Coexpression cluster:C4164

Full id: C4164_medial_amygdala_frontal_Mast_Hep2_paracentral_parietal

Phase1 CAGE Peaks

Hg19::chr2:196521674..196521689,+	p6@SLC39A10
Hg19::chr2:196521845..196521869,+	p3@SLC39A10
Hg19::chr2:196521879..196521894,+	p4@SLC39A10

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
cerebral hemisphere	8.72e-10	32
regional part of cerebral cortex	1.20e-09	22
gray matter	2.59e-09	34
brain grey matter	2.59e-09	34
telencephalon	5.48e-09	34
cerebral cortex	6.86e-09	25
pallium	6.86e-09	25
neocortex	8.84e-09	20
regional part of telencephalon	1.88e-08	33
larynx	1.72e-07	9
regional part of forebrain	3.40e-07	41
forebrain	3.40e-07	41
future forebrain	3.40e-07	41
central nervous system	4.20e-07	82

Disease

Ontology term	p-value	n
myeloid leukemia	3.12e-08	31
leukemia	4.60e-07	39

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280159969363192
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326205045841609
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321333421646053
FOSL1#8061	3	39.713579716373	1.59554825631833e-05	0.000371709713008321
FOXA2#3170	2	16.4203091684435	0.00481068235210548	0.0225960357171821
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.0155845241927498
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434797589693878
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00471979752645544
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00665673847714537
REST#5978	3	9.65002871612802	0.00111263624711459	0.00769197173577816
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00485449967681785
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.00035943414879536
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370819481277416
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00643689611920239
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00615043599428572
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00248710801453034
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.006170276833023

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.