Coexpression cluster:C3408

Full id: C3408_cerebellum_pineal_rhabdomyosarcoma_neuroectodermal_brain_Pericytes_iPS

Phase1 CAGE Peaks

Hg19::chr14:21994337..21994442,-	p1@SALL2
Hg19::chr14:21994449..21994524,-	p2@SALL2
Hg19::chr19:49149553..49149602,-	p4@CA11

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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No GOStat results

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
neurectodermal cell	1.53e-07	59
neural cell	7.25e-07	25

Uber Anatomy

Ontology term	p-value	n
central nervous system	1.60e-39	81
nervous system	1.83e-39	89
neurectoderm	5.83e-37	86
neural plate	7.65e-35	82
presumptive neural plate	7.65e-35	82
brain	1.08e-32	68
future brain	1.08e-32	68
neural tube	1.18e-32	56
neural rod	1.18e-32	56
future spinal cord	1.18e-32	56
neural keel	1.18e-32	56
regional part of nervous system	7.96e-31	53
regional part of brain	7.96e-31	53
ectoderm-derived structure	9.82e-31	171
ectoderm	9.82e-31	171
presumptive ectoderm	9.82e-31	171
anatomical cluster	2.71e-29	373
adult organism	2.84e-28	114
structure with developmental contribution from neural crest	2.23e-27	132
pre-chordal neural plate	1.31e-26	61
ecto-epithelium	1.40e-25	104
organ system subdivision	1.47e-25	223
multi-tissue structure	1.26e-24	342
regional part of forebrain	1.19e-23	41
forebrain	1.19e-23	41
anterior neural tube	1.19e-23	41
future forebrain	1.19e-23	41
cell layer	5.56e-20	309
brain grey matter	1.18e-19	34
gray matter	1.18e-19	34
telencephalon	2.52e-19	34
epithelium	3.83e-19	306
regional part of telencephalon	2.20e-18	32
cerebral hemisphere	2.61e-18	32
tube	1.52e-15	192
anatomical conduit	7.62e-15	240
cerebral cortex	2.61e-14	25
pallium	2.61e-14	25
regional part of cerebral cortex	1.37e-13	22
neocortex	1.54e-12	20
posterior neural tube	4.58e-10	15
chordal neural plate	4.58e-10	15
embryo	7.19e-10	592
organ part	1.72e-09	218
segmental subdivision of nervous system	9.20e-09	13
multi-cellular organism	1.02e-08	656
segmental subdivision of hindbrain	2.31e-08	12
hindbrain	2.31e-08	12
presumptive hindbrain	2.31e-08	12
developing anatomical structure	1.38e-07	581
compound organ	7.23e-07	68
neural nucleus	7.74e-07	9
nucleus of brain	7.74e-07	9
regional part of metencephalon	7.89e-07	9
metencephalon	7.89e-07	9
future metencephalon	7.89e-07	9

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
BCL3#602	2	23.0314018691589	0.00246467476084291	0.0138495731920624
CTBP2#1488	2	41.8113335595521	0.000754340825991485	0.00593376527270654
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321207453625705
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319685244901288
GATA3#2625	2	18.1576775714707	0.00394454681927962	0.0189426395649597
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156401298968889
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245887012854144
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00628487971055167
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328544814207018
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139829331590944
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109118037366963

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.