Coexpression cluster:C499

Full id: C499_medulla_thalamus_spinal_globus_optic_caudate_hippocampus

Phase1 CAGE Peaks

Hg19::chr12:41365353..41365362,+	p@chr12:41365353..41365362 +
Hg19::chr15:59664884..59664903,+	p4@FAM81A
Hg19::chr17:42991223..42991232,-	p@chr17:42991223..42991232 -
Hg19::chr18:24434129..24434169,-	p8@AQP4
Hg19::chr18:24434187..24434198,-	p13@AQP4
Hg19::chr18:24435190..24435201,-	p@chr18:24435190..24435201 -
Hg19::chr18:74691180..74691220,-	p@chr18:74691180..74691220 -
Hg19::chr18:74691599..74691602,+	p@chr18:74691599..74691602 +
Hg19::chr1:204991565..204991578,+	p@chr1:204991565..204991578 +
Hg19::chr1:68849935..68849943,-	p@chr1:68849935..68849943 -
Hg19::chr1:85786236..85786252,-	p30@DDAH1
Hg19::chr6:164348089..164348100,+	p@chr6:164348089..164348100 +
Hg19::chr8:26491964..26491967,+	p@chr8:26491964..26491967 +
Hg19::chr8:28965684..28965712,-	p4@KIF13B
Hg19::chr9:87426149..87426182,+	p25@NTRK2
Hg19::chr9:87426979..87426990,+	p54@NTRK2
Hg19::chr9:87427842..87427853,+	p46@NTRK2
Hg19::chr9:87429337..87429348,+	p57@NTRK2
Hg19::chrX:13792037..13792048,-	p@chrX:13792037..13792048 -

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:0016403	dimethylargininase activity	0.0259898459425752
GO:0043121	neurotrophin binding	0.0259898459425752
GO:0007263	nitric oxide mediated signal transduction	0.0259898459425752
GO:0006527	arginine catabolic process	0.0259898459425752
GO:0015250	water channel activity	0.0259898459425752
GO:0005372	water transporter activity	0.0297760869891295
GO:0009065	glutamine family amino acid catabolic process	0.0396763042251676
GO:0016813	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines	0.0396763042251676
GO:0007399	nervous system development	0.0396763042251676
GO:0006525	arginine metabolic process	0.040578659960201
GO:0000051	urea cycle intermediate metabolic process	0.0472042095940519

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
neural tube	1.15e-128	56
neural rod	1.15e-128	56
future spinal cord	1.15e-128	56
neural keel	1.15e-128	56
regional part of nervous system	3.04e-117	53
regional part of brain	3.04e-117	53
regional part of forebrain	2.42e-98	41
forebrain	2.42e-98	41
anterior neural tube	2.42e-98	41
future forebrain	2.42e-98	41
central nervous system	4.49e-98	81
brain	1.37e-97	68
future brain	1.37e-97	68
nervous system	1.02e-91	89
neural plate	1.11e-89	82
presumptive neural plate	1.11e-89	82
brain grey matter	2.43e-86	34
gray matter	2.43e-86	34
telencephalon	1.57e-85	34
neurectoderm	4.15e-85	86
regional part of telencephalon	9.27e-79	32
cerebral hemisphere	2.04e-78	32
ecto-epithelium	7.77e-69	104
pre-chordal neural plate	3.00e-68	61
adult organism	1.11e-65	114
regional part of cerebral cortex	9.35e-62	22
structure with developmental contribution from neural crest	1.58e-57	132
neocortex	3.29e-54	20
cerebral cortex	4.83e-54	25
pallium	4.83e-54	25
ectoderm-derived structure	9.15e-44	171
ectoderm	9.15e-44	171
presumptive ectoderm	9.15e-44	171
neural nucleus	1.36e-34	9
nucleus of brain	1.36e-34	9
basal ganglion	2.54e-34	9
nuclear complex of neuraxis	2.54e-34	9
aggregate regional part of brain	2.54e-34	9
collection of basal ganglia	2.54e-34	9
cerebral subcortex	2.54e-34	9
organ system subdivision	7.82e-33	223
tube	4.18e-31	192
posterior neural tube	1.52e-29	15
chordal neural plate	1.52e-29	15
telencephalic nucleus	5.90e-27	7
brainstem	2.26e-23	6
anatomical conduit	6.14e-23	240
segmental subdivision of nervous system	8.89e-23	13
gyrus	5.40e-22	6
limbic system	5.20e-20	5
segmental subdivision of hindbrain	1.84e-19	12
hindbrain	1.84e-19	12
presumptive hindbrain	1.84e-19	12
occipital lobe	5.68e-19	5
epithelium	4.88e-18	306
cell layer	9.14e-18	309
anatomical cluster	1.27e-16	373
regional part of diencephalon	4.87e-16	4
corpus striatum	7.74e-16	4
striatum	7.74e-16	4
ventral part of telencephalon	7.74e-16	4
future corpus striatum	7.74e-16	4
organ part	1.78e-15	218
diencephalon	7.07e-14	7
future diencephalon	7.07e-14	7
temporal lobe	1.43e-13	6
spinal cord	5.14e-13	3
dorsal region element	5.14e-13	3
dorsum	5.14e-13	3
multi-tissue structure	5.35e-13	342
medulla oblongata	1.23e-12	3
myelencephalon	1.23e-12	3
future myelencephalon	1.23e-12	3
caudate-putamen	1.43e-12	3
dorsal striatum	1.43e-12	3
pons	1.74e-12	3
parietal lobe	2.62e-12	5
frontal cortex	3.24e-12	3
regional part of metencephalon	2.02e-10	9
metencephalon	2.02e-10	9
future metencephalon	2.02e-10	9
Ammon's horn	2.20e-09	2
lobe parts of cerebral cortex	2.20e-09	2
hippocampal formation	2.20e-09	2
limbic lobe	2.20e-09	2
locus ceruleus	2.29e-09	2
brainstem nucleus	2.29e-09	2
hindbrain nucleus	2.29e-09	2
dorsal plus ventral thalamus	2.39e-09	2
globus pallidus	2.39e-09	2
pallidum	2.39e-09	2
thalamic complex	2.39e-09	2
amygdala	4.36e-09	2
caudate nucleus	4.36e-09	2
future caudate nucleus	4.36e-09	2
multi cell component structure	4.53e-09	2
neuron projection bundle	4.53e-09	2
middle frontal gyrus	6.73e-09	2
organ	6.76e-09	503
middle temporal gyrus	1.58e-08	2

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.