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Coexpression cluster:C4820

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Full id: C4820_cerebellum_parietal_occipital_pineal_duodenum_pituitary_temporal



Phase1 CAGE Peaks

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


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism5.63e-32114
central nervous system4.39e-2881
neural tube8.58e-2856
neural rod8.58e-2856
future spinal cord8.58e-2856
neural keel8.58e-2856
nervous system5.40e-2789
regional part of nervous system3.37e-2653
regional part of brain3.37e-2653
regional part of forebrain4.69e-2441
forebrain4.69e-2441
anterior neural tube4.69e-2441
future forebrain4.69e-2441
brain5.02e-2468
future brain5.02e-2468
brain grey matter1.61e-2034
gray matter1.61e-2034
telencephalon3.31e-2034
regional part of telencephalon2.15e-1932
cerebral hemisphere2.29e-1932
neurectoderm3.81e-1886
neural plate1.80e-1782
presumptive neural plate1.80e-1782
cerebral cortex2.22e-1525
pallium2.22e-1525
regional part of cerebral cortex1.42e-1422
pre-chordal neural plate2.91e-1461
neocortex2.38e-1320
organ system subdivision9.86e-10223
ecto-epithelium2.62e-09104
ectoderm-derived structure2.11e-08171
ectoderm2.11e-08171
presumptive ectoderm2.11e-08171
structure with developmental contribution from neural crest7.56e-07132
basal ganglion9.16e-079
nuclear complex of neuraxis9.16e-079
aggregate regional part of brain9.16e-079
collection of basal ganglia9.16e-079
cerebral subcortex9.16e-079


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.90467
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.111.3342
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.24.86005
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.12.37721
MA0160.12.02335
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.28.15771
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

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 clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.