Coexpression cluster:C4510

Full id: C4510_bone_mesenchymal_Small_squamous_Fibroblast_thyroid_glioblastoma

Phase1 CAGE Peaks

Hg19::chr5:60600415..60600431,-	p@chr5:60600415..60600431 -
Hg19::chr5:60600469..60600488,-	p@chr5:60600469..60600488 -
Hg19::chr5:60600512..60600563,-	p@chr5:60600512..60600563 -

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
embryonic cell	3.37e-16	250
smooth muscle cell	1.73e-14	43
smooth muscle myoblast	1.73e-14	43
muscle precursor cell	1.86e-14	58
myoblast	1.86e-14	58
multi-potent skeletal muscle stem cell	1.86e-14	58
vascular associated smooth muscle cell	4.17e-14	32
muscle cell	4.86e-14	55
endo-epithelial cell	7.79e-14	42
contractile cell	4.31e-12	59
electrically responsive cell	3.13e-11	61
electrically active cell	3.13e-11	61
endodermal cell	1.03e-09	58
mesodermal cell	2.13e-09	121
aortic smooth muscle cell	2.41e-08	10
respiratory epithelial cell	6.01e-08	13
epithelial cell	6.82e-08	253
squamous epithelial cell	7.58e-08	63

Uber Anatomy

Ontology term	p-value	n
artery	4.13e-16	42
arterial blood vessel	4.13e-16	42
arterial system	4.13e-16	42
endoderm-derived structure	3.92e-15	160
endoderm	3.92e-15	160
presumptive endoderm	3.92e-15	160
unilaminar epithelium	8.62e-15	148
systemic artery	1.36e-14	33
systemic arterial system	1.36e-14	33
organism subdivision	1.51e-13	264
multilaminar epithelium	1.16e-12	83
skeletal muscle tissue	1.57e-12	62
striated muscle tissue	1.57e-12	62
myotome	1.57e-12	62
multi-tissue structure	1.99e-12	342
trunk mesenchyme	2.22e-12	122
digestive system	6.64e-12	145
digestive tract	6.64e-12	145
primitive gut	6.64e-12	145
somite	1.00e-11	71
presomitic mesoderm	1.00e-11	71
presumptive segmental plate	1.00e-11	71
dermomyotome	1.00e-11	71
trunk paraxial mesoderm	1.00e-11	71
dense mesenchyme tissue	1.01e-11	73
muscle tissue	1.13e-11	64
musculature	1.13e-11	64
musculature of body	1.13e-11	64
paraxial mesoderm	2.40e-11	72
presumptive paraxial mesoderm	2.40e-11	72
aorta	1.90e-10	21
aortic system	1.90e-10	21
trunk	1.99e-10	199
epithelial tube open at both ends	4.18e-10	59
blood vessel	4.18e-10	59
blood vasculature	4.18e-10	59
vascular cord	4.18e-10	59
endo-epithelium	9.44e-10	82
respiratory system	1.66e-09	74
splanchnic layer of lateral plate mesoderm	1.99e-09	83
anatomical conduit	2.43e-09	240
epithelial vesicle	2.54e-09	78
epithelium	1.43e-08	306
cell layer	1.93e-08	309
blood vessel smooth muscle	2.41e-08	10
arterial system smooth muscle	2.41e-08	10
artery smooth muscle tissue	2.41e-08	10
aorta smooth muscle tissue	2.41e-08	10
thoracic cavity element	3.43e-08	34
thoracic cavity	3.43e-08	34
mucosa	5.95e-08	20
surface structure	6.05e-08	99
anatomical cluster	6.56e-08	373
orifice	6.84e-08	36
thoracic segment organ	9.98e-08	35
mouth	1.05e-07	29
stomodeum	1.05e-07	29
mesenchyme	1.22e-07	160
entire embryonic mesenchyme	1.22e-07	160
mouth mucosa	3.46e-07	13
vessel	3.64e-07	68
epithelial tube	3.74e-07	117
reproductive structure	5.49e-07	59
reproductive system	5.49e-07	59
tracheobronchial tree	7.60e-07	15
lower respiratory tract	7.60e-07	15

Disease

Ontology term	p-value	n
squamous cell carcinoma	8.78e-09	14

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
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164465025779676
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115644243573549
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280949315868959
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168168877039914
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.00067872767834425
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435585130610177
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00445975240637885
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157466625944682
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187259350099651
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00722600532584657
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295724904620184
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309876401315713
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.004862802021733
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203816924592201
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00310464430010346
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00644939135216079
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00249246008686632
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00618273458180723

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.