Coexpression cluster:C696

Full id: C696_medial_occipital_temporal_amygdala_parietal_duodenum_cerebellum

Phase1 CAGE Peaks

Hg19::chr12:57980107..57980120,+	p6@KIF5A
Hg19::chr14:24038741..24038779,-	p@chr14:24038741..24038779 -
Hg19::chr14:60063171..60063197,-	p@chr14:60063171..60063197 -
Hg19::chr14:60063407..60063420,-	p@chr14:60063407..60063420 -
Hg19::chr19:42471468..42471486,-	p@chr19:42471468..42471486 -
Hg19::chr1:183387432..183387443,-	p9@NMNAT2
Hg19::chr1:6219506..6219520,-	p@chr1:6219506..6219520 -
Hg19::chr2:149818477..149818509,+	p4@KIF5C
Hg19::chr2:149880852..149880863,+	p@chr2:149880852..149880863 +
Hg19::chr2:241679747..241679778,-	p@chr2:241679747..241679778 -
Hg19::chr2:241727586..241727616,-	p2@KIF1A
Hg19::chrX:102318624..102318646,-	p2@BEX1

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:0003777	microtubule motor activity	4.31307061549663e-05
GO:0007018	microtubule-based movement	4.31307061549663e-05
GO:0005875	microtubule associated complex	4.31307061549663e-05
GO:0030705	cytoskeleton-dependent intracellular transport	4.31307061549663e-05
GO:0005871	kinesin complex	0.000101134960161195
GO:0005874	microtubule	0.000101134960161195
GO:0007017	microtubule-based process	0.000102363837873752
GO:0015630	microtubule cytoskeleton	0.000393922153268168
GO:0007010	cytoskeleton organization and biogenesis	0.000813017179920108
GO:0046907	intracellular transport	0.00157929267129455
GO:0044430	cytoskeletal part	0.00157929267129455
GO:0051649	establishment of cellular localization	0.00244448456790267
GO:0051641	cellular localization	0.00244448456790267
GO:0035253	ciliary rootlet	0.00270779369921599
GO:0000309	nicotinamide-nucleotide adenylyltransferase activity	0.00270779369921599
GO:0005856	cytoskeleton	0.00390852402056889
GO:0008089	anterograde axon cargo transport	0.00398158069513317
GO:0006996	organelle organization and biogenesis	0.00431841749717366
GO:0044441	cilium part	0.00498686646998808
GO:0008088	axon cargo transport	0.00541399340658784
GO:0009435	NAD biosynthetic process	0.00966386179691905
GO:0019674	NAD metabolic process	0.00983898908286267
GO:0019363	pyridine nucleotide biosynthetic process	0.0135230356149226
GO:0006769	nicotinamide metabolic process	0.0157157848394654
GO:0005524	ATP binding	0.0157157848394654
GO:0032559	adenyl ribonucleotide binding	0.0157157848394654
GO:0042364	water-soluble vitamin biosynthetic process	0.0157157848394654
GO:0043234	protein complex	0.0157157848394654
GO:0043232	intracellular non-membrane-bound organelle	0.0157157848394654
GO:0043228	non-membrane-bound organelle	0.0157157848394654
GO:0019362	pyridine nucleotide metabolic process	0.0157157848394654
GO:0009110	vitamin biosynthetic process	0.0157157848394654
GO:0030554	adenyl nucleotide binding	0.0157157848394654
GO:0005929	cilium	0.016289917483026
GO:0044463	cell projection part	0.0181338635138292
GO:0006733	oxidoreduction coenzyme metabolic process	0.0187521610759297
GO:0016043	cellular component organization and biogenesis	0.019199745731352
GO:0044424	intracellular part	0.0195380484406782
GO:0006767	water-soluble vitamin metabolic process	0.0210586210832302
GO:0032553	ribonucleotide binding	0.0210586210832302
GO:0032555	purine ribonucleotide binding	0.0210586210832302
GO:0017076	purine nucleotide binding	0.0228038418528482
GO:0043005	neuron projection	0.025386786923073
GO:0032991	macromolecular complex	0.0257483418226147
GO:0006766	vitamin metabolic process	0.0257483418226147
GO:0006810	transport	0.0278101633781098
GO:0044446	intracellular organelle part	0.0279625372272735
GO:0044422	organelle part	0.0279625372272735
GO:0051234	establishment of localization	0.0279625372272735
GO:0000166	nucleotide binding	0.0293260869871864
GO:0005622	intracellular	0.0293260869871864
GO:0051179	localization	0.0329773797637642
GO:0009108	coenzyme biosynthetic process	0.0492532669303054

