Coexpression cluster:C4355

Full id: C4355_Smooth_CD14_Alveolar_Astrocyte_Meningeal_Fibroblast_Renal

Phase1 CAGE Peaks

Hg19::chr4:10118348..10118395,-	p1@WDR1
Hg19::chr4:10118405..10118430,-	p2@WDR1
Hg19::chr4:10118443..10118454,-	p4@WDR1

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
somatic cell	6.60e-46	588
animal cell	7.29e-33	679
eukaryotic cell	7.29e-33	679
mesodermal cell	1.31e-25	121
native cell	3.37e-23	722
embryonic cell	5.63e-18	250
multi fate stem cell	2.34e-17	427
somatic stem cell	3.09e-17	433
contractile cell	1.45e-16	59
stem cell	7.22e-16	441
smooth muscle cell	1.16e-15	43
smooth muscle myoblast	1.16e-15	43
muscle cell	5.91e-15	55
muscle precursor cell	6.05e-15	58
myoblast	6.05e-15	58
multi-potent skeletal muscle stem cell	6.05e-15	58
vascular associated smooth muscle cell	1.15e-14	32
non-terminally differentiated cell	4.82e-13	106
electrically responsive cell	5.17e-12	61
electrically active cell	5.17e-12	61
fibroblast	8.33e-11	76
endothelial cell	4.19e-10	36
meso-epithelial cell	6.74e-10	45
lining cell	1.84e-09	58
barrier cell	1.84e-09	58
defensive cell	6.44e-09	48
phagocyte	6.44e-09	48
classical monocyte	1.42e-08	42
CD14-positive, CD16-negative classical monocyte	1.42e-08	42
monopoietic cell	7.76e-08	59
monocyte	7.76e-08	59
monoblast	7.76e-08	59
promonocyte	7.76e-08	59
macrophage dendritic cell progenitor	8.77e-08	61
myeloid leukocyte	9.62e-08	72
endothelial cell of vascular tree	1.46e-07	24
connective tissue cell	2.11e-07	361
epithelial cell of nephron	2.18e-07	15
stuff accumulating cell	3.60e-07	87
blood vessel endothelial cell	5.32e-07	18
embryonic blood vessel endothelial progenitor cell	5.32e-07	18
mesenchymal cell	6.26e-07	354
motile cell	9.72e-07	386

Uber Anatomy

Ontology term	p-value	n
mesoderm	3.26e-24	315
mesoderm-derived structure	3.26e-24	315
presumptive mesoderm	3.26e-24	315
vasculature	3.47e-23	78
vascular system	3.47e-23	78
lateral plate mesoderm	6.83e-23	203
cardiovascular system	4.07e-21	109
circulatory system	1.03e-20	112
vessel	8.40e-20	68
musculoskeletal system	1.37e-18	167
epithelial tube	2.45e-18	117
epithelial tube open at both ends	1.27e-17	59
blood vessel	1.27e-17	59
blood vasculature	1.27e-17	59
vascular cord	1.27e-17	59
artery	1.55e-17	42
arterial blood vessel	1.55e-17	42
arterial system	1.55e-17	42
splanchnic layer of lateral plate mesoderm	2.21e-17	83
epithelial vesicle	3.96e-17	78
somite	4.76e-14	71
presomitic mesoderm	4.76e-14	71
presumptive segmental plate	4.76e-14	71
dermomyotome	4.76e-14	71
trunk paraxial mesoderm	4.76e-14	71
multilaminar epithelium	1.17e-13	83
systemic artery	1.36e-13	33
systemic arterial system	1.36e-13	33
unilaminar epithelium	1.99e-13	148
dense mesenchyme tissue	2.33e-13	73
paraxial mesoderm	2.80e-13	72
presumptive paraxial mesoderm	2.80e-13	72
skeletal muscle tissue	3.10e-13	62
striated muscle tissue	3.10e-13	62
myotome	3.10e-13	62
muscle tissue	5.56e-13	64
musculature	5.56e-13	64
musculature of body	5.56e-13	64
trunk mesenchyme	1.48e-11	122
mesenchyme	3.53e-10	160
entire embryonic mesenchyme	3.53e-10	160
trunk	3.80e-08	199
aorta	6.79e-08	21
aortic system	6.79e-08	21
skeletal element	1.44e-07	90
organism subdivision	1.81e-07	264
nephron epithelium	2.18e-07	15
renal tubule	2.18e-07	15
nephron tubule	2.18e-07	15
nephron	2.18e-07	15
uriniferous tubule	2.18e-07	15
nephrogenic mesenchyme	2.18e-07	15
skeletal system	3.05e-07	100
parenchyma	3.32e-07	15
excretory tube	3.94e-07	16
kidney epithelium	3.94e-07	16
bone element	4.33e-07	82

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	6.33620157696263	0.00393075003576489	0.0190701724803851
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326796171849236
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323595706587624
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321788115565316
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464038734033716
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.0076407528250551
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154590506571428
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000629043227297818
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435134758253868
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.010898044740391
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157288064748312
MAX#4149	3	6.45255550900712	0.00372191383426551	0.018715115981553
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295510378029962
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270389192606881
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00472601955499818
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173436719248728
PBX3#5090	2	14.6096751244961	0.00605612247321789	0.0268541321691676
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00884348948449475
RDBP#7936	3	153.638403990025	2.75057764221434e-07	1.4033589564007e-05
REST#5978	3	9.65002871612802	0.00111263624711459	0.00769859659549494
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277684957510501
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.0020359940386158
SP1#6667	3	5.6983813781409	0.00540396270171217	0.024741767594762
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00375906833093368
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.0054459541388343
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00630770891400446
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330540324851197
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140652561438675
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243361152081256

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.