Coexpression cluster:C3468

Full id: C3468_non_iPS_pons_H9_teratocarcinoma_caudate_brain

Phase1 CAGE Peaks

Hg19::chr14:96342981..96343004,+	p2@LOC100507043
Hg19::chr14:96343050..96343059,+	p4@LOC100507043
Hg19::chr14:96343100..96343115,+	p1@LOC100507043

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	6.47e-13	5
oligodendrocyte	9.56e-08	7
macroglial cell	9.56e-08	7
astrocyte	9.56e-08	7
oligodendrocyte precursor cell	9.56e-08	7
astrocyte of the cerebral cortex	8.74e-07	3

Uber Anatomy

Ontology term	p-value	n
neural tube	2.20e-59	57
neural rod	2.20e-59	57
future spinal cord	2.20e-59	57
neural keel	2.20e-59	57
central nervous system	4.26e-56	82
regional part of nervous system	3.86e-53	94
nervous system	3.86e-53	94
brain	2.81e-51	69
future brain	2.81e-51	69
regional part of brain	4.04e-51	59
telencephalon	6.69e-49	34
cerebral hemisphere	9.16e-49	32
gray matter	1.29e-48	34
brain grey matter	1.29e-48	34
regional part of telencephalon	7.67e-47	33
regional part of forebrain	1.67e-45	41
forebrain	1.67e-45	41
future forebrain	1.67e-45	41
anterior neural tube	3.26e-44	42
neural plate	1.73e-43	86
presumptive neural plate	1.73e-43	86
neurectoderm	5.77e-41	90
cerebral cortex	7.69e-35	25
pallium	7.69e-35	25
pre-chordal neural plate	6.25e-34	61
regional part of cerebral cortex	1.01e-29	22
head	1.44e-27	123
neocortex	3.63e-26	20
anterior region of body	1.11e-25	129
craniocervical region	1.11e-25	129
adult organism	2.80e-24	115
ectoderm-derived structure	2.93e-23	169
ectoderm	2.15e-22	173
presumptive ectoderm	2.15e-22	173
posterior neural tube	1.13e-15	15
chordal neural plate	1.13e-15	15
nucleus of brain	4.91e-15	9
neural nucleus	4.91e-15	9
segmental subdivision of hindbrain	1.93e-13	12
hindbrain	1.93e-13	12
presumptive hindbrain	1.93e-13	12
tube	8.59e-13	194
gyrus	1.63e-12	6
segmental subdivision of nervous system	2.95e-12	13
basal ganglion	1.40e-11	9
nuclear complex of neuraxis	1.40e-11	9
aggregate regional part of brain	1.40e-11	9
collection of basal ganglia	1.40e-11	9
cerebral subcortex	1.40e-11	9
telencephalic nucleus	1.57e-11	7
corpus striatum	5.73e-10	4
striatum	5.73e-10	4
ventral part of telencephalon	5.73e-10	4
future corpus striatum	5.73e-10	4
organ part	9.08e-10	219
brainstem	2.50e-09	8
anatomical conduit	3.24e-09	241
temporal lobe	4.47e-09	7
testis	1.22e-08	8
regional part of metencephalon	1.28e-08	9
metencephalon	1.28e-08	9
future metencephalon	1.28e-08	9
caudate-putamen	7.48e-08	3
dorsal striatum	7.48e-08	3
parietal lobe	1.17e-07	5
pons	1.79e-07	3
limbic system	3.05e-07	5
occipital lobe	4.79e-07	5
epithelium	5.48e-07	309
medulla oblongata	6.80e-07	3
myelencephalon	6.80e-07	3
future myelencephalon	6.80e-07	3
cell layer	8.35e-07	312
middle temporal gyrus	9.50e-07	3

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	0.027892685061692
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00662952214895741

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.