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
regional part of nervous system	4.92e-35	94
nervous system	4.92e-35	94
central nervous system	5.38e-35	82
adult organism	7.56e-33	115
neural plate	1.56e-32	86
presumptive neural plate	1.56e-32	86
neurectoderm	1.82e-32	90
neural tube	1.29e-31	57
neural rod	1.29e-31	57
future spinal cord	1.29e-31	57
neural keel	1.29e-31	57
ectoderm	1.06e-28	173
presumptive ectoderm	1.06e-28	173
brain	1.99e-28	69
future brain	1.99e-28	69
ectoderm-derived structure	2.38e-28	169
pre-chordal neural plate	2.00e-27	61
regional part of brain	3.24e-27	59
anterior region of body	2.17e-26	129
craniocervical region	2.17e-26	129
anterior neural tube	1.39e-25	42
regional part of forebrain	1.52e-25	41
forebrain	1.52e-25	41
future forebrain	1.52e-25	41
head	9.43e-25	123
telencephalon	1.50e-21	34
gray matter	1.88e-21	34
brain grey matter	1.88e-21	34
regional part of telencephalon	7.68e-21	33
cerebral hemisphere	8.90e-21	32
cerebral cortex	8.09e-17	25
pallium	8.09e-17	25
regional part of cerebral cortex	4.87e-16	22
neocortex	5.21e-15	20
organism subdivision	6.39e-08	365
posterior neural tube	2.69e-07	15
chordal neural plate	2.69e-07	15
multi-cellular organism	3.62e-07	659
embryo	6.05e-07	612
organ part	6.10e-07	219

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.