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Coexpression cluster:C1804

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Full id: C1804_hippocampus_temporal_duodenum_amygdala_brain_merkel_Neurons



Phase1 CAGE Peaks

Hg19::chr18:67068228..67068257,+p2@DOK6
Hg19::chr22:26779052..26779057,+p@chr22:26779052..26779057
+
Hg19::chr5:175223625..175223636,+p15@CPLX2
Hg19::chr8:65492915..65492932,+p1@BHLHE22
Hg19::chr8:65492973..65492989,+p5@BHLHE22


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


GO IDGO nameFDR corrected p-value
GO:0002448mast cell mediated immunity0.00402637148661542
GO:0043303mast cell degranulation0.00402637148661542
GO:0045576mast cell activation0.00402637148661542
GO:0043299leukocyte degranulation0.00402637148661542
GO:0002444myeloid leukocyte mediated immunity0.00402637148661542
GO:0019905syntaxin binding0.00642968469553287
GO:0000149SNARE binding0.00642968469553287
GO:0005158insulin receptor binding0.00642968469553287
GO:0002274myeloid leukocyte activation0.00670884107822723
GO:0006904vesicle docking during exocytosis0.00708040750904987
GO:0048278vesicle docking0.00708040750904987
GO:0022406membrane docking0.00708040750904987
GO:0045055regulated secretory pathway0.00911365272578224
GO:0006836neurotransmitter transport0.011619925588591
GO:0002443leukocyte mediated immunity0.011619925588591
GO:0032403protein complex binding0.0137733392856842
GO:0002252immune effector process0.0137733392856842
GO:0006887exocytosis0.0137733392856842
GO:0045321leukocyte activation0.0211380868929689
GO:0001775cell activation0.0233065056081194
GO:0045045secretory pathway0.0254773357295268
GO:0032940secretion by cell0.0300697653881253
GO:0046903secretion0.0371399017736141



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>disease_data<br>


Cell Type
Ontology termp-valuen
neuronal stem cell1.03e-078
Uber Anatomy
Ontology termp-valuen
nervous system7.98e-8189
central nervous system1.53e-7581
neural tube5.48e-6856
neural rod5.48e-6856
future spinal cord5.48e-6856
neural keel5.48e-6856
regional part of nervous system1.83e-6553
regional part of brain1.83e-6553
brain5.27e-6268
future brain5.27e-6268
brain grey matter2.32e-5234
gray matter2.32e-5234
telencephalon4.52e-5234
cerebral hemisphere7.41e-5232
regional part of forebrain3.71e-5141
forebrain3.71e-5141
anterior neural tube3.71e-5141
future forebrain3.71e-5141
neurectoderm4.82e-5186
neural plate2.81e-4982
presumptive neural plate2.81e-4982
regional part of cerebral cortex2.20e-4822
regional part of telencephalon4.87e-4832
ectoderm-derived structure1.70e-44171
ectoderm1.70e-44171
presumptive ectoderm1.70e-44171
neocortex1.97e-4320
adult organism3.33e-42114
cerebral cortex5.33e-4225
pallium5.33e-4225
ecto-epithelium2.64e-40104
pre-chordal neural plate4.91e-3861
organ system subdivision3.13e-36223
structure with developmental contribution from neural crest1.13e-28132
posterior neural tube3.30e-1715
chordal neural plate3.30e-1715
anatomical cluster6.40e-17373
segmental subdivision of hindbrain6.37e-1512
hindbrain6.37e-1512
presumptive hindbrain6.37e-1512
gyrus4.14e-146
brainstem6.00e-146
tube6.40e-14192
segmental subdivision of nervous system1.27e-1313
limbic system2.39e-135
temporal lobe6.28e-136
occipital lobe7.35e-135
parietal lobe1.59e-125
basal ganglion4.63e-129
nuclear complex of neuraxis4.63e-129
aggregate regional part of brain4.63e-129
collection of basal ganglia4.63e-129
cerebral subcortex4.63e-129
neural nucleus8.93e-129
nucleus of brain8.93e-129
organ part1.76e-11218
sympathetic nervous system2.18e-115
autonomic nervous system2.18e-115
anatomical conduit4.41e-10240
germ layer1.19e-09560
germ layer / neural crest1.19e-09560
embryonic tissue1.19e-09560
presumptive structure1.19e-09560
germ layer / neural crest derived structure1.19e-09560
epiblast (generic)1.19e-09560
embryonic structure1.90e-09564
regional part of metencephalon2.12e-099
metencephalon2.12e-099
future metencephalon2.12e-099
embryo3.13e-09592
developing anatomical structure3.65e-09581
frontal cortex5.81e-083
pons6.69e-083
telencephalic nucleus7.36e-087
medulla oblongata1.02e-073
myelencephalon1.02e-073
future myelencephalon1.02e-073
epithelium1.54e-07306
cell layer2.37e-07309
multi-tissue structure3.21e-07342
Disease
Ontology termp-valuen
neuroectodermal tumor2.84e-1010
neuroendocrine tumor2.00e-096


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
SUZ12#23512220.04631236442520.003824075654154750.0188735238053149



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.