Coexpression cluster:C699

Full id: C699_medulloblastoma_Lens_neuroblastoma_Ciliary_eye_small_cerebellum

Phase1 CAGE Peaks

Hg19::chr13:36045322..36045356,+	p9@NBEA
Hg19::chr13:36046061..36046077,+	p@chr13:36046061..36046077 +
Hg19::chr13:36046127..36046134,+	p@chr13:36046127..36046134 +
Hg19::chr13:36046521..36046554,+	p@chr13:36046521..36046554 +
Hg19::chr13:36050790..36050807,-	p2@MAB21L1
Hg19::chr13:36050819..36050834,-	p1@MAB21L1
Hg19::chr13:36050881..36050887,+	p3@NBEA
Hg19::chr13:36050940..36050952,+	p2@NBEA
Hg19::chr13:36050956..36050969,+	p4@NBEA
Hg19::chr13:36050976..36050990,+	p8@NBEA
Hg19::chr13:36052762..36052767,-	p@chr13:36052762..36052767 -
Hg19::chr13:36052779..36052793,-	p@chr13:36052779..36052793 -

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:0005802	trans-Golgi network	0.0296627598117251

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	6.95e-16	180
fibroblast	1.10e-13	75
stuff accumulating cell	2.18e-09	39
skin fibroblast	7.51e-09	23
fat cell	1.58e-07	15

Uber Anatomy

Ontology term	p-value	n
anterior region of body	6.90e-24	129
craniocervical region	6.90e-24	129
head	8.91e-24	123
ectoderm-derived structure	3.92e-23	169
neural plate	4.26e-23	86
presumptive neural plate	4.26e-23	86
ectoderm	1.17e-22	173
presumptive ectoderm	1.17e-22	173
neurectoderm	4.00e-22	90
organism subdivision	1.84e-20	365
regional part of nervous system	1.44e-18	94
nervous system	1.44e-18	94
pre-chordal neural plate	1.33e-16	61
neural tube	1.49e-16	57
neural rod	1.49e-16	57
future spinal cord	1.49e-16	57
neural keel	1.49e-16	57
regional part of brain	7.44e-15	59
central nervous system	8.74e-15	82
brain	9.90e-14	69
future brain	9.90e-14	69
adult organism	1.86e-13	115
subdivision of head	6.55e-13	48
surface structure	3.04e-11	95
face	6.36e-10	21
eye	9.18e-10	20
sense organ	1.38e-09	23
posterior neural tube	1.66e-09	15
chordal neural plate	1.66e-09	15
anterior neural tube	2.35e-09	42
camera-type eye	4.99e-09	19
simple eye	4.99e-09	19
ocular region	4.99e-09	19
optic cup	4.99e-09	19
eye primordium	4.99e-09	19
optic vesicle	4.99e-09	19
visual system	6.78e-09	21
multi-tissue structure	7.16e-09	347
regional part of forebrain	7.92e-09	41
forebrain	7.92e-09	41
future forebrain	7.92e-09	41
sensory system	8.28e-09	24
entire sense organ system	8.28e-09	24
gray matter	7.50e-08	34
brain grey matter	7.50e-08	34
pigment epithelium of eye	8.26e-08	11
segmental subdivision of hindbrain	1.03e-07	12
hindbrain	1.03e-07	12
presumptive hindbrain	1.03e-07	12
integument	2.16e-07	45
integumental system	2.16e-07	45
cell layer	2.40e-07	312
telencephalon	4.41e-07	34
regional part of telencephalon	5.11e-07	33
somite	5.54e-07	83
paraxial mesoderm	5.54e-07	83
presomitic mesoderm	5.54e-07	83
presumptive segmental plate	5.54e-07	83
trunk paraxial mesoderm	5.54e-07	83
presumptive paraxial mesoderm	5.54e-07	83
ectodermal placode	8.54e-07	29
cerebral hemisphere	9.98e-07	32

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
REST#5978	7	5.62918341774135	6.32358000930756e-05	0.00103224190777129
SUZ12#23512	12	50.1157809110629	3.91454139263279e-21	1.04293568496218e-18

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.