Coexpression cluster:C3981

Full id: C3981_Astrocyte_trachea_Chondrocyte_Ciliary_retina_Retinal_merkel

Phase1 CAGE Peaks

Hg19::chr1:40782923..40782936,-	p4@COL9A2
Hg19::chr1:40782938..40782974,-	p1@COL9A2
Hg19::chr1:40782976..40782993,-	p5@COL9A2

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
neuronal stem cell	3.03e-08	8
neural cell	6.01e-08	25
oligodendrocyte	6.35e-07	7
macroglial cell	6.35e-07	7
astrocyte	6.35e-07	7
oligodendrocyte precursor cell	6.35e-07	7
kidney tubule cell	6.75e-07	10
nephron tubule epithelial cell	6.75e-07	10

Uber Anatomy

Ontology term	p-value	n
neural plate	3.20e-42	82
presumptive neural plate	3.20e-42	82
neurectoderm	3.93e-39	86
central nervous system	2.50e-37	81
neural tube	5.02e-36	56
neural rod	5.02e-36	56
future spinal cord	5.02e-36	56
neural keel	5.02e-36	56
nervous system	2.93e-35	89
ecto-epithelium	6.90e-34	104
regional part of nervous system	2.02e-33	53
regional part of brain	2.02e-33	53
pre-chordal neural plate	2.60e-32	61
ectoderm-derived structure	9.55e-28	171
ectoderm	9.55e-28	171
presumptive ectoderm	9.55e-28	171
brain	1.81e-27	68
future brain	1.81e-27	68
adult organism	3.67e-25	114
regional part of forebrain	2.55e-24	41
forebrain	2.55e-24	41
anterior neural tube	2.55e-24	41
future forebrain	2.55e-24	41
structure with developmental contribution from neural crest	3.10e-23	132
telencephalon	2.03e-21	34
brain grey matter	2.77e-21	34
gray matter	2.77e-21	34
organ system subdivision	9.51e-20	223
regional part of telencephalon	1.47e-19	32
anatomical cluster	1.88e-19	373
cerebral hemisphere	2.08e-19	32
epithelium	2.84e-15	306
organ part	6.60e-15	218
cell layer	8.19e-15	309
multi-tissue structure	8.34e-15	342
cerebral cortex	5.86e-14	25
pallium	5.86e-14	25
posterior neural tube	7.30e-13	15
chordal neural plate	7.30e-13	15
tube	2.13e-12	192
segmental subdivision of nervous system	1.88e-11	13
neocortex	3.95e-11	20
regional part of cerebral cortex	4.54e-11	22
pigment epithelium of eye	1.68e-10	11
segmental subdivision of hindbrain	2.30e-10	12
hindbrain	2.30e-10	12
presumptive hindbrain	2.30e-10	12
eye	4.47e-10	21
visual system	4.47e-10	21
anatomical conduit	4.49e-10	240
sense organ	2.55e-09	24
sensory system	2.55e-09	24
entire sense organ system	2.55e-09	24
embryo	3.69e-09	592
neural nucleus	4.00e-09	9
nucleus of brain	4.00e-09	9
camera-type eye	4.09e-09	20
simple eye	4.09e-09	20
immature eye	4.09e-09	20
ocular region	4.09e-09	20
eyeball of camera-type eye	4.09e-09	20
optic cup	4.09e-09	20
optic vesicle	4.09e-09	20
eye primordium	4.09e-09	20
cavitated compound organ	1.91e-08	31
face	7.05e-08	22
regional part of metencephalon	1.31e-07	9
metencephalon	1.31e-07	9
future metencephalon	1.31e-07	9
telencephalic nucleus	2.30e-07	7
brainstem	3.18e-07	6
basal ganglion	3.86e-07	9
nuclear complex of neuraxis	3.86e-07	9
aggregate regional part of brain	3.86e-07	9
collection of basal ganglia	3.86e-07	9
cerebral subcortex	3.86e-07	9
developing anatomical structure	3.99e-07	581
nephron tubule epithelium	6.75e-07	10
vasculature of eye	6.82e-07	6
uvea	6.82e-07	6
vasculature of head	6.82e-07	6

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.027973233244626
SUZ12#23512	3	50.1157809110629	7.93834897779404e-06	0.000222749389815108
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329749085294402

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.