Coexpression cluster:C4186

Full id: C4186_retina_corpus_Retinal_medulla_eye_pons_spinal

Phase1 CAGE Peaks

Hg19::chr2:219610834..219610846,+	p11@TTLL4
Hg19::chr2:219610848..219610865,+	p6@TTLL4
Hg19::chr2:219610868..219610888,+	p9@TTLL4

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
pigment cell	1.96e-08	14
visual pigment cell	4.32e-07	4

Uber Anatomy

Ontology term	p-value	n
neural tube	5.81e-57	57
neural rod	5.81e-57	57
future spinal cord	5.81e-57	57
neural keel	5.81e-57	57
regional part of nervous system	1.50e-49	94
nervous system	1.50e-49	94
central nervous system	6.17e-49	82
neural plate	5.82e-47	86
presumptive neural plate	5.82e-47	86
regional part of brain	8.56e-47	59
brain	4.62e-45	69
future brain	4.62e-45	69
regional part of forebrain	8.93e-45	41
forebrain	8.93e-45	41
future forebrain	8.93e-45	41
neurectoderm	4.99e-44	90
telencephalon	1.82e-43	34
anterior neural tube	2.02e-43	42
gray matter	3.40e-43	34
brain grey matter	3.40e-43	34
regional part of telencephalon	7.10e-42	33
adult organism	7.55e-41	115
cerebral hemisphere	2.98e-40	32
pre-chordal neural plate	5.35e-36	61
ectoderm-derived structure	1.74e-34	169
head	4.77e-34	123
ectoderm	3.72e-33	173
presumptive ectoderm	3.72e-33	173
anterior region of body	9.24e-33	129
craniocervical region	9.24e-33	129
cerebral cortex	4.35e-30	25
pallium	4.35e-30	25
regional part of cerebral cortex	6.78e-27	22
neocortex	3.38e-24	20
tube	5.64e-20	194
anatomical conduit	5.19e-16	241
nucleus of brain	1.60e-14	9
neural nucleus	1.60e-14	9
basal ganglion	2.30e-14	9
nuclear complex of neuraxis	2.30e-14	9
aggregate regional part of brain	2.30e-14	9
collection of basal ganglia	2.30e-14	9
cerebral subcortex	2.30e-14	9
posterior neural tube	3.70e-14	15
chordal neural plate	3.70e-14	15
epithelium	3.24e-12	309
cell layer	6.82e-12	312
organism subdivision	8.64e-12	365
telencephalic nucleus	1.25e-11	7
segmental subdivision of nervous system	1.61e-11	13
organ part	1.84e-11	219
anatomical cluster	1.86e-11	286
brainstem	1.50e-10	8
segmental subdivision of hindbrain	3.59e-10	12
hindbrain	3.59e-10	12
presumptive hindbrain	3.59e-10	12
organ	4.16e-10	511
gyrus	5.24e-10	6
temporal lobe	1.83e-09	7
multi-tissue structure	1.92e-09	347
limbic system	1.28e-08	5
parietal lobe	1.67e-08	5
embryo	7.63e-08	612
corpus striatum	2.06e-07	4
striatum	2.06e-07	4
ventral part of telencephalon	2.06e-07	4
future corpus striatum	2.06e-07	4

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
EP300#2033	3	6.7739417262232	0.00321688050010379	0.016781607519997
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00243505279166128
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00392144522886912
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123039146119282
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000758175675696141
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00665768095746212
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247103529161172
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00615224681012387

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.