Coexpression cluster:C876

Full id: C876_skeletal_spinal_medulla_hippocampus_parietal_thalamus_occipital

Phase1 CAGE Peaks

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

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:0001843	neural tube closure	0.010383953248564
GO:0014020	primary neural tube formation	0.010383953248564
GO:0001839	neural plate morphogenesis	0.010383953248564
GO:0001841	neural tube formation	0.010383953248564
GO:0001840	neural plate development	0.010383953248564
GO:0001838	embryonic epithelial tube formation	0.010383953248564
GO:0021915	neural tube development	0.010383953248564
GO:0016331	morphogenesis of embryonic epithelium	0.0105201195496108
GO:0002009	morphogenesis of an epithelium	0.0236325170582736
GO:0007254	JNK cascade	0.0236325170582736
GO:0031098	stress-activated protein kinase signaling pathway	0.0236325170582736
GO:0035239	tube morphogenesis	0.0242021142259976
GO:0048598	embryonic morphogenesis	0.0242021142259976
GO:0009792	embryonic development ending in birth or egg hatching	0.0242021142259976
GO:0043009	chordate embryonic development	0.0242021142259976
GO:0035295	tube development	0.0274244371401497
GO:0048503	GPI anchor binding	0.0274244371401497
GO:0009986	cell surface	0.0274244371401497
GO:0000165	MAPKKK cascade	0.0274244371401497
GO:0005089	Rho guanyl-nucleotide exchange factor activity	0.0274244371401497
GO:0035023	regulation of Rho protein signal transduction	0.0274244371401497
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.0274244371401497
GO:0032502	developmental process	0.0274244371401497
GO:0007266	Rho protein signal transduction	0.0298931627822005
GO:0009790	embryonic development	0.0358469119443389
GO:0035091	phosphoinositide binding	0.0368062548747997
GO:0005085	guanyl-nucleotide exchange factor activity	0.0435957043134591
GO:0005543	phospholipid binding	0.0441627868691779
GO:0016337	cell-cell adhesion	0.0441627868691779
GO:0005096	GTPase activator activity	0.0441627868691779
GO:0046578	regulation of Ras protein signal transduction	0.044715327201792
GO:0007243	protein kinase cascade	0.044715327201792
GO:0007265	Ras protein signal transduction	0.049776947180899

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

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.