Coexpression cluster:C3308

Full id: C3308_hippocampus_medial_cerebellum_middle_occipital_parietal_olfactory

Phase1 CAGE Peaks

Hg19::chr12:58005170..58005192,+	p2@ARHGEF25
Hg19::chr12:58005204..58005235,+	p1@ARHGEF25
Hg19::chr12:58005243..58005248,+	p3@ARHGEF25

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
non-terminally differentiated cell	5.02e-13	180

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	2.41e-32	94
nervous system	2.41e-32	94
central nervous system	7.59e-31	82
brain	4.40e-27	69
future brain	4.40e-27	69
neural tube	2.24e-26	57
neural rod	2.24e-26	57
future spinal cord	2.24e-26	57
neural keel	2.24e-26	57
neurectoderm	9.40e-26	90
ectoderm	5.40e-25	173
presumptive ectoderm	5.40e-25	173
regional part of brain	2.61e-24	59
neural plate	3.69e-24	86
presumptive neural plate	3.69e-24	86
ectoderm-derived structure	1.65e-23	169
organism subdivision	3.85e-21	365
anterior neural tube	2.31e-20	42
adult organism	4.30e-20	115
regional part of forebrain	5.09e-20	41
forebrain	5.09e-20	41
future forebrain	5.09e-20	41
head	7.32e-20	123
gray matter	1.09e-18	34
brain grey matter	1.09e-18	34
telencephalon	2.54e-18	34
cerebral hemisphere	2.66e-18	32
anterior region of body	3.92e-18	129
craniocervical region	3.92e-18	129
regional part of telencephalon	9.88e-18	33
pre-chordal neural plate	1.22e-17	61
regional part of cerebral cortex	7.84e-16	22
cerebral cortex	1.97e-15	25
pallium	1.97e-15	25
multi-tissue structure	4.01e-15	347
neocortex	1.78e-14	20
tube	2.80e-13	194
epithelium	1.85e-12	309
cell layer	2.12e-12	312
anatomical conduit	2.46e-12	241
anatomical cluster	4.12e-10	286
multi-cellular organism	7.08e-10	659
organ part	6.30e-09	219
embryo	7.31e-09	612
embryonic structure	4.28e-08	605
developing anatomical structure	4.28e-08	605
germ layer	7.97e-08	604
embryonic tissue	7.97e-08	604
presumptive structure	7.97e-08	604
epiblast (generic)	7.97e-08	604
posterior neural tube	3.33e-07	15
chordal neural plate	3.33e-07	15
anatomical system	8.33e-07	625

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189478262247415
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320995484885685
HNF4A#3172	2	15.4215269086358	0.00544421048668661	0.0246707987598847
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.010906103351647

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.