Coexpression cluster:C3243

Full id: C3243_occipital_temporal_pons_paracentral_insula_parietal_postcentral

Phase1 CAGE Peaks

Hg19::chr12:117176090..117176112,+	p2@RNFT2
Hg19::chr12:117176113..117176135,+	p1@RNFT2
Hg19::chr12:117176138..117176147,+	p3@RNFT2

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	7.27e-10	25
neurectodermal cell	3.04e-09	59
migratory neural crest cell	1.01e-08	41

Uber Anatomy

Ontology term	p-value	n
nervous system	2.68e-38	89
central nervous system	2.59e-35	81
brain	4.89e-29	68
future brain	4.89e-29	68
neural tube	1.47e-28	56
neural rod	1.47e-28	56
future spinal cord	1.47e-28	56
neural keel	1.47e-28	56
neurectoderm	5.30e-28	86
regional part of nervous system	3.94e-27	53
regional part of brain	3.94e-27	53
neural plate	7.91e-27	82
presumptive neural plate	7.91e-27	82
pre-chordal neural plate	9.98e-24	61
organ system subdivision	1.47e-23	223
regional part of forebrain	9.13e-23	41
forebrain	9.13e-23	41
anterior neural tube	9.13e-23	41
future forebrain	9.13e-23	41
ectoderm-derived structure	7.11e-21	171
ectoderm	7.11e-21	171
presumptive ectoderm	7.11e-21	171
telencephalon	6.35e-19	34
brain grey matter	1.56e-18	34
gray matter	1.56e-18	34
ecto-epithelium	2.08e-18	104
cerebral hemisphere	4.70e-18	32
regional part of telencephalon	1.23e-17	32
anatomical cluster	5.44e-15	373
cerebral cortex	2.61e-14	25
pallium	2.61e-14	25
structure with developmental contribution from neural crest	3.03e-13	132
regional part of cerebral cortex	3.49e-13	22
neocortex	3.86e-12	20
organ part	1.84e-10	218
multi-tissue structure	4.10e-09	342
tube	2.24e-07	192
posterior neural tube	4.73e-07	15
chordal neural plate	4.73e-07	15
cell layer	9.23e-07	309

Disease

Ontology term	p-value	n
cell type cancer	1.36e-19	143
carcinoma	3.62e-15	106
disease of cellular proliferation	2.63e-14	239
cancer	2.70e-14	235

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	0.00129310875500823
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000283886553507358
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00163955320121267
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189338438790356
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.0065884826080292
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323944881838967
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320758909470137
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319345515629342
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460421699073584
ELK4#2005	3	16.235681658468	0.000233604395574599	0.0025512296841384
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167006900904876
FOS#2353	3	8.9979553088944	0.00137249927241713	0.0089533074023718
FOSL1#8061	3	39.713579716373	1.59554825631833e-05	0.000370305476314734
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153690883962262
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00387060062521022
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00432896794470632
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108411035706888
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127721855535264
IRF3#3661	3	46.9819522114896	9.63568551583244e-06	0.000253295081698471
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156273147138936
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185924790231432
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000734672488333436
NFE2#4778	3	77.204260651629	2.17039522930409e-06	7.82173593351588e-05
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268767340556106
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199126311501555
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245100977278296
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00469814885240502
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172442593432929
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00136228862789095
REST#5978	3	9.65002871612802	0.00111263624711459	0.00765699901241438
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00483367166071882
SIRT6#51548	3	153.638403990025	2.75057764221434e-07	1.39721584812852e-05
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245640868995524
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000938218553260926
SREBF1#6720	3	47.0058494404883	9.62099323994382e-06	0.000254252761383222
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154530255651081
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00541011162224112
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247541398240389
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00613547859620868
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000645370752360822
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189660236297778
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00420651337459323
YY1#7528	3	4.91117074985386	0.00844145534180826	0.032821456924281
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242191930903659
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00387963141200019

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.