Coexpression cluster:C1580

Full id: C1580_acute_Neutrophils_Mallassezderived_migratory_Smooth_Preadipocyte_small

Phase1 CAGE Peaks

Hg19::chr10:44101729..44101736,-	p1@CAP1P2
Hg19::chr1:40506327..40506338,+	p5@CAP1
Hg19::chr1:40506344..40506355,+	p3@CAP1
Hg19::chr1:40506371..40506382,+	p2@CAP1
Hg19::chr1:40506393..40506453,+	p1@CAP1

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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GO ID	GO name	FDR corrected p-value
GO:0007190	adenylate cyclase activation	0.00508261705718434
GO:0031281	positive regulation of cyclase activity	0.00508261705718434
GO:0045762	positive regulation of adenylate cyclase activity	0.00508261705718434
GO:0051349	positive regulation of lyase activity	0.00508261705718434
GO:0007163	establishment and/or maintenance of cell polarity	0.00508261705718434
GO:0007189	G-protein signaling, adenylate cyclase activating pathway	0.00508261705718434
GO:0045761	regulation of adenylate cyclase activity	0.00508261705718434
GO:0031279	regulation of cyclase activity	0.00508261705718434
GO:0051339	regulation of lyase activity	0.00508261705718434
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.00861404579172152
GO:0019933	cAMP-mediated signaling	0.00861404579172152
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.010221087049063
GO:0019935	cyclic-nucleotide-mediated signaling	0.010221087049063
GO:0043085	positive regulation of catalytic activity	0.0194591624475058
GO:0019932	second-messenger-mediated signaling	0.0194591624475058
GO:0003779	actin binding	0.0289225113492157
GO:0032989	cellular structure morphogenesis	0.0289225113492157
GO:0000902	cell morphogenesis	0.0289225113492157
GO:0008092	cytoskeletal protein binding	0.03294624985282
GO:0050790	regulation of catalytic activity	0.03294624985282
GO:0065009	regulation of a molecular function	0.0339611230639136
GO:0007010	cytoskeleton organization and biogenesis	0.0339611230639136
GO:0009653	anatomical structure morphogenesis	0.0495791930950809

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
myeloid leukocyte	7.56e-27	72
monopoietic cell	8.45e-23	59
monocyte	8.45e-23	59
monoblast	8.45e-23	59
promonocyte	8.45e-23	59
macrophage dendritic cell progenitor	9.82e-23	61
granulocyte monocyte progenitor cell	1.58e-21	67
myeloid lineage restricted progenitor cell	9.19e-21	66
defensive cell	1.78e-19	48
phagocyte	1.78e-19	48
somatic cell	8.82e-19	588
classical monocyte	1.02e-16	42
CD14-positive, CD16-negative classical monocyte	1.02e-16	42
somatic stem cell	7.33e-15	433
multi fate stem cell	1.58e-14	427
stuff accumulating cell	1.80e-14	87
myeloid cell	2.70e-14	108
common myeloid progenitor	2.70e-14	108
stem cell	1.95e-13	441
native cell	5.44e-12	722
animal cell	1.32e-11	679
eukaryotic cell	1.32e-11	679
vascular associated smooth muscle cell	2.58e-10	32
mesenchymal cell	2.81e-08	354
smooth muscle cell	2.98e-08	43
smooth muscle myoblast	2.98e-08	43
connective tissue cell	1.58e-07	361
muscle precursor cell	4.34e-07	58
myoblast	4.34e-07	58
multi-potent skeletal muscle stem cell	4.34e-07	58

