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Coexpression cluster:C4820

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Full id: C4820_cerebellum_parietal_occipital_pineal_duodenum_pituitary_temporal



Phase1 CAGE Peaks

Hg19::chr9:3525867..3525902,-p3@RFX3
Hg19::chr9:3525910..3525955,-p4@RFX3
Hg19::chr9:3525968..3526016,-p1@RFX3


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism2.02e-33115
neural tube8.28e-2957
neural rod8.28e-2957
future spinal cord8.28e-2957
neural keel8.28e-2957
central nervous system1.29e-2882
regional part of nervous system1.49e-2694
nervous system1.49e-2694
anterior neural tube8.62e-2542
brain1.27e-2469
future brain1.27e-2469
regional part of forebrain1.70e-2441
forebrain1.70e-2441
future forebrain1.70e-2441
regional part of brain8.09e-2459
gray matter7.31e-2134
brain grey matter7.31e-2134
telencephalon1.83e-2034
regional part of telencephalon5.20e-2033
cerebral hemisphere1.15e-1932
neurectoderm2.52e-1890
neural plate6.80e-1886
presumptive neural plate6.80e-1886
cerebral cortex1.16e-1525
pallium1.16e-1525
pre-chordal neural plate3.69e-1561
regional part of cerebral cortex1.18e-1422
neocortex1.95e-1320
anterior region of body4.73e-11129
craniocervical region4.73e-11129
head6.18e-10123
ectoderm3.11e-08173
presumptive ectoderm3.11e-08173
ectoderm-derived structure7.93e-08169
basal ganglion8.65e-079
nuclear complex of neuraxis8.65e-079
aggregate regional part of brain8.65e-079
collection of basal ganglia8.65e-079
cerebral subcortex8.65e-079


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066435.360256373075030.0064925092527670.0281766538063467
E2F6#187635.017155731697390.00791769806886330.0324777686899185
EGR1#195834.988179094810140.008056488137383440.0322899518220965
ELK4#2005210.8237877723120.01091284719516480.0402133529114323
EP300#203336.77394172622320.003216880500103790.0168650059008253
ESR1#2099330.76860329615453.43136389821584e-050.000680144646357495
GABPB1#255337.067683836182170.002832212825417420.0154938701625777
HDAC2#3066313.41562023662630.0004140761399857210.00394002350437033
HSF1#32973164.2906666666672.24910326529255e-071.19296138102534e-05
JUND#372736.994663941871030.002921845042734990.0157816805139739
MAX#414936.452555509007120.003721913834265510.0187611834034874
MXI1#460139.96157162875930.001011470541259020.00724086447724662
MYC#460935.22228187160940.007020843755740150.0296466219627925
NFKB1#479035.488063424193840.006049381815655430.027100389801623
PBX3#5090321.91451268674419.49854535978121e-050.00137455809731217
POU2F2#545239.106124057742520.001324165192682130.00886048747812205
RAD21#5885310.35503389545630.0009004912073565420.0066960769814959
SIN3A#2594235.408884726815140.006318961977991520.0278599320339183
SIX5#147912317.0867153554590.0002004060546325010.00240466543425595
SMARCB1#6598318.25271578115740.000164397760679890.00204180493847628
SP1#666735.69838137814090.005403962701712170.0248168349575287
YY1#752834.911170749853860.008441455341808260.0331572136764494
ZNF263#1012738.221841637010680.001799043925565870.0110264289050572
ZZZ3#260093239.4132124352337.25894005043406e-084.39487791262193e-06



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.