Coexpression cluster:C2825

Full id: C2825_cervical_gall_bile_rectal_epitheloid_large_umbilical

Phase1 CAGE Peaks

Hg19::chr5:58571724..58571727,-	p8@uc003jsd.1
Hg19::chr5:58571770..58571781,-	p7@uc003jsd.1
Hg19::chr5:58571807..58571821,-	p24@PDE4D
Hg19::chr5:58571829..58571862,-	p9@PDE4D

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:0004115	3',5'-cyclic-AMP phosphodiesterase activity	0.00638761332862357
GO:0005626	insoluble fraction	0.00912516189803367
GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	0.0107220652301896
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.0107220652301896
GO:0005813	centrosome	0.0191628399858707
GO:0008081	phosphoric diester hydrolase activity	0.0191628399858707
GO:0005815	microtubule organizing center	0.0191628399858707
GO:0005625	soluble fraction	0.0266910985517485

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.02e-39	115
neural tube	7.30e-18	57
neural rod	7.30e-18	57
future spinal cord	7.30e-18	57
neural keel	7.30e-18	57
regional part of brain	1.10e-16	59
anatomical cluster	1.41e-16	286
regional part of forebrain	1.84e-16	41
forebrain	1.84e-16	41
future forebrain	1.84e-16	41
neural plate	2.03e-16	86
presumptive neural plate	2.03e-16	86
anterior neural tube	9.22e-16	42
central nervous system	1.21e-15	82
neurectoderm	1.93e-15	90
telencephalon	1.03e-14	34
brain	1.92e-14	69
future brain	1.92e-14	69
gray matter	2.36e-14	34
brain grey matter	2.36e-14	34
cerebral hemisphere	2.67e-14	32
regional part of telencephalon	4.54e-14	33
neocortex	1.73e-13	20
multi-tissue structure	7.09e-13	347
regional part of cerebral cortex	7.78e-13	22
regional part of nervous system	2.12e-12	94
nervous system	2.12e-12	94
organ part	3.58e-12	219
cerebral cortex	2.13e-11	25
pallium	2.13e-11	25
pre-chordal neural plate	2.70e-11	61
organ	6.49e-11	511
anatomical conduit	9.92e-11	241
anterior region of body	3.91e-10	129
craniocervical region	3.91e-10	129
larynx	9.52e-10	9
multi-cellular organism	1.12e-09	659
anatomical system	1.25e-09	625
anatomical group	1.63e-09	626
head	1.80e-09	123
ectoderm-derived structure	1.85e-09	169
subdivision of digestive tract	2.58e-09	129
endodermal part of digestive tract	2.58e-09	129
ectoderm	4.28e-09	173
presumptive ectoderm	4.28e-09	173
digestive system	6.69e-09	155
digestive tract	6.69e-09	155
primitive gut	6.69e-09	155
embryo	9.44e-09	612
embryonic structure	4.18e-08	605
developing anatomical structure	4.18e-08	605
endoderm-derived structure	4.25e-08	169
endoderm	4.25e-08	169
presumptive endoderm	4.25e-08	169
germ layer	7.30e-08	604
embryonic tissue	7.30e-08	604
presumptive structure	7.30e-08	604
epiblast (generic)	7.30e-08	604
upper respiratory tract	9.25e-08	19
tube	1.46e-07	194
epithelium	4.76e-07	309
cell layer	6.20e-07	312
mixed endoderm/mesoderm-derived structure	6.63e-07	130

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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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.