Uber Anatomy

Ontology term	p-value	n
mesoderm	1.06e-25	315
mesoderm-derived structure	1.06e-25	315
presumptive mesoderm	1.06e-25	315
lateral plate mesoderm	3.53e-23	203
musculoskeletal system	4.35e-22	167
bone marrow	7.29e-20	76
hemolymphoid system	9.71e-20	108
hematopoietic system	9.85e-20	98
blood island	9.85e-20	98
immune system	1.49e-17	93
skeletal element	2.02e-17	90
bone element	2.11e-17	82
skeletal system	7.24e-17	100
anatomical system	2.72e-11	624
anatomical group	4.99e-11	625
artery	2.21e-10	42
arterial blood vessel	2.21e-10	42
arterial system	2.21e-10	42
cardiovascular system	2.90e-10	109
circulatory system	2.14e-09	112
embryonic structure	7.27e-09	564
epithelial tube open at both ends	8.42e-09	59
blood vessel	8.42e-09	59
blood vasculature	8.42e-09	59
vascular cord	8.42e-09	59
multi-cellular organism	8.69e-09	656
vessel	1.82e-08	68
systemic artery	2.20e-08	33
systemic arterial system	2.20e-08	33
splanchnic layer of lateral plate mesoderm	2.21e-08	83
developing anatomical structure	2.36e-08	581
vasculature	2.92e-08	78
vascular system	2.92e-08	78
germ layer	4.34e-08	560
germ layer / neural crest	4.34e-08	560
embryonic tissue	4.34e-08	560
presumptive structure	4.34e-08	560
germ layer / neural crest derived structure	4.34e-08	560
epiblast (generic)	4.34e-08	560
connective tissue	2.96e-07	371
embryo	7.02e-07	592

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
BCLAF1#9774	4	17.3221180880975	2.18923511079637e-05	0.000481350580497816
CCNT2#905	4	5.06896126157011	0.00270999809128077	0.0148884529539859
CEBPB#1051	4	6.37691810065985	0.00111394417667732	0.00765238544155773
E2F1#1869	4	3.92591137190346	0.00721498454710636	0.0298650775282486
E2F6#1876	4	4.01372458535791	0.00663211823393388	0.0282853559389832
EGR1#1958	4	3.99054327584811	0.006780098300144	0.0287544337841606
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.00572440244626931
ELK4#2005	5	16.235681658468	8.85705446514576e-07	3.82082573847731e-05
GABPB1#2553	5	7.06768383618217	5.6685482528729e-05	0.000947682905365443
GATA1#2623	4	10.8482465150404	0.000139095691709438	0.00181519616974159
GTF2F1#2962	4	10.1917287014061	0.00017783388942764	0.00215812149406615
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00673506272880161
HMGN3#9324	5	8.17854772335059	2.73180911341838e-05	0.000581192528002245
IRF1#3659	4	6.10973100285112	0.00131552526476799	0.00880549529751358
MAX#4149	5	6.45255550900712	8.93743970843928e-05	0.00130511362655158
NANOG#79923	4	23.3958227848101	6.64263001833934e-06	0.000194382078028955
NFKB1#4790	5	5.48806342419384	0.000200816284746232	0.00238764252761973
PAX5#5079	4	5.33565242494226	0.00222338958618779	0.0127727494494976
POU2F2#5452	5	9.10612405774252	1.59639992500654e-05	0.000369681622544919
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00247708279302816
SIX5#147912	5	17.086715355459	6.86007756253503e-07	3.09753411393686e-05
SP1#6667	4	4.55870510251272	0.0040757356578168	0.0194750311738449
STAT3#6774	4	8.41557199772339	0.000377152721159863	0.00374139941538896
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135103256923129
TAF7#6879	4	9.14645552393913	0.000272066287241299	0.00290208670954898
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00917641932174204
TFAP2C#7022	4	8.64738288788818	0.000339051887817405	0.00344759420813572
USF1#7391	5	6.36149927720796	9.59569864925045e-05	0.00136665099035738
USF2#7392	4	10.3937579080557	0.000164617972868753	0.00202574955442909
YY1#7528	5	4.91117074985386	0.0003499314082136	0.0035239115169627
ZEB1#6935	4	13.5107456140351	5.85221769500384e-05	0.000966782290174796
ZNF143#7702	5	13.5008765522279	2.22790360787208e-06	7.97122387470201e-05

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.