Coexpression cluster:C3219

Full id: C3219_smooth_granulocyte_liposarcoma_bladder_colon_hippocampus_endometrial

Phase1 CAGE Peaks

Hg19::chr12:104234966..104234984,-	p3@NT5DC3
Hg19::chr12:104234989..104235022,-	p1@NT5DC3
Hg19::chr12:104235025..104235067,-	p2@NT5DC3

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
brain	5.10e-21	68
future brain	5.10e-21	68
ecto-epithelium	1.65e-19	104
neural tube	1.21e-18	56
neural rod	1.21e-18	56
future spinal cord	1.21e-18	56
neural keel	1.21e-18	56
regional part of nervous system	2.49e-18	53
regional part of brain	2.49e-18	53
ectoderm-derived structure	3.77e-18	171
ectoderm	3.77e-18	171
presumptive ectoderm	3.77e-18	171
central nervous system	9.80e-18	81
neural plate	7.71e-17	82
presumptive neural plate	7.71e-17	82
nervous system	8.89e-17	89
neurectoderm	4.95e-16	86
regional part of forebrain	4.05e-15	41
forebrain	4.05e-15	41
anterior neural tube	4.05e-15	41
future forebrain	4.05e-15	41
cerebral hemisphere	1.09e-14	32
telencephalon	1.59e-14	34
organ system subdivision	1.83e-14	223
brain grey matter	2.27e-14	34
gray matter	2.27e-14	34
pre-chordal neural plate	3.05e-14	61
cerebral cortex	7.70e-14	25
pallium	7.70e-14	25
regional part of telencephalon	1.01e-13	32
regional part of cerebral cortex	8.67e-13	22
neocortex	1.52e-11	20
adult organism	9.24e-11	114
structure with developmental contribution from neural crest	1.54e-08	132
multi-tissue structure	2.24e-07	342

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
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00138886175357738
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278525846724064
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323897386071525
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320721587330417
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00912717686292777
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319309158885883
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00760386572545714
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000849525934627137
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127694027907281
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185889225257929
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00718618856180619
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293382107392368
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268710185201275
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172417252860786
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275632155544191
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308217401566362
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245598111664107
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00540927394915569
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189642502755347
USF2#7392	3	12.9921973850696	0.000455897939342781	0.0042057702399983
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139702964112498

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.