Coexpression cluster:C2166

Full id: C2166_pineal_cerebellum_pituitary_lung_Mast_spinal_occipital

Phase1 CAGE Peaks

Hg19::chr11:76156045..76156099,+	p1@C11orf30
Hg19::chr2:233562028..233562056,+	p1@GIGYF2
Hg19::chr2:71558882..71558936,+	p1@ZNF638
Hg19::chr5:102455968..102456013,+	p2@PPIP5K2

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
hematopoietic stem cell	1.87e-10	168
angioblastic mesenchymal cell	1.87e-10	168
hematopoietic oligopotent progenitor cell	2.10e-10	161
hematopoietic multipotent progenitor cell	2.10e-10	161
leukocyte	4.09e-10	136
hematopoietic lineage restricted progenitor cell	2.31e-09	120
hematopoietic cell	7.78e-09	177
nongranular leukocyte	1.01e-07	115
myeloid cell	4.31e-07	108
common myeloid progenitor	4.31e-07	108

Uber Anatomy

Ontology term	p-value	n
adult organism	3.72e-37	114
neural tube	1.33e-22	56
neural rod	1.33e-22	56
future spinal cord	1.33e-22	56
neural keel	1.33e-22	56
central nervous system	1.17e-21	81
regional part of nervous system	2.99e-21	53
regional part of brain	2.99e-21	53
nervous system	1.62e-20	89
regional part of forebrain	4.12e-20	41
forebrain	4.12e-20	41
anterior neural tube	4.12e-20	41
future forebrain	4.12e-20	41
brain	1.05e-18	68
future brain	1.05e-18	68
brain grey matter	2.85e-16	34
gray matter	2.85e-16	34
telencephalon	3.69e-16	34
regional part of telencephalon	2.74e-15	32
cerebral hemisphere	3.26e-15	32
neurectoderm	2.58e-12	86
regional part of cerebral cortex	3.00e-12	22
neural plate	5.52e-12	82
presumptive neural plate	5.52e-12	82
cerebral cortex	1.50e-11	25
pallium	1.50e-11	25
neocortex	3.23e-11	20
pre-chordal neural plate	1.86e-09	61
organ system subdivision	1.30e-08	223
hematopoietic system	1.92e-07	98
blood island	1.92e-07	98
ectoderm-derived structure	6.58e-07	171
ectoderm	6.58e-07	171
presumptive ectoderm	6.58e-07	171

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	3	4.75215118272197	0.0138620699668949	0.0487061204842058
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160601591872505
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185606785562444
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319911693874413
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186243646320078
NRF1#4899	4	12.2102794477109	4.49717228915276e-05	0.000792174357744688
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434780906831527
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.0123811954815199
RXRA#6256	2	10.0373085695666	0.0139170380592011	0.0488729501635811
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321331143872214
TBP#6908	4	3.70677068709639	0.00529637781478435	0.024354896204573
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0482764728791248
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106642840391351
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.00976185443996488
ZNF263#10127	3	6.16638122775801	0.00653981434797598	0.0279590515652816

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.