Coexpression cluster:C2519

Full id: C2519_cerebellum_CD8_Natural_CD4_Mast_Basophils_Peripheral

Phase1 CAGE Peaks

Hg19::chr1:144533782..144533805,+	p@chr1:144533782..144533805 +
Hg19::chr4:2420335..2420354,-	p2@ZFYVE28
Hg19::chr4:2420357..2420413,-	p1@ZFYVE28
Hg19::chr4:2420416..2420440,-	p4@ZFYVE28

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
leukocyte	1.12e-12	140
nongranular leukocyte	9.57e-11	119
hematopoietic lineage restricted progenitor cell	2.75e-10	124
myeloid leukocyte	4.27e-10	76
CD14-positive, CD16-negative classical monocyte	6.65e-10	42
granulocyte monocyte progenitor cell	9.11e-10	71
mature alpha-beta T cell	9.21e-10	18
alpha-beta T cell	9.21e-10	18
immature T cell	9.21e-10	18
mature T cell	9.21e-10	18
immature alpha-beta T cell	9.21e-10	18
classical monocyte	4.02e-09	45
macrophage dendritic cell progenitor	1.26e-08	65
myeloid lineage restricted progenitor cell	1.69e-08	70
monopoietic cell	2.15e-08	63
monocyte	2.15e-08	63
monoblast	2.15e-08	63
promonocyte	2.15e-08	63
T cell	1.41e-07	25
pro-T cell	1.41e-07	25
hematopoietic cell	1.85e-07	182
hematopoietic stem cell	5.35e-07	172
angioblastic mesenchymal cell	5.35e-07	172

Uber Anatomy

Ontology term	p-value	n
adult organism	2.80e-30	115
neural tube	7.44e-23	57
neural rod	7.44e-23	57
future spinal cord	7.44e-23	57
neural keel	7.44e-23	57
regional part of brain	2.00e-19	59
brain	2.17e-18	69
future brain	2.17e-18	69
anterior neural tube	7.81e-18	42
central nervous system	1.61e-17	82
regional part of forebrain	1.88e-17	41
forebrain	1.88e-17	41
future forebrain	1.88e-17	41
regional part of nervous system	1.38e-16	94
nervous system	1.38e-16	94
neural plate	5.12e-16	86
presumptive neural plate	5.12e-16	86
neurectoderm	1.66e-15	90
gray matter	2.00e-14	34
brain grey matter	2.00e-14	34
telencephalon	3.50e-14	34
regional part of telencephalon	1.15e-13	33
cerebral hemisphere	2.60e-13	32
hematopoietic system	1.03e-12	102
blood island	1.03e-12	102
hemolymphoid system	1.06e-12	112
regional part of cerebral cortex	5.30e-12	22
neocortex	5.89e-11	20
pre-chordal neural plate	9.26e-11	61
cerebral cortex	1.33e-09	25
pallium	1.33e-09	25
bone marrow	1.61e-08	80
anterior region of body	4.15e-08	129
craniocervical region	4.15e-08	129
tube	6.60e-08	194
bone element	9.13e-08	86
head	1.55e-07	123

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
ATF3#467	3	16.8473808945066	0.000340998682365564	0.00346435422058143
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00512252409447469
CHD2#1106	3	7.75801712558764	0.00335152246453634	0.0172982285482437
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00817493779573956
E2F4#1874	4	12.6680603152844	3.88145892637771e-05	0.00072687051965566
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00997078061838762
EBF1#1879	3	6.67985013492675	0.00518429411827891	0.0240491469049894
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160918889850368
ESR1#2099	3	23.0764524721159	0.000133910524496857	0.00175807432657791
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.019205956349166
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186117953347944
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.00248140654903433
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.0030754606463689
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466237814062163
MXI1#4601	4	9.9615716287593	0.000101522475495045	0.00142397338412933
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434977647121437
RFX5#5993	4	12.0479108271951	4.74457429336527e-05	0.000826691015390015
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00796466612514825
SIX5#147912	3	12.8150365165942	0.000766447113693038	0.0060167596292083
SMARCC2#6601	3	70.6165308201732	4.74678670742709e-06	0.000147194078662998
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00684324139619552
SREBF1#6720	4	47.0058494404883	2.04523668136926e-07	1.10274896110235e-05
SRF#6722	4	13.7971782621678	2.75840773062708e-05	0.000584588768220294
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00507967882022681
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.00976780280047915

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.