Coexpression cluster:C2555

Full id: C2555_Mast_brain_Hepatic_thymus_optic_cervical_corpus

Phase1 CAGE Peaks

Hg19::chr1:204463845..204463857,-	p3@PIK3C2B
Hg19::chr1:204463865..204463876,-	p4@PIK3C2B
Hg19::chr1:204463880..204463915,-	p2@PIK3C2B
Hg19::chr1:204463918..204463963,-	p1@PIK3C2B

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><br>

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Cell Type

Ontology term	p-value	n
endothelial cell of vascular tree	1.69e-07	24
endothelial cell	2.23e-07	35

Uber Anatomy

Ontology term	p-value	n
adult organism	1.57e-31	115
neural tube	2.58e-17	57
neural rod	2.58e-17	57
future spinal cord	2.58e-17	57
neural keel	2.58e-17	57
central nervous system	4.58e-14	82
anterior neural tube	6.22e-14	42
regional part of forebrain	1.81e-13	41
forebrain	1.81e-13	41
future forebrain	1.81e-13	41
regional part of nervous system	9.33e-13	94
nervous system	9.33e-13	94
regional part of brain	1.05e-12	59
neurectoderm	1.64e-12	90
brain	1.68e-12	69
future brain	1.68e-12	69
neural plate	3.45e-12	86
presumptive neural plate	3.45e-12	86
gray matter	5.08e-12	34
brain grey matter	5.08e-12	34
telencephalon	6.51e-12	34
regional part of telencephalon	1.49e-11	33
cerebral hemisphere	1.03e-10	32
organ part	4.20e-10	219
regional part of cerebral cortex	9.93e-10	22
neocortex	4.61e-09	20
pre-chordal neural plate	2.13e-08	61
subdivision of digestive tract	2.78e-08	129
endodermal part of digestive tract	2.78e-08	129
cerebral cortex	5.57e-08	25
pallium	5.57e-08	25
anatomical conduit	5.72e-08	241
anatomical cluster	9.98e-08	286
tube	3.12e-07	194
foregut	7.87e-07	98
mixed endoderm/mesoderm-derived structure	8.53e-07	130

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	4	6.33620157696263	0.000620310058721564	0.00512455008881676
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00817652311011495
CTCFL#140690	4	19.7464743589744	6.5732084880439e-06	0.000193053802385494
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106535217431222
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00997259063544288
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101486273198822
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160975973528924
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00390440579253117
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186188680292024
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.0024819343394308
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00485659723083141
MYC#4609	4	5.2222818716094	0.00134430939527274	0.0088814732371514
NANOG#79923	4	29.2447784810127	1.36586687657858e-06	5.33868902406402e-05
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00768185655689104
NR3C1#2908	4	14.973023331173	1.98868032687801e-05	0.000443415424122144
NRF1#4899	4	12.2102794477109	4.49717228915276e-05	0.000794317904121132
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00444122775194969
RAD21#5885	4	10.3550338954563	8.6948481184721e-05	0.00129466957890663
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00796778707582424
SMARCB1#6598	4	18.2527157811574	9.00423392720929e-06	0.000241684190985302
SMC3#9126	4	15.0449328449328	1.95092670935632e-05	0.000438083927324156
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322446446724065
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244409863290148
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106909606281549
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00249045316913467

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.