Coexpression cluster:C2840

Full id: C2840_retinoblastoma_embryonic_carcinoid_medulloblastoma_argyrophil_merkel_neuroblastoma

Phase1 CAGE Peaks

Hg19::chr6:119399805..119399860,-	p1@FAM184A
Hg19::chr6:119399865..119399887,-	p4@FAM184A
Hg19::chr6:119399895..119399915,-	p3@FAM184A
Hg19::chr6:119399919..119399944,-	p2@FAM184A

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.05e-37	115
regional part of nervous system	2.81e-35	94
nervous system	2.81e-35	94
central nervous system	1.23e-32	82
neural tube	3.64e-30	57
neural rod	3.64e-30	57
future spinal cord	3.64e-30	57
neural keel	3.64e-30	57
brain	2.32e-26	69
future brain	2.32e-26	69
neurectoderm	1.48e-25	90
neural plate	2.32e-25	86
presumptive neural plate	2.32e-25	86
anterior neural tube	9.08e-25	42
regional part of forebrain	9.92e-25	41
forebrain	9.92e-25	41
future forebrain	9.92e-25	41
regional part of brain	3.74e-24	59
gray matter	1.69e-20	34
brain grey matter	1.69e-20	34
telencephalon	2.39e-20	34
pre-chordal neural plate	4.28e-20	61
ectoderm	5.15e-20	173
presumptive ectoderm	5.15e-20	173
regional part of telencephalon	1.01e-19	33
ectoderm-derived structure	1.42e-19	169
cerebral hemisphere	1.43e-19	32
anterior region of body	3.04e-17	129
craniocervical region	3.04e-17	129
head	1.05e-16	123
cerebral cortex	1.79e-15	25
pallium	1.79e-15	25
regional part of cerebral cortex	9.03e-15	22
neocortex	1.52e-13	20
posterior neural tube	9.69e-07	15
chordal neural plate	9.69e-07	15

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
BHLHE40#8553	4	44.8718135469774	2.46312701995675e-07	1.28687605221242e-05
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00513389034177205
CHD2#1106	4	10.3440228341169	8.73193255208051e-05	0.00129336874742127
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00819453307291256
CTCFL#140690	4	19.7464743589744	6.5732084880439e-06	0.000193434579116037
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106768958124115
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00998891040919625
HDAC2#3066	4	13.4156202366263	3.0859005065161e-05	0.000628242423002017
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.00248563516814015
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00486247783774636
SMC3#9126	4	15.0449328449328	1.95092670935632e-05	0.000439406587445471
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0323206786638642
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244940177389303
ZBTB33#10009	4	31.6647250299812	9.93721537730495e-07	4.20686192456567e-05
ZNF263#10127	3	6.16638122775801	0.00653981434797598	0.0279922815855846

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.