Coexpression cluster:C3515

Full id: C3515_neuroblastoma_neuroectodermal_brain_pineal_Retinal_Mesothelial_amygdala

Phase1 CAGE Peaks

Hg19::chr15:77363355..77363369,-	p3@TSPAN3
Hg19::chr15:77363375..77363406,-	p2@TSPAN3
Hg19::chr15:77363411..77363423,-	p4@TSPAN3

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
nervous system	5.84e-28	89
central nervous system	7.61e-26	81
brain	2.73e-23	68
future brain	2.73e-23	68
neural tube	2.01e-20	56
neural rod	2.01e-20	56
future spinal cord	2.01e-20	56
neural keel	2.01e-20	56
anatomical cluster	4.75e-20	373
neurectoderm	8.31e-20	86
regional part of nervous system	5.57e-19	53
regional part of brain	5.57e-19	53
neural plate	5.66e-19	82
presumptive neural plate	5.66e-19	82
ectoderm-derived structure	2.57e-17	171
ectoderm	2.57e-17	171
presumptive ectoderm	2.57e-17	171
structure with developmental contribution from neural crest	1.41e-16	132
regional part of forebrain	3.22e-16	41
forebrain	3.22e-16	41
anterior neural tube	3.22e-16	41
future forebrain	3.22e-16	41
pre-chordal neural plate	1.06e-15	61
ecto-epithelium	6.89e-15	104
cell layer	2.01e-14	309
tube	2.13e-14	192
epithelium	2.73e-14	306
telencephalon	3.08e-13	34
brain grey matter	3.71e-13	34
gray matter	3.71e-13	34
anatomical conduit	7.10e-13	240
cerebral hemisphere	8.67e-13	32
regional part of telencephalon	2.09e-12	32
organ system subdivision	5.97e-12	223
cerebral cortex	1.00e-09	25
pallium	1.00e-09	25
regional part of cerebral cortex	2.89e-09	22
multi-tissue structure	1.83e-08	342
neocortex	1.91e-08	20

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324623213210512
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321457187301358
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00914015843907318
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108552830066925
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127847230100331
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186236565224634
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00719401878633553
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199316544423935
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245453601526262
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470469974893478
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00483994050618947
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00202805784640291
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246026355973896
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000939124461101216
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247859234403334
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00614414130656967
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189980008146163
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328679549059804
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139888877777078
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.010918778971535

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.