Coexpression cluster:C3962

Full id: C3962_occipital_brain_duodenum_merkel_Neurons_retinoblastoma_parietal

Phase1 CAGE Peaks

Hg19::chr1:26232902..26232918,-	p1@STMN1
Hg19::chr1:26232930..26232945,-	p1@MIR3917
Hg19::chr1:26232951..26232959,-	p2@STMN1

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0007052	mitotic spindle organization and biogenesis	0.0115094783939715
GO:0007051	spindle organization and biogenesis	0.0115094783939715
GO:0007019	microtubule depolymerization	0.0115094783939715
GO:0031109	microtubule polymerization or depolymerization	0.0120098904980572
GO:0051261	protein depolymerization	0.0138113740727658
GO:0015631	tubulin binding	0.0167638054868715
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0218751576928899
GO:0005874	microtubule	0.0489403037795832
GO:0007017	microtubule-based process	0.0489403037795832
GO:0000278	mitotic cell cycle	0.0489403037795832

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>

---

Cell Type

Ontology term	p-value	n
neural cell	2.23e-08	25
neurectodermal cell	2.19e-07	59

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.88e-13	94
nervous system	1.88e-13	94
central nervous system	3.62e-12	82
ectoderm	1.27e-10	173
presumptive ectoderm	1.27e-10	173
ectoderm-derived structure	1.07e-09	169
pre-chordal neural plate	1.87e-09	61
brain	3.37e-09	69
future brain	3.37e-09	69
neurectoderm	4.83e-09	90
cerebral hemisphere	6.93e-09	32
cerebral cortex	9.23e-09	25
pallium	9.23e-09	25
telencephalon	1.49e-08	34
anterior region of body	3.56e-08	129
craniocervical region	3.56e-08	129
regional part of forebrain	3.91e-08	41
forebrain	3.91e-08	41
future forebrain	3.91e-08	41
regional part of telencephalon	3.96e-08	33
neural plate	4.89e-08	86
presumptive neural plate	4.89e-08	86
gray matter	5.45e-08	34
brain grey matter	5.45e-08	34
neocortex	7.46e-08	20
head	8.31e-08	123
anterior neural tube	1.50e-07	42
regional part of cerebral cortex	1.81e-07	22
neural tube	6.21e-07	57
neural rod	6.21e-07	57
future spinal cord	6.21e-07	57
neural keel	6.21e-07	57

Disease

Ontology term	p-value	n
cancer	1.34e-21	235
disease of cellular proliferation	4.33e-21	239
hematologic cancer	5.75e-20	51
immune system cancer	5.75e-20	51
leukemia	2.87e-18	39
organ system cancer	5.06e-17	137
myeloid leukemia	4.70e-14	31

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

---

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

---

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

---

This analysis result is provided for C0 - C305 clusters.