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
neuron	2.02e-14	6
neuroblast	2.02e-14	6
electrically signaling cell	2.02e-14	6
neuronal stem cell	3.11e-14	8
embryonic stem cell	3.36e-11	5

Uber Anatomy

Ontology term	p-value	n
central nervous system	3.82e-98	81
nervous system	1.04e-96	89
neural tube	1.21e-96	56
neural rod	1.21e-96	56
future spinal cord	1.21e-96	56
neural keel	1.21e-96	56
regional part of nervous system	8.68e-90	53
regional part of brain	8.68e-90	53
brain	6.51e-77	68
future brain	6.51e-77	68
regional part of forebrain	3.01e-74	41
forebrain	3.01e-74	41
anterior neural tube	3.01e-74	41
future forebrain	3.01e-74	41
brain grey matter	3.81e-67	34
gray matter	3.81e-67	34
telencephalon	9.24e-67	34
neural plate	9.16e-65	82
presumptive neural plate	9.16e-65	82
cerebral hemisphere	1.44e-62	32
regional part of telencephalon	1.86e-62	32
neurectoderm	3.72e-61	86
regional part of cerebral cortex	2.03e-53	22
ecto-epithelium	7.34e-53	104
pre-chordal neural plate	1.89e-49	61
ectoderm-derived structure	7.91e-49	171
ectoderm	7.91e-49	171
presumptive ectoderm	7.91e-49	171
neocortex	1.81e-48	20
cerebral cortex	1.80e-46	25
pallium	1.80e-46	25
adult organism	4.57e-43	114
structure with developmental contribution from neural crest	3.55e-37	132
organ system subdivision	2.60e-35	223
posterior neural tube	2.56e-22	15
chordal neural plate	2.56e-22	15
basal ganglion	2.69e-22	9
nuclear complex of neuraxis	2.69e-22	9
aggregate regional part of brain	2.69e-22	9
collection of basal ganglia	2.69e-22	9
cerebral subcortex	2.69e-22	9
neural nucleus	7.04e-22	9
nucleus of brain	7.04e-22	9
tube	2.43e-21	192
telencephalic nucleus	2.41e-17	7
gyrus	2.55e-16	6
segmental subdivision of hindbrain	3.52e-16	12
hindbrain	3.52e-16	12
presumptive hindbrain	3.52e-16	12
anatomical cluster	1.51e-15	373
segmental subdivision of nervous system	8.64e-15	13
brainstem	9.40e-15	6
anatomical conduit	1.66e-14	240
occipital lobe	2.65e-14	5
temporal lobe	3.61e-14	6
parietal lobe	7.28e-14	5
limbic system	1.11e-13	5
corpus striatum	4.47e-11	4
striatum	4.47e-11	4
ventral part of telencephalon	4.47e-11	4
future corpus striatum	4.47e-11	4
organ part	5.48e-11	218
epithelium	1.34e-10	306
cell layer	2.26e-10	309
regional part of metencephalon	2.56e-10	9
metencephalon	2.56e-10	9
future metencephalon	2.56e-10	9
diencephalon	3.87e-09	7
future diencephalon	3.87e-09	7
frontal cortex	4.45e-09	3
caudate-putamen	6.63e-09	3
dorsal striatum	6.63e-09	3
embryo	7.59e-09	592
pons	2.08e-08	3
spinal cord	4.11e-08	3
dorsal region element	4.11e-08	3
dorsum	4.11e-08	3
medulla oblongata	5.01e-08	3
myelencephalon	5.01e-08	3
future myelencephalon	5.01e-08	3
germ layer	5.45e-07	560
germ layer / neural crest	5.45e-07	560
embryonic tissue	5.45e-07	560
presumptive structure	5.45e-07	560
germ layer / neural crest derived structure	5.45e-07	560
epiblast (generic)	5.45e-07	560
embryonic structure	7.95e-07	564
middle temporal gyrus	8.30e-07	2
middle frontal gyrus	9.52e-07	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.