protein of unknown function, DUF617) |
Chr5_-_967432 | 0.80 |
AT5G03700.1
|
AT5G03700
|
D-mannose binding lectin protein with Apple-like carbohydrate-binding domain-containing protein |
Chr3_+_22421344 | 0.80 |
AT3G60660.1
|
AT3G60660
|
spindle/kinetochore-associated-like protein |
Chr1_-_1330402 | 0.76 |
AT1G04730.3
|
CTF18
|
P-loop containing nucleoside triphosphate hydrolases superfamily protein |
Chr2_-_12651753 | 0.75 |
AT2G29570.1
|
PCNA2
|
proliferating cell nuclear antigen 2 |
Chr3_-_23444006 | 0.72 |
AT3G63480.1
AT3G63480.2 |
AT3G63480
|
ATP binding microtubule motor family protein |
Chr4_-_15019771 | 0.71 |
AT4G30840.1
|
AT4G30840
|
Transducin/WD40 repeat-like superfamily protein |
Chr1_+_25562118 | 0.62 |
AT1G68200.6
|
AT1G68200
|
Zinc finger C-x8-C-x5-C-x3-H type family protein |
Chr3_-_8828316 | 0.60 |
AT3G24320.2
|
MSH1
|
MUTL protein homolog 1 |
Chr3_-_8180122 | 0.58 |
AT3G23020.1
|
AT3G23020
|
Tetratricopeptide repeat (TPR)-like superfamily protein |
Chr1_+_30048739 | 0.56 |
AT1G79890.3
|
AT1G79890
|
RAD3-like DNA-binding helicase protein |
Chr5_-_8297159 | 0.55 |
AT5G24330.1
|
ATXR6
|
TRITHORAX-RELATED PROTEIN 6 |
Chr3_-_8829728 | 0.55 |
AT3G24320.1
|
MSH1
|
MUTL protein homolog 1 |
Chr2_-_10621307 | 0.54 |
AT2G24970.1
|
AT2G24970
|
spindle/kinetochore-associated protein |
Chr1_+_30049612 | 0.44 |
AT1G79890.4
|
AT1G79890
|
RAD3-like DNA-binding helicase protein |
Chr1_-_7209013 | 0.39 |
AT1G20750.1
|
AT1G20750
|
RAD3-like DNA-binding helicase protein |
Chr1_+_30048519 | 0.38 |
AT1G79890.1
AT1G79890.2 |
AT1G79890
|
RAD3-like DNA-binding helicase protein |
Chr2_-_13462431 | 0.35 |
AT2G31650.1
|
ATX1
|
homologue of trithorax |
Chr3_-_3346360 | 0.32 |
AT3G10690.1
|
GYRA
|
DNA GYRASE A |
Chr3_-_5296636 | 0.23 |
AT3G15620.2
|
UVR3
|
DNA photolyase family protein |
Chr3_-_5296811 | 0.22 |
AT3G15620.1
|
UVR3
|
DNA photolyase family protein |
Chr1_+_25561638 | 0.18 |
AT1G68200.1
AT1G68200.3 AT1G68200.2 AT1G68200.4 AT1G68200.5 |
AT1G68200
|
Zinc finger C-x8-C-x5-C-x3-H type family protein |
Chr1_+_30336097 | 0.15 |
AT1G80720.2
AT1G80720.1 |
AT1G80720
|
Mitochondrial glycoprotein family protein |
Chr5_+_19866231 | 0.13 |
AT5G49010.1
AT5G49010.2 |
SLD5
|
DNA replication protein-like protein |
Chr4_+_15237191 | 0.12 |
AT4G31400.1
AT4G31400.2 |
CTF7
|
protein CTF7 |
Chr5_+_2016566 | 0.04 |
AT5G06590.2
AT5G06590.1 |
AT5G06590
|
hypothetical protein |
Chr4_-_1080722 | 0.03 |
AT4G02460.3
AT4G02460.4 AT4G02460.2 AT4G02460.1 |
PMS1
|
DNA mismatch repair protein |
Chr5_+_25599514 | 0.02 |
AT5G63960.2
AT5G63960.1 |
AT5G63960
|
DNA polymerase delta subunit 1 |
Log-likelihood per target | Total log-likelihood | Term | Description |
---|---|---|---|
2.6 | 10.4 | GO:1902975 | cell cycle DNA replication initiation(GO:1902292) nuclear cell cycle DNA replication initiation(GO:1902315) mitotic DNA replication initiation(GO:1902975) |
2.1 | 6.4 | GO:0010069 | zygote asymmetric cytokinesis in embryo sac(GO:0010069) |
2.0 | 12.1 | GO:0009263 | deoxyribonucleotide biosynthetic process(GO:0009263) |
1.4 | 4.1 | GO:0071163 | DNA replication preinitiation complex assembly(GO:0071163) |
1.1 | 5.3 | GO:0006272 | leading strand elongation(GO:0006272) |
0.8 | 3.9 | GO:0000085 | mitotic G1 phase(GO:0000080) mitotic S phase(GO:0000084) mitotic G2 phase(GO:0000085) G1 phase(GO:0051318) G2 phase(GO:0051319) S phase(GO:0051320) interphase(GO:0051325) mitotic interphase(GO:0051329) |
