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Coexpression cluster:C2776

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Full id: C2776_NK_Hep2_plasma_medial_neuroblastoma_caudate_frontal



Phase1 CAGE Peaks

  Short description
Hg19::chr4:134076051..134076081,+ p3@PCDH10
Hg19::chr4:134076088..134076099,+ p5@PCDH10
Hg19::chr4:134076101..134076115,+ p9@PCDH10
Hg19::chr4:134076121..134076131,+ p15@PCDH10


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


uberon_data


Uber Anatomy
Ontology termp-valuen
cerebral hemisphere1.21e-5032
telencephalon1.98e-5034
brain grey matter4.36e-5034
gray matter4.36e-5034
regional part of forebrain1.20e-4941
forebrain1.20e-4941
anterior neural tube1.20e-4941
future forebrain1.20e-4941
regional part of nervous system6.16e-4953
regional part of brain6.16e-4953
brain7.71e-4768
future brain7.71e-4768
regional part of telencephalon8.35e-4732
neural tube9.33e-4656
neural rod9.33e-4656
future spinal cord9.33e-4656
neural keel9.33e-4656
central nervous system8.54e-4281
pre-chordal neural plate7.74e-3961
neurectoderm9.41e-3986
nervous system1.44e-3889
cerebral cortex1.22e-3625
pallium1.22e-3625
neocortex4.75e-3520
neural plate6.26e-3582
presumptive neural plate6.26e-3582
regional part of cerebral cortex6.68e-3522
ecto-epithelium4.32e-25104
ectoderm-derived structure1.95e-23171
ectoderm1.95e-23171
presumptive ectoderm1.95e-23171
larynx3.26e-229
organ system subdivision3.64e-22223
structure with developmental contribution from neural crest7.11e-21132
adult organism2.33e-15114
neural nucleus1.19e-149
nucleus of brain1.19e-149
gyrus3.80e-146
organ part2.37e-12218
upper respiratory tract1.08e-1119
parietal lobe1.24e-115
basal ganglion1.66e-119
nuclear complex of neuraxis1.66e-119
aggregate regional part of brain1.66e-119
collection of basal ganglia1.66e-119
cerebral subcortex1.66e-119
telencephalic nucleus1.71e-117
occipital lobe3.21e-115
anatomical cluster6.20e-11373
corpus striatum6.32e-104
striatum6.32e-104
ventral part of telencephalon6.32e-104
future corpus striatum6.32e-104
multi-tissue structure5.30e-09342
frontal cortex3.94e-083
brainstem4.81e-086
temporal lobe6.80e-086
caudate-putamen8.07e-083
dorsal striatum8.07e-083
tube5.52e-07192


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.12.80052
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.14.90158
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.11.54523
MA0091.16.95519
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.12.2938
MA0143.12.05538
MA0144.15.03067
MA0145.10.195821
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.23.4512
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.13.43559
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#1066445.360256373075030.001211145381643620.00819081865657439
GATA2#2624412.7449317335543.78864877853583e-050.000723633302453372
RAD21#5885410.35503389545638.6948481184721e-050.00129762966939855
SMC3#9126415.04493284493281.95092670935632e-050.00043912248835876



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.