Coexpression cluster:C4312

Full id: C4312_cervical_Small_malignant_Sebocyte_oral_epidermoid_squamous

Phase1 CAGE Peaks

Hg19::chr3:189507432..189507459,+	p1@TP63
Hg19::chr3:189507460..189507471,+	p3@TP63
Hg19::chr5:122758885..122758934,-	p4@CEP120

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:0045747	positive regulation of Notch signaling pathway	0.00588720122453785
GO:0008593	regulation of Notch signaling pathway	0.00588720122453785
GO:0002347	response to tumor cell	0.00588720122453785
GO:0051289	protein homotetramerization	0.00662310137760509
GO:0051262	protein tetramerization	0.0100082420817143
GO:0051260	protein homooligomerization	0.0165912034509703
GO:0007219	Notch signaling pathway	0.0165912034509703
GO:0030308	negative regulation of cell growth	0.0165912034509703
GO:0045792	negative regulation of cell size	0.0165912034509703
GO:0045926	negative regulation of growth	0.0165912034509703
GO:0051259	protein oligomerization	0.0165912034509703
GO:0009967	positive regulation of signal transduction	0.0312582350731415
GO:0001558	regulation of cell growth	0.0312582350731415
GO:0016049	cell growth	0.0312582350731415
GO:0040008	regulation of growth	0.0312582350731415
GO:0045892	negative regulation of transcription, DNA-dependent	0.0312582350731415
GO:0008361	regulation of cell size	0.0312582350731415
GO:0006917	induction of apoptosis	0.0312582350731415
GO:0012502	induction of programmed cell death	0.0312582350731415
GO:0016564	transcription repressor activity	0.0312582350731415
GO:0045893	positive regulation of transcription, DNA-dependent	0.0312582350731415
GO:0043065	positive regulation of apoptosis	0.0317254732655651
GO:0043068	positive regulation of programmed cell death	0.0317254732655651
GO:0045941	positive regulation of transcription	0.0317254732655651
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0317254732655651
GO:0009607	response to biotic stimulus	0.0317254732655651
GO:0016481	negative regulation of transcription	0.0317254732655651
GO:0016563	transcription activator activity	0.0323796067349582
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0323796067349582
GO:0006461	protein complex assembly	0.0333608069390478
GO:0042802	identical protein binding	0.0335754444836924
GO:0031325	positive regulation of cellular metabolic process	0.0335754444836924
GO:0031324	negative regulation of cellular metabolic process	0.0338514070410927
GO:0009893	positive regulation of metabolic process	0.0338514070410927
GO:0009892	negative regulation of metabolic process	0.0366688533414072
GO:0000902	cell morphogenesis	0.0380281376395824
GO:0032989	cellular structure morphogenesis	0.0380281376395824
GO:0042981	regulation of apoptosis	0.0434747167350488
GO:0043067	regulation of programmed cell death	0.0434747167350488

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
endo-epithelial cell	3.13e-29	42
endodermal cell	1.18e-21	58
epithelial cell of alimentary canal	1.28e-17	20
respiratory epithelial cell	1.99e-15	13
epithelial cell	7.18e-15	253
general ecto-epithelial cell	1.23e-11	14
acinar cell	2.10e-10	5
epithelial cell of tracheobronchial tree	5.01e-09	9
epithelial cell of lower respiratory tract	5.01e-09	9
protein secreting cell	1.51e-08	6
transitional epithelial cell	2.82e-08	4
urothelial cell	2.82e-08	4
ecto-epithelial cell	4.71e-08	34
squamous epithelial cell	1.57e-07	63
acinar cell of salivary gland	8.48e-07	3

Uber Anatomy

Ontology term	p-value	n
orifice	3.31e-18	36
respiratory system	4.46e-18	74
endoderm-derived structure	1.84e-16	160
endoderm	1.84e-16	160
presumptive endoderm	1.84e-16	160
oral opening	2.38e-15	22
anterior region of body	3.70e-13	62
craniocervical region	3.70e-13	62
surface structure	2.08e-12	99
mouth	2.21e-12	29
stomodeum	2.21e-12	29
digestive system	3.94e-11	145
digestive tract	3.94e-11	145
primitive gut	3.94e-11	145
respiratory tract	1.02e-10	54
head	1.45e-10	56
mucosa	1.80e-10	20
neck	1.84e-10	10
urothelium	8.37e-10	5
subdivision of digestive tract	9.21e-10	118
mucosa of oral region	2.31e-08	4
respiratory system mucosa	2.31e-08	4
foregut	2.32e-08	87
subdivision of head	2.69e-08	49
mouth mucosa	3.00e-08	13
transitional epithelium	4.66e-08	6
gland of gut	5.69e-08	10
tracheobronchial tree	6.90e-08	15
lower respiratory tract	6.90e-08	15
saliva-secreting gland	1.20e-07	6
gland of oral region	1.20e-07	6
gland of foregut	1.20e-07	6
oral gland	1.20e-07	6
oral cavity	1.20e-07	6
thoracic cavity element	1.27e-07	34
thoracic cavity	1.27e-07	34
anatomical space	1.40e-07	95
thoracic segment organ	2.67e-07	35
organism subdivision	5.38e-07	264
pharynx	7.62e-07	11

Disease

Ontology term	p-value	n
squamous cell carcinoma	9.66e-18	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)
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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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No analysis results for this cluster

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.