Coexpression cluster:C3469

Full id: C3469_pons_iPS_non_H9_diencephalon_teratocarcinoma_HES3GFP

Phase1 CAGE Peaks

Hg19::chr14:96343250..96343261,+	p3@ENST00000554321
Hg19::chr14:96343264..96343291,+	p2@ENST00000554321
Hg19::chr14:96343299..96343304,+	p4@ENST00000554321

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
embryonic stem cell	9.26e-18	5
astrocyte of the cerebral cortex	1.13e-09	3
oligodendrocyte	3.68e-07	7
macroglial cell	3.68e-07	7
astrocyte	3.68e-07	7
oligodendrocyte precursor cell	3.68e-07	7

Uber Anatomy

Ontology term	p-value	n
neural tube	2.18e-67	56
neural rod	2.18e-67	56
future spinal cord	2.18e-67	56
neural keel	2.18e-67	56
regional part of nervous system	2.05e-63	53
regional part of brain	2.05e-63	53
central nervous system	4.32e-58	81
nervous system	2.62e-54	89
brain	1.07e-49	68
future brain	1.07e-49	68
neural plate	1.54e-48	82
presumptive neural plate	1.54e-48	82
regional part of forebrain	1.60e-47	41
forebrain	1.60e-47	41
anterior neural tube	1.60e-47	41
future forebrain	1.60e-47	41
neurectoderm	7.63e-46	86
brain grey matter	3.15e-45	34
gray matter	3.15e-45	34
telencephalon	4.23e-45	34
cerebral hemisphere	4.29e-44	32
regional part of telencephalon	5.73e-40	32
ecto-epithelium	2.90e-36	104
pre-chordal neural plate	6.61e-35	61
cerebral cortex	5.35e-30	25
pallium	5.35e-30	25
structure with developmental contribution from neural crest	1.55e-26	132
ectoderm-derived structure	1.84e-26	171
ectoderm	1.84e-26	171
presumptive ectoderm	1.84e-26	171
adult organism	4.31e-25	114
regional part of cerebral cortex	4.28e-23	22
neocortex	6.63e-22	20
posterior neural tube	3.26e-20	15
chordal neural plate	3.26e-20	15
brainstem	1.04e-19	6
organ system subdivision	9.02e-18	223
neural nucleus	6.65e-17	9
nucleus of brain	6.65e-17	9
segmental subdivision of hindbrain	1.51e-16	12
hindbrain	1.51e-16	12
presumptive hindbrain	1.51e-16	12
segmental subdivision of nervous system	3.66e-15	13
tube	3.03e-14	192
basal ganglion	1.29e-12	9
nuclear complex of neuraxis	1.29e-12	9
aggregate regional part of brain	1.29e-12	9
collection of basal ganglia	1.29e-12	9
cerebral subcortex	1.29e-12	9
gyrus	1.41e-12	6
telencephalic nucleus	1.87e-11	7
pons	6.55e-11	3
medulla oblongata	1.58e-10	3
myelencephalon	1.58e-10	3
future myelencephalon	1.58e-10	3
anatomical conduit	1.30e-09	240
regional part of metencephalon	3.84e-09	9
metencephalon	3.84e-09	9
future metencephalon	3.84e-09	9
organ part	3.73e-08	218
corpus striatum	7.96e-08	4
striatum	7.96e-08	4
ventral part of telencephalon	7.96e-08	4
future corpus striatum	7.96e-08	4
anatomical cluster	1.12e-07	373
dorsal plus ventral thalamus	1.33e-07	2
thalamic complex	1.33e-07	2
locus ceruleus	1.42e-07	2
brainstem nucleus	1.42e-07	2
hindbrain nucleus	1.42e-07	2
globus pallidus	1.46e-07	2
pallidum	1.46e-07	2
epithelium	1.96e-07	306
temporal lobe	2.53e-07	6
cell layer	2.83e-07	309
middle temporal gyrus	7.17e-07	2

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	0.0278938324838428
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00662998951040605

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.