0.8 | 4.7 | GO:0045005 | DNA-dependent DNA replication maintenance of fidelity(GO:0045005) |
0.6 | 5.0 | GO:0033314 | mitotic DNA replication checkpoint(GO:0033314) |
0.5 | 2.3 | GO:0031507 | heterochromatin assembly(GO:0031507) |
0.3 | 1.0 | GO:0006297 | nucleotide-excision repair, DNA gap filling(GO:0006297) |
0.3 | 1.2 | GO:0000012 | single strand break repair(GO:0000012) |
0.2 | 3.0 | GO:0006268 | DNA unwinding involved in DNA replication(GO:0006268) |
0.2 | 0.9 | GO:0036388 | pre-replicative complex assembly involved in nuclear cell cycle DNA replication(GO:0006267) pre-replicative complex assembly(GO:0036388) pre-replicative complex assembly involved in cell cycle DNA replication(GO:1902299) |
0.2 | 1.1 | GO:0045003 | double-strand break repair via synthesis-dependent strand annealing(GO:0045003) |
0.2 | 7.6 | GO:0007062 | sister chromatid cohesion(GO:0007062) |
0.2 | 1.2 | GO:0006285 | base-excision repair, AP site formation(GO:0006285) |
0.1 | 0.9 | GO:1900036 | positive regulation of cellular response to heat(GO:1900036) |
0.1 | 1.8 | GO:0006265 | DNA topological change(GO:0006265) |
0.1 | 1.7 | GO:0010274 | hydrotropism(GO:0010274) |
0.1 | 0.3 | GO:0080182 | histone H3-K4 trimethylation(GO:0080182) |
0.1 | 1.2 | GO:0032042 | mitochondrial DNA metabolic process(GO:0032042) |
0.1 | 1.0 | GO:0000077 | DNA damage checkpoint(GO:0000077) |
0.1 | 2.8 | GO:0000741 | karyogamy(GO:0000741) polar nucleus fusion(GO:0010197) |
0.1 | 2.1 | GO:1900150 | regulation of defense response to fungus(GO:1900150) |
0.1 | 0.5 | GO:0043153 | entrainment of circadian clock by photoperiod(GO:0043153) |
0.1 | 1.9 | GO:0000122 | negative regulation of transcription from RNA polymerase II promoter(GO:0000122) |
0.1 | 0.5 | GO:0006270 | DNA replication initiation(GO:0006270) |
0.0 | 4.6 | GO:0006260 | DNA replication(GO:0006260) |
0.0 | 0.9 | GO:0009294 | genetic transfer(GO:0009292) DNA mediated transformation(GO:0009294) |
0.0 | 0.8 | GO:0048544 | recognition of pollen(GO:0048544) |
Log-likelihood per target | Total log-likelihood | Term | Description |
---|---|---|---|
2.5 | 7.5 | GO:0005658 | alpha DNA polymerase:primase complex(GO:0005658) |
0.9 | 2.8 | GO:0036387 | nuclear pre-replicative complex(GO:0005656) pre-replicative complex(GO:0036387) |
0.9 | 8.8 | GO:0042555 | MCM complex(GO:0042555) |
0.6 | 3.7 | GO:0000808 | origin recognition complex(GO:0000808) nuclear origin of replication recognition complex(GO:0005664) |
0.3 | 2.0 | GO:0031298 | replication fork protection complex(GO:0031298) |
0.3 | 1.0 | GO:0030896 | checkpoint clamp complex(GO:0030896) |
0.3 | 2.5 | GO:0005662 | DNA replication factor A complex(GO:0005662) |
0.3 | 1.8 | GO:0030892 | nuclear cohesin complex(GO:0000798) mitotic cohesin complex(GO:0030892) meiotic cohesin complex(GO:0030893) nuclear mitotic cohesin complex(GO:0034990) nuclear meiotic cohesin complex(GO:0034991) |
0.2 | 0.9 | GO:0043625 | delta DNA polymerase complex(GO:0043625) |
0.2 | 1.3 | GO:0000796 | condensin complex(GO:0000796) |
0.2 | 1.8 | GO:0032300 | mismatch repair complex(GO:0032300) |
0.1 | 0.6 | GO:0030915 | Smc5-Smc6 complex(GO:0030915) |
0.1 | 0.3 | GO:0009330 | DNA topoisomerase complex (ATP-hydrolyzing)(GO:0009330) |
0.1 | 0.5 | GO:0000777 | condensed chromosome kinetochore(GO:0000777) |
