Coexpression cluster:C2104

Full id: C2104_putamen_occipital_temporal_nucleus_caudate_postcentral_paracentral

Phase1 CAGE Peaks

Hg19::chr11:12030188..12030199,-	p5@DKK3
Hg19::chr11:12030681..12030692,-	p10@DKK3
Hg19::chr11:12030770..12030824,-	p3@DKK3
Hg19::chr15:73925651..73925773,-	p1@NPTN

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0048170	positive regulation of long-term neuronal synaptic plasticity	0.00335570469798658
GO:0048169	regulation of long-term neuronal synaptic plasticity	0.00670973011129312
GO:0048168	regulation of neuronal synaptic plasticity	0.00670973011129312
GO:0042734	presynaptic membrane	0.00670973011129312
GO:0050839	cell adhesion molecule binding	0.00670973011129312
GO:0050769	positive regulation of neurogenesis	0.00670973011129312
GO:0048167	regulation of synaptic plasticity	0.00670973011129312
GO:0050803	regulation of synapse structure and activity	0.00670973011129312
GO:0030178	negative regulation of Wnt receptor signaling pathway	0.00670973011129312
GO:0030111	regulation of Wnt receptor signaling pathway	0.00905693545560676
GO:0050767	regulation of neurogenesis	0.0115861213784452
GO:0048856	anatomical structure development	0.0165377437012502
GO:0051094	positive regulation of developmental process	0.0175356073319971
GO:0007275	multicellular organismal development	0.0186383030498096
GO:0009968	negative regulation of signal transduction	0.0232309476756626
GO:0016055	Wnt receptor signaling pathway	0.0303466189282252
GO:0044456	synapse part	0.0307294334108857
GO:0032502	developmental process	0.0307294334108857
GO:0007156	homophilic cell adhesion	0.0360647672442287
GO:0032501	multicellular organismal process	0.0360647672442287
GO:0050793	regulation of developmental process	0.0367818168635349
GO:0048699	generation of neurons	0.0367818168635349
GO:0022008	neurogenesis	0.0380790084458743
GO:0007268	synaptic transmission	0.040375621903325
GO:0019226	transmission of nerve impulse	0.0440808079690554
GO:0016337	cell-cell adhesion	0.0445576761873194

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>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	6.57e-13	180
fibroblast	5.21e-09	75
smooth muscle cell	2.71e-07	42
smooth muscle myoblast	2.71e-07	42
embryonic cell	6.16e-07	248

Uber Anatomy

Ontology term	p-value	n
ectoderm-derived structure	1.87e-33	169
organism subdivision	8.17e-33	365
head	2.27e-32	123
ectoderm	5.24e-32	173
presumptive ectoderm	5.24e-32	173
anterior region of body	1.15e-29	129
craniocervical region	1.15e-29	129
multi-cellular organism	4.66e-29	659
neural plate	4.92e-28	86
presumptive neural plate	4.92e-28	86
anatomical system	7.83e-28	625
anatomical group	1.63e-27	626
neural tube	4.51e-27	57
neural rod	4.51e-27	57
future spinal cord	4.51e-27	57
neural keel	4.51e-27	57
neurectoderm	6.06e-26	90
regional part of brain	1.29e-25	59
brain	1.34e-25	69
future brain	1.34e-25	69
central nervous system	1.69e-25	82
epithelium	3.51e-24	309
anatomical conduit	3.97e-24	241
cell layer	4.41e-24	312
anatomical cluster	1.02e-23	286
regional part of nervous system	3.58e-23	94
nervous system	3.58e-23	94
multi-tissue structure	3.77e-22	347
organ part	6.82e-21	219
adult organism	2.90e-20	115
tube	6.15e-20	194
regional part of forebrain	1.27e-19	41
forebrain	1.27e-19	41
future forebrain	1.27e-19	41
gray matter	1.80e-19	34
brain grey matter	1.80e-19	34
organ	1.83e-19	511
telencephalon	2.28e-19	34
pre-chordal neural plate	2.48e-19	61
anterior neural tube	2.59e-19	42
cerebral hemisphere	7.32e-19	32
regional part of telencephalon	1.00e-18	33
embryonic structure	1.06e-17	605
developing anatomical structure	1.06e-17	605
embryo	1.15e-17	612
germ layer	1.61e-17	604
embryonic tissue	1.61e-17	604
presumptive structure	1.61e-17	604
epiblast (generic)	1.61e-17	604
cerebral cortex	1.50e-14	25
pallium	1.50e-14	25
regional part of cerebral cortex	2.71e-14	22
neocortex	4.31e-13	20
posterior neural tube	6.06e-09	15
chordal neural plate	6.06e-09	15
surface structure	8.45e-09	95
somite	3.73e-08	83
paraxial mesoderm	3.73e-08	83
presomitic mesoderm	3.73e-08	83
presumptive segmental plate	3.73e-08	83
trunk paraxial mesoderm	3.73e-08	83
presumptive paraxial mesoderm	3.73e-08	83
splanchnic layer of lateral plate mesoderm	9.47e-08	84
segmental subdivision of hindbrain	2.49e-07	12
hindbrain	2.49e-07	12
presumptive hindbrain	2.49e-07	12
segmental subdivision of nervous system	3.68e-07	13
vasculature	3.93e-07	79
vascular system	3.93e-07	79

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

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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

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No analysis results for this cluster

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

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This analysis result is provided for C0 - C305 clusters.