Coexpression cluster:C3425

Full id: C3425_prostate_papillary_bronchioalveolar_small_lung_thyroid_nonsmall

Phase1 CAGE Peaks

Hg19::chr14:36982432..36982437,-	p10@SFTA3
Hg19::chr14:36982707..36982717,-	p8@SFTA3
Hg19::chr14:36982724..36982767,-	p1@SFTA3

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
respiratory epithelial cell	1.77e-22	13
epithelial cell of tracheobronchial tree	6.63e-11	9
epithelial cell of lower respiratory tract	6.63e-11	9
epithelial cell of lung	9.14e-10	19

Uber Anatomy

Ontology term	p-value	n
respiratory tract	1.11e-17	53
thoracic cavity element	1.93e-17	34
thoracic cavity	1.93e-17	34
lung	4.73e-17	22
respiratory tube	4.73e-17	22
respiration organ	4.73e-17	22
pair of lungs	4.73e-17	22
lung primordium	4.73e-17	22
lung bud	4.73e-17	22
thoracic segment organ	7.42e-17	35
corpus striatum	7.76e-16	4
striatum	7.76e-16	4
ventral part of telencephalon	7.76e-16	4
future corpus striatum	7.76e-16	4
respiratory primordium	2.74e-15	38
endoderm of foregut	2.74e-15	38
thyroid gland	6.32e-14	5
pharyngeal pouch	6.32e-14	5
thyroid diverticulum	6.32e-14	5
pharyngeal pouch 2	6.32e-14	5
thyroid primordium	6.32e-14	5
telencephalic nucleus	1.09e-13	7
tracheobronchial tree	4.89e-13	14
lower respiratory tract	4.89e-13	14
caudate-putamen	1.66e-12	3
dorsal striatum	1.66e-12	3
respiratory system	6.02e-12	72
epithelial bud	2.15e-11	37
nucleus of brain	1.38e-10	9
basal ganglion	1.38e-10	9
neural nucleus	1.38e-10	9
nuclear complex of neuraxis	1.38e-10	9
aggregate regional part of brain	1.38e-10	9
collection of basal ganglia	1.38e-10	9
cerebral subcortex	1.38e-10	9
thoracic segment of trunk	2.21e-10	52
respiratory tract epithelium	9.14e-10	19
lung epithelium	9.14e-10	19
throat	4.42e-09	2
caudate nucleus	5.62e-09	2
future caudate nucleus	5.62e-09	2
open tracheal system trachea	6.09e-09	2
regional part of forebrain	6.55e-09	41
forebrain	6.55e-09	41
future forebrain	6.55e-09	41
anterior neural tube	1.18e-08	42
endo-epithelium	5.41e-08	82
regional part of brain	6.24e-08	59
epithelial fold	1.23e-07	51
tube	1.96e-07	194
anatomical cluster	2.46e-07	286
neural tube	5.10e-07	57
neural rod	5.10e-07	57
future spinal cord	5.10e-07	57
neural keel	5.10e-07	57
epithelium	7.06e-07	309
segment of respiratory tract	7.23e-07	46
cell layer	9.67e-07	312

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.