Coexpression cluster:C876

Full id: C876_skeletal_spinal_medulla_hippocampus_parietal_thalamus_occipital

Phase1 CAGE Peaks

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Hg19::chr10:94001015..94001051,-	p@chr10:94001015..94001051 -
Hg19::chr15:93632396..93632407,-	p3@RGMA
Hg19::chr1:160103394..160103410,+	p@chr1:160103394..160103410 +
Hg19::chr1:160103559..160103576,+	p@chr1:160103559..160103576 +
Hg19::chr1:160103656..160103669,+	p@chr1:160103656..160103669 +
Hg19::chr1:160103687..160103724,+	p@chr1:160103687..160103724 +
Hg19::chr1:160103733..160103769,+	p@chr1:160103733..160103769 +
Hg19::chr1:160107625..160107629,+	p@chr1:160107625..160107629 +
Hg19::chrX:135849340..135849399,-	p6@ARHGEF6
Id	Short description

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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 ID	GO name	FDR corrected p-value
GO:0000165	MAPKKK cascade	2.74e-2
GO:0001838	embryonic epithelial tube formation	1.04e-2
GO:0001839	neural plate morphogenesis	1.04e-2
GO:0001840	neural plate development	1.04e-2
GO:0001841	neural tube formation	1.04e-2
GO:0001843	neural tube closure	1.04e-2
GO:0002009	morphogenesis of an epithelium	2.36e-2
GO:0005085	guanyl-nucleotide exchange factor activity	4.36e-2
GO:0005088	Ras guanyl-nucleotide exchange factor activity	2.74e-2
GO:0005089	Rho guanyl-nucleotide exchange factor activity	2.74e-2

Showing 1 to 10 of 33 entries

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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

Ontology term	p-value	n
cell layer	1.05e-10	309
regional part of forebrain	1.05e-61	41
forebrain	1.05e-61	41
anterior neural tube	1.05e-61	41
future forebrain	1.05e-61	41
ecto-epithelium	1.16e-44	104
nervous system	1.18e-57	89
tube	1.26e-19	192
anatomical conduit	1.26e-19	240
brain	1.28e-61	68
future brain	1.28e-61	68
caudate-putamen	1.31e-07	3
dorsal striatum	1.31e-07	3
neural nucleus	1.42e-20	9
nucleus of brain	1.42e-20	9
regional part of cerebral cortex	1.42e-41	22
central nervous system	1.42e-65	81
multi-tissue structure	1.55e-13	342
organ part	1.73e-10	218
ectoderm-derived structure	1.80e-32	171
ectoderm	1.80e-32	171
presumptive ectoderm	1.80e-32	171
regional part of metencephalon	1.90e-09	9
metencephalon	1.90e-09	9
future metencephalon	1.90e-09	9
regional part of telencephalon	1.90e-50	32
neural plate	1.90e-60	82
presumptive neural plate	1.90e-60	82
germ layer	1.96e-08	560
germ layer / neural crest	1.96e-08	560
embryonic tissue	1.96e-08	560
presumptive structure	1.96e-08	560
germ layer / neural crest derived structure	1.96e-08	560
epiblast (generic)	1.96e-08	560
basal ganglion	1.96e-20	9
nuclear complex of neuraxis	1.96e-20	9
aggregate regional part of brain	1.96e-20	9
collection of basal ganglia	1.96e-20	9
cerebral subcortex	1.96e-20	9
posterior neural tube	2.01e-21	15
chordal neural plate	2.01e-21	15
cerebral hemisphere	2.13e-50	32
regional part of nervous system	2.33e-76	53
regional part of brain	2.33e-76	53
diencephalon	2.40e-08	7
future diencephalon	2.40e-08	7
multi-cellular organism	2.43e-08	656
parietal lobe	2.48e-12	5
pons	2.50e-08	3
adult organism	2.51e-95	114
organ	2.65e-10	503
segmental subdivision of hindbrain	3.01e-15	12
hindbrain	3.01e-15	12
presumptive hindbrain	3.01e-15	12
spinal cord	3.02e-08	3
dorsal region element	3.02e-08	3
dorsum	3.02e-08	3
embryonic structure	3.07e-08	564
telencephalic nucleus	3.62e-16	7
structure with developmental contribution from neural crest	3.63e-42	132
gyrus	3.81e-14	6
neural tube	4.01e-83	56
neural rod	4.01e-83	56
future spinal cord	4.01e-83	56
neural keel	4.01e-83	56
medulla oblongata	4.31e-08	3
myelencephalon	4.31e-08	3
future myelencephalon	4.31e-08	3
organ system subdivision	4.56e-25	223
anatomical system	4.75e-07	624
cerebral cortex	5.07e-36	25
pallium	5.07e-36	25
frontal cortex	5.09e-08	3
anatomical group	5.24e-07	625
embryo	5.54e-09	592
neurectoderm	5.58e-57	86
epithelium	5.98e-11	306
limbic system	6.01e-13	5
developing anatomical structure	6.34e-08	581
regional part of diencephalon	6.34e-10	4
segmental subdivision of nervous system	6.45e-14	13
corpus striatum	6.80e-10	4
striatum	6.80e-10	4
ventral part of telencephalon	6.80e-10	4
future corpus striatum	6.80e-10	4
neocortex	6.83e-37	20
brain grey matter	6.98e-55	34
gray matter	6.98e-55	34
anatomical cluster	7.24e-16	373
temporal lobe	7.26e-12	6
telencephalon	7.26e-55	34
male genital duct	8.84e-07	3
internal male genitalia	8.84e-07	3
pre-chordal neural plate	9.03e-41	61
occipital lobe	9.51e-08	5
brainstem	9.69e-15	6

Showing 1 to 96 of 96 entries

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

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Motifs	-log10(p-value)

Motifs	-log10(p-value)
motif123_TTGATGCAGTGA	2.90
motif152_GCKYRMKCGS	2.40
motif12_ACTAAG	2.34
motif95_AGCGAGCTAGC	2.09
motif140_WTAAATAACG	2.00
motif148_NTCSYSTYT	1.84
motif141_TTAAACGGC	1.60
motif90_TTATATCGC	1.54
motif154_GRWGGCAARCG	1.47
motif68_CTTTTAAAC	1.44

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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.