Coexpression cluster:C3962

Full id: C3962_occipital_brain_duodenum_merkel_Neurons_retinoblastoma_parietal

Phase1 CAGE Peaks

Hg19::chr1:26232902..26232918,-	p1@STMN1
Hg19::chr1:26232930..26232945,-	p1@MIR3917
Hg19::chr1:26232951..26232959,-	p2@STMN1

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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GO ID	GO name	FDR corrected p-value
GO:0007052	mitotic spindle organization and biogenesis	0.0115094783939715
GO:0007051	spindle organization and biogenesis	0.0115094783939715
GO:0007019	microtubule depolymerization	0.0115094783939715
GO:0031109	microtubule polymerization or depolymerization	0.0120098904980572
GO:0051261	protein depolymerization	0.0138113740727658
GO:0015631	tubulin binding	0.0167638054868715
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0218751576928899
GO:0005874	microtubule	0.0489403037795832
GO:0007017	microtubule-based process	0.0489403037795832
GO:0000278	mitotic cell cycle	0.0489403037795832

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	1.20e-08	25
neurectodermal cell	2.35e-07	59

Uber Anatomy

Ontology term	p-value	n
nervous system	2.39e-10	89
central nervous system	1.55e-09	81
ectoderm-derived structure	6.18e-08	171
ectoderm	6.18e-08	171
presumptive ectoderm	6.18e-08	171
cerebral cortex	1.04e-07	25
pallium	1.04e-07	25
cerebral hemisphere	1.27e-07	32
pre-chordal neural plate	2.44e-07	61
brain	4.23e-07	68
future brain	4.23e-07	68
neocortex	5.51e-07	20
regional part of telencephalon	6.43e-07	32
telencephalon	6.78e-07	34

Disease

Ontology term	p-value	n
cancer	3.77e-20	235
disease of cellular proliferation	1.17e-19	239
hematologic cancer	1.67e-19	51
immune system cancer	1.67e-19	51
leukemia	3.42e-18	39
organ system cancer	4.33e-16	137
myeloid leukemia	3.29e-14	31

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
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.00129674977642174
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000284726247528085
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190206923497776
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00660786321242318
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325640053316751
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437541225786574
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322548062805326
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320916726259655
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462705380621291
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00762944385289745
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00898135661102585
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434348843579117
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108794113571577
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128182768787236
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156899878872024
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186719645949109
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294773829550049
NFE2#4778	3	77.204260651629	2.17039522930409e-06	7.83254690232516e-05
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269800310648349
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.0019981763953143
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246025373642962
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173053009692868
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00882937422961942
RDBP#7936	3	153.638403990025	2.75057764221434e-07	1.39925756636738e-05
REST#5978	3	9.65002871612802	0.00111263624711459	0.00768230973240782
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277067076711641
SIRT6#51548	3	153.638403990025	2.75057764221434e-07	1.3999394657662e-05
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239887770083252
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203261959602782
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246757808938491
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.0054353630183776
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000720269108604249
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00629718691625119
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00614230049693878
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190443809105018
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421881312130256
YY1#7528	3	4.91117074985386	0.00844145534180826	0.032972442009242
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140337095905169
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389351520949221

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.