Coexpression cluster:C1999

Full id: C1999_Neutrophils_Alveolar_Olfactory_Smooth_Monocytederived_Renal_Dendritic

Phase1 CAGE Peaks

Hg19::chr7:5567947..5567983,-	p10@ACTB
Hg19::chr7:5567987..5568010,-	p7@ACTB
Hg19::chr7:5568016..5568065,-	p3@ACTB
Hg19::chr7:5568084..5568101,-	p14@ACTB
Hg19::chr7:5568284..5568346,-	p4@ACTB

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	8.24e-22	591
animal cell	4.66e-19	679
eukaryotic cell	4.66e-19	679
native cell	1.77e-13	722
mesodermal cell	2.63e-11	119
somatic stem cell	5.31e-11	436
multi fate stem cell	9.81e-11	430
stem cell	3.92e-10	444
non-terminally differentiated cell	6.61e-10	180
smooth muscle cell	1.05e-09	42
smooth muscle myoblast	1.05e-09	42
electrically responsive cell	1.24e-09	60
electrically active cell	1.24e-09	60
contractile cell	3.23e-09	59
embryonic cell	4.72e-09	248
muscle precursor cell	1.50e-08	57
myoblast	1.50e-08	57
multi-potent skeletal muscle stem cell	1.50e-08	57
muscle cell	3.00e-08	54
vascular associated smooth muscle cell	2.54e-07	32
myeloid leukocyte	3.08e-07	76
macrophage dendritic cell progenitor	5.44e-07	65
monopoietic cell	5.68e-07	63
monocyte	5.68e-07	63
monoblast	5.68e-07	63
promonocyte	5.68e-07	63

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	1.04e-11	216
musculoskeletal system	5.97e-11	167
trunk mesenchyme	6.67e-09	143
vasculature	1.04e-08	79
vascular system	1.04e-08	79
somite	2.27e-08	83
paraxial mesoderm	2.27e-08	83
presomitic mesoderm	2.27e-08	83
presumptive segmental plate	2.27e-08	83
trunk paraxial mesoderm	2.27e-08	83
presumptive paraxial mesoderm	2.27e-08	83
multilaminar epithelium	2.32e-08	82
dermomyotome	4.58e-08	70
muscle tissue	1.30e-07	63
musculature	1.30e-07	63
musculature of body	1.30e-07	63
skeletal muscle tissue	2.12e-07	61
striated muscle tissue	2.12e-07	61
myotome	2.12e-07	61
cardiovascular system	2.91e-07	110
vessel	2.94e-07	69
artery	3.04e-07	42
arterial blood vessel	3.04e-07	42
arterial system	3.04e-07	42
blood vessel	8.98e-07	60
epithelial tube open at both ends	8.98e-07	60
blood vasculature	8.98e-07	60
vascular cord	8.98e-07	60

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	5	21.6526476101218	2.09874458450681e-07	1.12118048931615e-05
CTCF#10664	4	4.28820509846002	0.00515201558824328	0.0239462107708295
EBF1#1879	5	8.906466846569	1.78355672307702e-05	0.000406798166851804
ETS1#2113	5	9.72876092220234	1.14685159850452e-05	0.000292421958242709
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00675052839368579
JUND#3727	5	6.99466394187103	5.97069468343598e-05	0.000985575125720515
MYC#4609	5	5.2222818716094	0.000257394484885061	0.00276791830796034
POU2F2#5452	4	7.28489924619402	0.000663122328874386	0.00542757311170157
SIN3A#25942	4	4.32710778145211	0.00497705285576288	0.0232509582753184
SP1#6667	5	5.6983813781409	0.00016639184371255	0.00204565011954032
TAF7#6879	5	11.4330694049239	5.11611886715123e-06	0.000157570727916959
ZBTB33#10009	5	31.6647250299812	3.13617771034015e-08	2.11588671763705e-06

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.