Coexpression cluster:C1045

Full id: C1045_Whole_blood_occipital_Neutrophils_cerebral_medial_hippocampus

Phase1 CAGE Peaks

Hg19::chr16:75600247..75600325,+	p1@GABARAPL2
Hg19::chr1:51701924..51702001,+	p1@RNF11
Hg19::chr1:51702002..51702030,+	p2@RNF11
Hg19::chr1:51702031..51702042,+	p4@RNF11
Hg19::chr2:68479614..68479685,-	p1@PPP3R1
Hg19::chr5:14872052..14872082,-	p5@ANKH
Hg19::chr6:44095263..44095325,+	p1@TMEM63B
Hg19::chr9:131534188..131534227,-	p1@ZER1

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:0000151	ubiquitin ligase complex	0.00662310137760508
GO:0005517	calmodulin inhibitor activity	0.00662310137760508
GO:0031462	Cul2-RING ubiquitin ligase complex	0.00662310137760508
GO:0030504	inorganic diphosphate transmembrane transporter activity	0.00662310137760508
GO:0004723	calcium-dependent protein serine/threonine phosphatase activity	0.0105961823506016
GO:0051438	regulation of ubiquitin-protein ligase activity	0.0132432785339017
GO:0005315	inorganic phosphate transmembrane transporter activity	0.0132432785339017
GO:0005955	calcineurin complex	0.0132432785339017
GO:0042787	protein ubiquitination during ubiquitin-dependent protein catabolic process	0.0144450866570246
GO:0051340	regulation of ligase activity	0.0144450866570246
GO:0050811	GABA receptor binding	0.0144450866570246
GO:0048487	beta-tubulin binding	0.022062386928359
GO:0030500	regulation of bone mineralization	0.0224001597406885
GO:0015114	phosphate transmembrane transporter activity	0.0264670722043128
GO:0030278	regulation of ossification	0.0311239866203646
GO:0031461	cullin-RING ubiquitin ligase complex	0.0311239866203646
GO:0030282	bone mineralization	0.0311239866203646
GO:0006512	ubiquitin cycle	0.031212021879642
GO:0046850	regulation of bone remodeling	0.0334074980632568

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	3.03e-45	114
neural tube	4.12e-26	56
neural rod	4.12e-26	56
future spinal cord	4.12e-26	56
neural keel	4.12e-26	56
regional part of nervous system	1.26e-24	53
regional part of brain	1.26e-24	53
brain	3.98e-22	68
future brain	3.98e-22	68
central nervous system	4.09e-22	81
regional part of forebrain	1.13e-20	41
forebrain	1.13e-20	41
anterior neural tube	1.13e-20	41
future forebrain	1.13e-20	41
neural plate	3.33e-20	82
presumptive neural plate	3.33e-20	82
nervous system	3.72e-20	89
neurectoderm	7.77e-18	86
multi-cellular organism	3.50e-17	656
telencephalon	5.07e-17	34
brain grey matter	5.31e-17	34
gray matter	5.31e-17	34
ecto-epithelium	2.08e-16	104
cerebral hemisphere	4.83e-16	32
regional part of telencephalon	6.96e-16	32
structure with developmental contribution from neural crest	1.03e-15	132
anatomical system	2.30e-15	624
anatomical group	4.15e-15	625
pre-chordal neural plate	1.11e-14	61
ectoderm-derived structure	1.92e-14	171
ectoderm	1.92e-14	171
presumptive ectoderm	1.92e-14	171
regional part of cerebral cortex	2.53e-14	22
embryonic structure	4.60e-14	564
germ layer	6.60e-14	560
germ layer / neural crest	6.60e-14	560
embryonic tissue	6.60e-14	560
presumptive structure	6.60e-14	560
germ layer / neural crest derived structure	6.60e-14	560
epiblast (generic)	6.60e-14	560
neocortex	3.64e-13	20
developing anatomical structure	7.30e-13	581
embryo	3.31e-12	592
cerebral cortex	5.19e-12	25
pallium	5.19e-12	25
anatomical conduit	4.63e-11	240
tube	7.39e-11	192
organ	1.48e-08	503
anatomical cluster	8.22e-08	373
organ system subdivision	2.00e-07	223

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
CCNT2#905	8	6.33620157696263	3.84606837428661e-07	1.87525459823585e-05
E2F1#1869	7	4.29396556301941	9.58670853279727e-05	0.0013704164419064
E2F6#1876	7	4.39001126523521	8.25033297218753e-05	0.00124015043938154
EGR1#1958	7	4.36465670795887	8.58120841941444e-05	0.00128618373437891
ELF1#1997	8	4.25809795880754	9.24826870984006e-06	0.000246460815459808
ETS1#2113	4	4.86438046110117	0.005553791515982	0.0251368334620864
FOSL2#2355	3	6.34882522671063	0.00921194665864107	0.034825399879889
GABPB1#2553	7	6.1842233566594	7.95182205325426e-06	0.000221166536197023
HDAC2#3066	4	6.70781011831313	0.00169098738002969	0.0105662935851933
HEY1#23462	7	3.5350971627175	0.000356612305668408	0.0035677969720953
HMGN3#9324	7	7.15622925793177	2.91658210831366e-06	0.000100034456095294
IRF1#3659	7	6.68251828436841	4.6709523292352e-06	0.000145101008421474
MAX#4149	5	4.03284719312945	0.00331198131847205	0.0171313960140608
MYC#4609	6	3.91671140370705	0.000964927056924644	0.00693954117188768
NFKB1#4790	6	4.11604756814538	0.000729985658978431	0.00581577330368818
PAX5#5079	5	4.16847845698614	0.00284750870610728	0.0154368524140742
POLR2A#5430	8	2.14745317655807	0.00221072578897191	0.0127195896140611
REST#5978	4	4.82501435806401	0.00572073539826954	0.0257862703608059
SIN3A#25942	7	4.73277413596324	4.948745034002e-05	0.000847977001814823
SP1#6667	6	4.27378603360567	0.000590472686428894	0.00494375315840526
TAF1#6872	7	2.92516550002713	0.00126532535791574	0.00849124944132635
TBP#6908	7	3.24342435120934	0.000635422362049205	0.00521269940067999
TCF12#6938	5	6.64654056386651	0.000322376892081284	0.00329988437048684
TRIM28#10155	3	6.97144689197345	0.00710084720104505	0.0296061871064691
YY1#7528	7	4.29727440612212	9.53674534900876e-05	0.00136439472260976
ZBTB7A#51341	8	7.3519093078759	1.17052559937328e-07	6.76153335580455e-06
ZEB1#6935	5	10.5552700109649	3.50000145603859e-05	0.000682098623002826

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.