Coexpression cluster:C4500

Full id: C4500_small_frontal_insula_Hep2_non_amygdala_paracentral

Phase1 CAGE Peaks

Hg19::chr5:41870475..41870494,-	p2@OXCT1
Hg19::chr5:41870495..41870512,-	p4@OXCT1
Hg19::chr5:41870518..41870535,-	p1@OXCT1

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
lymphoid lineage restricted progenitor cell	6.77e-15	52
lymphocyte	2.02e-14	53
common lymphoid progenitor	2.02e-14	53
nucleate cell	9.92e-14	55
T cell	1.40e-09	25
pro-T cell	1.40e-09	25
mature alpha-beta T cell	4.28e-07	18
alpha-beta T cell	4.28e-07	18
immature T cell	4.28e-07	18
mature T cell	4.28e-07	18
immature alpha-beta T cell	4.28e-07	18

Uber Anatomy

Ontology term	p-value	n
cerebral hemisphere	9.36e-14	32
telencephalon	1.04e-12	34
regional part of forebrain	1.46e-12	41
forebrain	1.46e-12	41
anterior neural tube	1.46e-12	41
future forebrain	1.46e-12	41
brain grey matter	1.70e-12	34
gray matter	1.70e-12	34
regional part of nervous system	1.87e-12	53
regional part of brain	1.87e-12	53
brain	2.11e-12	68
future brain	2.11e-12	68
neural tube	2.28e-12	56
neural rod	2.28e-12	56
future spinal cord	2.28e-12	56
neural keel	2.28e-12	56
regional part of telencephalon	2.51e-12	32
central nervous system	2.81e-12	81
cerebral cortex	1.29e-11	25
pallium	1.29e-11	25
nervous system	1.36e-11	89
regional part of cerebral cortex	1.86e-11	22
neocortex	1.22e-10	20
neural plate	8.09e-09	82
presumptive neural plate	8.09e-09	82
ecto-epithelium	9.34e-09	104
structure with developmental contribution from neural crest	9.35e-09	132
neurectoderm	7.08e-08	86
pre-chordal neural plate	8.19e-08	61
ectoderm-derived structure	1.02e-07	171
ectoderm	1.02e-07	171
presumptive ectoderm	1.02e-07	171
larynx	1.33e-07	9
upper respiratory tract	9.21e-07	19

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
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164422429295402
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190879064018807
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327159144272616
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323912596895301
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109067621799045
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00722452276422863
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295689128561072
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270597647526657
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00472913672512267
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173539329347381
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00885028084977147
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.0048616142342338
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203744366057281
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109348604700656
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00155285256239896
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00631367169875446
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00616540718170265
YY1#7528	3	4.91117074985386	0.00844145534180826	0.03308876874505
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243552559728961
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109928825498581

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.