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

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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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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>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	6.19e-24	180
embryonic cell	1.51e-17	248
ectodermal cell	2.00e-13	71
neurectodermal cell	7.64e-13	59
electrically responsive cell	8.77e-11	60
electrically active cell	8.77e-11	60
neural cell	1.46e-10	25
contractile cell	2.98e-09	59
migratory neural crest cell	8.97e-09	41
muscle precursor cell	3.28e-08	57
myoblast	3.28e-08	57
multi-potent skeletal muscle stem cell	3.28e-08	57
muscle cell	4.13e-08	54
fibroblast	7.45e-08	75
mesodermal cell	1.42e-07	119
smooth muscle cell	3.32e-07	42
smooth muscle myoblast	3.32e-07	42

Uber Anatomy

Ontology term	p-value	n
epithelium	1.38e-29	309
cell layer	7.97e-29	312
regional part of nervous system	4.82e-28	94
nervous system	4.82e-28	94
ectoderm-derived structure	6.85e-28	169
ectoderm	9.38e-28	173
presumptive ectoderm	9.38e-28	173
organism subdivision	2.01e-27	365
central nervous system	2.49e-23	82
tube	1.06e-19	194
neural plate	9.76e-19	86
presumptive neural plate	9.76e-19	86
neurectoderm	2.10e-18	90
brain	6.64e-18	69
future brain	6.64e-18	69
anatomical conduit	2.52e-17	241
neural tube	6.26e-17	57
neural rod	6.26e-17	57
future spinal cord	6.26e-17	57
neural keel	6.26e-17	57
multi-cellular organism	1.39e-16	659
head	1.91e-16	123
multi-tissue structure	7.39e-16	347
regional part of brain	7.64e-15	59
anterior region of body	1.07e-14	129
craniocervical region	1.07e-14	129
embryo	6.64e-14	612
anatomical system	1.49e-13	625
anatomical group	1.81e-13	626
anatomical cluster	3.19e-13	286
pre-chordal neural plate	4.88e-13	61
embryonic structure	1.91e-11	605
developing anatomical structure	1.91e-11	605
germ layer	2.10e-11	604
embryonic tissue	2.10e-11	604
presumptive structure	2.10e-11	604
epiblast (generic)	2.10e-11	604
regional part of forebrain	5.65e-11	41
forebrain	5.65e-11	41
future forebrain	5.65e-11	41
anterior neural tube	2.07e-10	42
trunk mesenchyme	2.83e-10	143
somite	7.67e-10	83
paraxial mesoderm	7.67e-10	83
presomitic mesoderm	7.67e-10	83
presumptive segmental plate	7.67e-10	83
trunk paraxial mesoderm	7.67e-10	83
presumptive paraxial mesoderm	7.67e-10	83
organ part	1.05e-09	219
gray matter	3.75e-09	34
brain grey matter	3.75e-09	34
telencephalon	4.11e-09	34
dermomyotome	4.16e-09	70
multilaminar epithelium	6.26e-09	82
skeletal muscle tissue	7.26e-09	61
striated muscle tissue	7.26e-09	61
myotome	7.26e-09	61
regional part of telencephalon	8.47e-09	33
muscle tissue	2.22e-08	63
musculature	2.22e-08	63
musculature of body	2.22e-08	63
posterior neural tube	2.35e-08	15
chordal neural plate	2.35e-08	15
epithelial tube	3.04e-08	118
segmental subdivision of nervous system	3.34e-08	13
cerebral hemisphere	3.85e-08	32
segmental subdivision of hindbrain	1.08e-07	12
hindbrain	1.08e-07	12
presumptive hindbrain	1.08e-07	12

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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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

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This analysis result is provided for C0 - C305 clusters.