Coexpression cluster:C990

Full id: C990_pineal_occipital_merkel_Lens_medial_parietal_middle

Phase1 CAGE Peaks

Hg19::chr11:124589340..124589351,+	p@chr11:124589340..124589351 +
Hg19::chr12:57735480..57735493,-	p9@R3HDM2
Hg19::chr9:77112225..77112238,+	p2@RORB
Hg19::chr9:77112244..77112262,+	p1@RORB
Hg19::chr9:77114317..77114328,-	p3@ENST00000417576
Hg19::chr9:77114341..77114368,-	p1@ENST00000417576
Hg19::chr9:77114385..77114400,-	p2@ENST00000417576
Hg19::chr9:77302053..77302065,+	p@chr9:77302053..77302065 +

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0042462	eye photoreceptor cell development	0.00918254698947879
GO:0001754	eye photoreceptor cell differentiation	0.00918254698947879
GO:0042461	photoreceptor cell development	0.00918254698947879
GO:0043193	positive regulation of gene-specific transcription	0.00918254698947879
GO:0046530	photoreceptor cell differentiation	0.00918254698947879
GO:0032583	regulation of gene-specific transcription	0.00918254698947879
GO:0048592	eye morphogenesis	0.0170497870118158
GO:0001654	eye development	0.0269598341411594
GO:0007423	sensory organ development	0.0438243772124945

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><br>uberon_data<br><br>

---

Uber Anatomy

Ontology term	p-value	n
neural tube	4.19e-55	56
neural rod	4.19e-55	56
future spinal cord	4.19e-55	56
neural keel	4.19e-55	56
regional part of nervous system	2.00e-50	53
regional part of brain	2.00e-50	53
central nervous system	2.87e-50	81
regional part of forebrain	1.73e-49	41
forebrain	1.73e-49	41
anterior neural tube	1.73e-49	41
future forebrain	1.73e-49	41
nervous system	5.51e-48	89
neural plate	7.75e-48	82
presumptive neural plate	7.75e-48	82
brain	1.38e-47	68
future brain	1.38e-47	68
neurectoderm	4.05e-47	86
pre-chordal neural plate	1.41e-45	61
adult organism	6.01e-43	114
telencephalon	9.26e-41	34
brain grey matter	2.89e-40	34
gray matter	2.89e-40	34
neocortex	4.25e-38	20
ecto-epithelium	4.94e-38	104
cerebral hemisphere	8.49e-38	32
regional part of cerebral cortex	1.07e-37	22
regional part of telencephalon	2.27e-37	32
cerebral cortex	1.55e-32	25
pallium	1.55e-32	25
ectoderm-derived structure	1.21e-31	171
ectoderm	1.21e-31	171
presumptive ectoderm	1.21e-31	171
structure with developmental contribution from neural crest	1.75e-29	132
organ system subdivision	2.30e-17	223
gyrus	1.85e-13	6
occipital lobe	1.24e-11	5
anatomical cluster	1.24e-11	373
tube	1.47e-11	192
parietal lobe	2.04e-11	5
temporal lobe	8.89e-11	6
anatomical conduit	8.95e-11	240
epithelium	3.27e-10	306
diencephalon	5.82e-10	7
future diencephalon	5.82e-10	7
cell layer	5.85e-10	309
basal ganglion	1.36e-09	9
nuclear complex of neuraxis	1.36e-09	9
aggregate regional part of brain	1.36e-09	9
collection of basal ganglia	1.36e-09	9
cerebral subcortex	1.36e-09	9
neural nucleus	3.13e-09	9
nucleus of brain	3.13e-09	9
regional part of diencephalon	1.09e-08	4
embryo	1.09e-08	592
multi-tissue structure	2.11e-08	342
posterior neural tube	3.98e-08	15
chordal neural plate	3.98e-08	15
multi-cellular organism	4.99e-08	656
organ part	5.42e-08	218
embryonic structure	9.65e-08	564
frontal cortex	1.64e-07	3
germ layer	1.93e-07	560
germ layer / neural crest	1.93e-07	560
embryonic tissue	1.93e-07	560
presumptive structure	1.93e-07	560
germ layer / neural crest derived structure	1.93e-07	560
epiblast (generic)	1.93e-07	560
developing anatomical structure	2.63e-07	581
organ	2.71e-07	503
brainstem	3.08e-07	6
limbic system	9.97e-07	5

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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ZNF263#10127	5	5.13865102313167	0.00108253124903356	0.00764063533944823

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

---

This analysis result is provided for C0 - C305 clusters.