Coexpression cluster:C535

Full id: C535_medulloblastoma_small_pineal_retinoblastoma_eye_Retinal_retina

Phase1 CAGE Peaks

Hg19::chr11:67290913..67290920,-	p1@CABP2
Hg19::chr14:57268994..57269015,+	p@chr14:57268994..57269015 +
Hg19::chr14:57271021..57271034,-	p@chr14:57271021..57271034 -
Hg19::chr14:57271062..57271079,-	p@chr14:57271062..57271079 -
Hg19::chr14:57277178..57277203,-	p1@OTX2
Hg19::chr14:57278918..57278927,-	p@chr14:57278918..57278927 -
Hg19::chr15:75918721..75918732,-	p7@SNUPN
Hg19::chr17:55952035..55952049,-	p@chr17:55952035..55952049 -
Hg19::chr17:67712324..67712342,+	p@chr17:67712324..67712342 +
Hg19::chr1:205426201..205426247,-	p@chr1:205426201..205426247 -
Hg19::chr1:54791102..54791151,-	p6@SSBP3
Hg19::chr22:29025920..29025935,-	p@chr22:29025920..29025935 -
Hg19::chr2:20552002..20552029,-	p7@PUM2
Hg19::chr3:52001448..52001478,-	p2@PCBP4
Hg19::chr6:35480705..35480718,-	p4@TULP1
Hg19::chr7:105241331..105241343,-	p2@EFCAB10
Hg19::chrX:118425471..118425477,+	p1@ENST00000428222

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:0042706	eye photoreceptor cell fate commitment	0.0171023195572825
GO:0046552	photoreceptor cell fate commitment	0.0171023195572825
GO:0040036	regulation of fibroblast growth factor receptor signaling pathway	0.0265895153713653
GO:0003723	RNA binding	0.0265895153713653
GO:0008190	eukaryotic initiation factor 4E binding	0.0265895153713653
GO:0031369	translation initiation factor binding	0.0265895153713653
GO:0000339	RNA cap binding	0.0265895153713653
GO:0008589	regulation of smoothened signaling pathway	0.0265895153713653
GO:0001754	eye photoreceptor cell differentiation	0.0265895153713653
GO:0030901	midbrain development	0.0273468007267111
GO:0046530	photoreceptor cell differentiation	0.0310704218977338
GO:0007224	smoothened signaling pathway	0.0360475526660574
GO:0048663	neuron fate commitment	0.0360475526660574
GO:0001708	cell fate specification	0.0360475526660574
GO:0008543	fibroblast growth factor receptor signaling pathway	0.0360475526660574
GO:0003676	nucleic acid binding	0.0360475526660574
GO:0030426	growth cone	0.0360475526660574
GO:0030427	site of polarized growth	0.0360475526660574
GO:0048592	eye morphogenesis	0.0454975813188519
GO:0042472	inner ear morphogenesis	0.0454975813188519
GO:0009953	dorsal/ventral pattern formation	0.0454975813188519
GO:0042471	ear morphogenesis	0.0480699371691776

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>

---

Cell Type

Ontology term	p-value	n
embryonic stem cell	1.67e-22	5
neuron	3.42e-09	6
neuroblast	3.42e-09	6
electrically signaling cell	3.42e-09	6
pigment cell	1.79e-08	14
neural cell	1.03e-07	25
neuronal stem cell	4.15e-07	8
neurectodermal cell	5.15e-07	59

Uber Anatomy

Ontology term	p-value	n
pineal body	5.25e-26	2
regional part of epithalamus	5.25e-26	2
secretory circumventricular organ	5.25e-26	2
circumventricular organ	5.25e-26	2
epithalamus	5.25e-26	2
retina	1.51e-19	6
photoreceptor array	1.51e-19	6
posterior segment of eyeball	1.51e-19	6
gland of diencephalon	1.62e-13	4
neuroendocrine gland	1.62e-13	4
regional part of diencephalon	1.62e-13	4
eye	6.66e-10	21
visual system	6.66e-10	21
sense organ	1.09e-08	24
sensory system	1.09e-08	24
entire sense organ system	1.09e-08	24
diencephalon	4.12e-08	7
future diencephalon	4.12e-08	7
central nervous system	8.54e-07	81

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

---

No analysis results for this cluster

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.