Coexpression cluster:C4260

Full id: C4260_pineal_globus_thalamus_occipital_corpus_middle_extraskeletal

Phase1 CAGE Peaks

Hg19::chr3:106959530..106959548,+	p1@LOC344595
Hg19::chr3:106959552..106959576,+	p1@ENST00000473550
Hg19::chr3:106959578..106959602,+	p2@ENST00000473550

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
fibroblast	8.41e-08	76

Uber Anatomy

Ontology term	p-value	n
ectoderm-derived structure	2.79e-35	171
ectoderm	2.79e-35	171
presumptive ectoderm	2.79e-35	171
nervous system	1.77e-34	89
central nervous system	2.54e-34	81
brain	5.34e-33	68
future brain	5.34e-33	68
neural tube	6.27e-31	56
neural rod	6.27e-31	56
future spinal cord	6.27e-31	56
neural keel	6.27e-31	56
neural plate	2.23e-30	82
presumptive neural plate	2.23e-30	82
structure with developmental contribution from neural crest	1.13e-29	132
regional part of nervous system	3.60e-29	53
regional part of brain	3.60e-29	53
neurectoderm	6.59e-29	86
ecto-epithelium	3.64e-28	104
regional part of forebrain	1.70e-25	41
forebrain	1.70e-25	41
anterior neural tube	1.70e-25	41
future forebrain	1.70e-25	41
pre-chordal neural plate	3.07e-24	61
organ system subdivision	4.00e-22	223
adult organism	4.77e-22	114
multi-tissue structure	1.26e-21	342
telencephalon	1.87e-21	34
brain grey matter	2.31e-21	34
gray matter	2.31e-21	34
anatomical cluster	7.42e-21	373
regional part of telencephalon	3.93e-20	32
cerebral hemisphere	4.38e-20	32
cerebral cortex	1.03e-15	25
pallium	1.03e-15	25
epithelium	2.23e-15	306
cell layer	3.07e-15	309
regional part of cerebral cortex	6.62e-15	22
multi-cellular organism	2.19e-14	656
neocortex	8.72e-14	20
organ part	7.07e-12	218
anatomical system	1.21e-11	624
embryonic structure	1.66e-11	564
anatomical group	1.83e-11	625
anatomical conduit	4.31e-11	240
germ layer	1.11e-10	560
germ layer / neural crest	1.11e-10	560
embryonic tissue	1.11e-10	560
presumptive structure	1.11e-10	560
germ layer / neural crest derived structure	1.11e-10	560
epiblast (generic)	1.11e-10	560
developing anatomical structure	1.81e-10	581
embryo	1.10e-09	592
tube	3.10e-08	192
organ	1.03e-07	503
neural nucleus	4.04e-07	9
nucleus of brain	4.04e-07	9
basal ganglion	4.15e-07	9
nuclear complex of neuraxis	4.15e-07	9
aggregate regional part of brain	4.15e-07	9
collection of basal ganglia	4.15e-07	9
cerebral subcortex	4.15e-07	9
posterior neural tube	8.01e-07	15
chordal neural plate	8.01e-07	15

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326458123496503
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323304714631901
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321579042453732
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00721564015427261
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295319948852449
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00472290649147904

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.