Coexpression cluster:C4238

Full id: C4238_brain_nonsmall_spinal_Olfactory_insula_frontal_temporal

Phase1 CAGE Peaks

Hg19::chr2:56410948..56411039,+	p2@CCDC85A
Hg19::chr2:56411109..56411130,+	p4@CCDC85A
Hg19::chr2:56411131..56411187,+	p1@CCDC85A

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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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>

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Cell Type

Ontology term	p-value	n
mesodermal cell	2.97e-09	121
lining cell	1.44e-07	58
barrier cell	1.44e-07	58
endothelial cell of vascular tree	2.02e-07	24

Uber Anatomy

Ontology term	p-value	n
adult organism	1.37e-31	114
tube	1.09e-23	192
neural tube	1.29e-22	56
neural rod	1.29e-22	56
future spinal cord	1.29e-22	56
neural keel	1.29e-22	56
neural plate	1.46e-20	82
presumptive neural plate	1.46e-20	82
regional part of nervous system	1.68e-20	53
regional part of brain	1.68e-20	53
anatomical conduit	2.97e-19	240
regional part of forebrain	4.97e-19	41
forebrain	4.97e-19	41
anterior neural tube	4.97e-19	41
future forebrain	4.97e-19	41
brain	8.39e-19	68
future brain	8.39e-19	68
neurectoderm	2.08e-18	86
anatomical cluster	4.86e-18	373
telencephalon	5.60e-18	34
brain grey matter	1.12e-17	34
gray matter	1.12e-17	34
central nervous system	3.51e-17	81
cerebral hemisphere	9.16e-17	32
regional part of telencephalon	1.31e-16	32
regional part of cerebral cortex	2.37e-16	22
structure with developmental contribution from neural crest	4.44e-16	132
nervous system	6.74e-16	89
pre-chordal neural plate	2.83e-15	61
neocortex	3.56e-15	20
epithelial tube open at both ends	1.69e-14	59
blood vessel	1.69e-14	59
blood vasculature	1.69e-14	59
vascular cord	1.69e-14	59
vessel	3.52e-14	68
epithelium	9.43e-14	306
splanchnic layer of lateral plate mesoderm	1.02e-13	83
cerebral cortex	3.53e-13	25
pallium	3.53e-13	25
cell layer	3.65e-13	309
ecto-epithelium	3.85e-12	104
multi-cellular organism	4.41e-12	656
vasculature	6.37e-12	78
vascular system	6.37e-12	78
multi-tissue structure	9.92e-12	342
artery	6.37e-11	42
arterial blood vessel	6.37e-11	42
arterial system	6.37e-11	42
circulatory system	3.77e-09	112
cardiovascular system	2.55e-08	109
anatomical system	5.53e-08	624
systemic artery	6.13e-08	33
systemic arterial system	6.13e-08	33
aorta	6.13e-08	21
aortic system	6.13e-08	21
anatomical group	7.35e-08	625
organ part	9.47e-08	218
organ system subdivision	1.94e-07	223
epithelial tube	3.69e-07	117

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

TF	#promoters	Enrichment	p-value	q-value
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.019052471480264
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280264186926401
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108924480269722
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00665862370469484
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00309805669473797
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330218426265306
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389888162758854
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109691370507428

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.