Coexpression cluster:C798

Full id: C798_cerebellum_small_carcinosarcoma_argyrophil_Neural_gastric_Ciliary

Phase1 CAGE Peaks

Hg19::chr11:31816236..31816261,-	p@chr11:31816236..31816261 -
Hg19::chr11:31816304..31816311,-	p@chr11:31816304..31816311 -
Hg19::chr11:31819053..31819055,-	p@chr11:31819053..31819055 -
Hg19::chr11:31832581..31832601,-	p7@PAX6
Hg19::chr11:31832610..31832639,-	p5@PAX6
Hg19::chr11:31832658..31832681,-	p1@PAX6
Hg19::chr11:31832687..31832704,-	p6@PAX6
Hg19::chr11:31832807..31832823,-	p4@PAX6
Hg19::chr11:31832862..31832884,-	p2@PAX6
Hg19::chr11:31833011..31833025,+	p@chr11:31833011..31833025 +

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
neural cell	2.73e-09	25
neuron associated cell	2.02e-07	17
neuron associated cell (sensu Vertebrata)	2.02e-07	17

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	3.13e-45	94
nervous system	3.13e-45	94
neurectoderm	9.90e-42	90
central nervous system	1.72e-40	82
neural plate	3.12e-40	86
presumptive neural plate	3.12e-40	86
neural tube	7.53e-38	57
neural rod	7.53e-38	57
future spinal cord	7.53e-38	57
neural keel	7.53e-38	57
brain	1.96e-35	69
future brain	1.96e-35	69
regional part of brain	6.22e-34	59
pre-chordal neural plate	4.63e-33	61
ectoderm	3.57e-29	173
presumptive ectoderm	3.57e-29	173
regional part of forebrain	1.75e-28	41
forebrain	1.75e-28	41
future forebrain	1.75e-28	41
head	4.12e-28	123
anterior region of body	8.24e-28	129
craniocervical region	8.24e-28	129
ectoderm-derived structure	1.00e-27	169
anterior neural tube	2.60e-27	42
gray matter	3.42e-24	34
brain grey matter	3.42e-24	34
telencephalon	3.64e-24	34
regional part of telencephalon	1.25e-23	33
cerebral hemisphere	5.38e-23	32
cerebral cortex	1.98e-18	25
pallium	1.98e-18	25
regional part of cerebral cortex	5.06e-16	22
neocortex	1.55e-14	20
posterior neural tube	1.71e-11	15
chordal neural plate	1.71e-11	15
adult organism	2.75e-11	115
segmental subdivision of nervous system	1.68e-09	13
pigment epithelium of eye	1.82e-09	11
segmental subdivision of hindbrain	2.22e-09	12
hindbrain	2.22e-09	12
presumptive hindbrain	2.22e-09	12
visual system	2.94e-08	21
eye	4.85e-08	20
organ part	6.53e-08	219
sensory system	1.16e-07	24
entire sense organ system	1.16e-07	24
sense organ	1.95e-07	23
basal ganglion	2.02e-07	9
nuclear complex of neuraxis	2.02e-07	9
aggregate regional part of brain	2.02e-07	9
collection of basal ganglia	2.02e-07	9
cerebral subcortex	2.02e-07	9
regional part of metencephalon	2.27e-07	9
metencephalon	2.27e-07	9
future metencephalon	2.27e-07	9
camera-type eye	2.47e-07	19
simple eye	2.47e-07	19
ocular region	2.47e-07	19
optic cup	2.47e-07	19
eye primordium	2.47e-07	19
optic vesicle	2.47e-07	19
nucleus of brain	3.35e-07	9
neural nucleus	3.35e-07	9
temporal lobe	9.70e-07	7

Disease

Ontology term	p-value	n
cell type cancer	1.43e-12	143
cancer	4.66e-10	235
disease of cellular proliferation	5.66e-10	239
carcinoma	9.28e-09	106

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
CCNT2#905	7	4.43534110387384	0.000187529269757189	0.00226735001205963
CEBPB#1051	7	5.57980333807737	4.14051761029175e-05	0.000751532010255926
CTBP2#1488	7	43.9019002375297	2.99349477998484e-11	3.4698956862024e-09
E2F4#1874	7	8.86764222069911	1.84731179412716e-06	6.85369081587377e-05
E2F6#1876	7	3.51200901218817	0.000845395041948297	0.00637258843637951
ELF1#1997	7	2.98066857116528	0.00237820287046913	0.0134731288087294
FOS#2353	7	6.29856871622608	1.848304348188e-05	0.00041991528784078
HDAC2#3066	6	8.04937214197576	2.76518202234458e-05	0.000584600901278635
JUND#3727	7	4.89626475930972	9.81446965345405e-05	0.00139173577208023
MAX#4149	7	4.51678885630499	0.000166525450971397	0.00204152501162128
NANOG#79923	7	20.4713449367089	5.96944508093541e-09	4.74101045481227e-07
NFYA#4800	7	12.8979064898814	1.4357468212053e-07	8.1272608270927e-06
NFYB#4801	7	11.7318552774755	2.74641977103244e-07	1.40950041507055e-05
POU2F2#5452	7	6.37428684041977	1.70647444265859e-05	0.000390838781396536
SPI1#6688	7	5.74302645596591	3.41922598863134e-05	0.00067825364297563
SUZ12#23512	7	35.081046637744	1.42572395471382e-10	1.51322341571501e-08
TAF1#6872	7	2.3401324000217	0.0104083984434833	0.0386352973073269
TBP#6908	7	2.59473948096747	0.0055886690177364	0.0252727864708107
TRIM28#10155	7	13.0133675316838	1.35067750650695e-07	7.68737918812423e-06
ZNF263#10127	7	5.75528914590747	3.37110736015453e-05	0.000669217033999579

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.