0.0 | 0.8 | GO:0005657 | replication fork(GO:0005657) |
0.0 | 3.9 | GO:1990204 | oxidoreductase complex(GO:1990204) |
0.0 | 1.9 | GO:0090575 | RNA polymerase II transcription factor complex(GO:0090575) |
0.0 | 0.3 | GO:0048471 | perinuclear region of cytoplasm(GO:0048471) |
0.0 | 5.0 | GO:0005730 | nucleolus(GO:0005730) |
0.0 | 1.4 | GO:0080008 | Cul4-RING E3 ubiquitin ligase complex(GO:0080008) |
Log-likelihood per target | Total log-likelihood | Term | Description |
---|---|---|---|
2.5 | 7.4 | GO:0061731 | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor(GO:0004748) oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor(GO:0016728) ribonucleoside-diphosphate reductase activity(GO:0061731) |
0.9 | 18.3 | GO:0003688 | DNA replication origin binding(GO:0003688) |
0.6 | 6.4 | GO:0003886 | DNA (cytosine-5-)-methyltransferase activity(GO:0003886) |
0.6 | 2.2 | GO:0070182 | DNA polymerase binding(GO:0070182) |
0.5 | 4.7 | GO:0009378 | four-way junction helicase activity(GO:0009378) |
0.4 | 4.7 | GO:0047429 | nucleoside-triphosphate diphosphatase activity(GO:0047429) |
0.2 | 1.5 | GO:0003917 | DNA topoisomerase type I activity(GO:0003917) |
0.2 | 1.2 | GO:0003909 | DNA ligase activity(GO:0003909) DNA ligase (ATP) activity(GO:0003910) |
0.2 | 0.6 | GO:0046976 | histone methyltransferase activity (H3-K27 specific)(GO:0046976) |
0.2 | 0.7 | GO:0032135 | DNA insertion or deletion binding(GO:0032135) |
0.1 | 1.2 | GO:0030983 | mismatched DNA binding(GO:0030983) |
0.1 | 4.0 | GO:0003678 | DNA helicase activity(GO:0003678) |
0.1 | 0.5 | GO:0003913 | DNA photolyase activity(GO:0003913) |
0.1 | 1.2 | GO:0019104 | DNA N-glycosylase activity(GO:0019104) |
0.0 | 0.9 | GO:0031491 | nucleosome binding(GO:0031491) |
0.0 | 2.5 | GO:0003697 | single-stranded DNA binding(GO:0003697) |
0.0 | 1.9 | GO:0003899 | DNA-directed RNA polymerase activity(GO:0003899) |
0.0 | 2.5 | GO:0042393 | histone binding(GO:0042393) |
0.0 | 0.3 | GO:0003918 | DNA topoisomerase type II (ATP-hydrolyzing) activity(GO:0003918) DNA topoisomerase II activity(GO:0061505) |
0.0 | 1.8 | GO:0003682 | chromatin binding(GO:0003682) |
0.0 | 5.3 | GO:0030234 | enzyme regulator activity(GO:0030234) |
Log-likelihood per target | Total log-likelihood | Term | Description |
---|---|---|---|
1.1 | 10.7 | PID ATR PATHWAY | ATR signaling pathway |
0.5 | 3.2 | PID FANCONI PATHWAY | Fanconi anemia pathway |
0.4 | 2.9 | PID CMYB PATHWAY | C-MYB transcription factor network |
Log-likelihood per target | Total log-likelihood | Term | Description |
---|---|---|---|
1.3 | 9.0 | REACTOME UNWINDING OF DNA | Genes involved in Unwinding of DNA |
1.0 | 3.9 | REACTOME G1 S SPECIFIC TRANSCRIPTION | Genes involved in G1/S-Specific Transcription |
0.9 | 7.0 | REACTOME PROCESSIVE SYNTHESIS ON THE LAGGING STRAND | Genes involved in Processive synthesis on the lagging strand |
0.4 | 1.7 | REACTOME FANCONI ANEMIA PATHWAY | Genes involved in Fanconi Anemia pathway |
0.4 | 2.0 | REACTOME E2F ENABLED INHIBITION OF PRE REPLICATION COMPLEX FORMATION | Genes involved in E2F-enabled inhibition of pre-replication complex formation |
0.4 | 1.8 | REACTOME DOPAMINE NEUROTRANSMITTER RELEASE CYCLE | Genes involved in Dopamine Neurotransmitter Release Cycle |
0.1 | 1.5 | REACTOME MEIOTIC RECOMBINATION | Genes involved in Meiotic Recombination |