Coexpression cluster:C734

Full id: C734_brain_occipital_parietal_middle_medial_frontal_hippocampus

Phase1 CAGE Peaks

Hg19::chr11:133110104..133110106,-	p@chr11:133110104..133110106 -
Hg19::chr11:35280774..35280791,-	p18@SLC1A2
Hg19::chr11:35428629..35428633,-	p@chr11:35428629..35428633 -
Hg19::chr11:64490531..64490542,-	p15@NRXN2
Hg19::chr12:6806552..6806592,-	p@chr12:6806552..6806592 -
Hg19::chr16:24228379..24228398,+	p11@PRKCB
Hg19::chr17:36689327..36689331,-	p@chr17:36689327..36689331 -
Hg19::chr5:11385202..11385207,-	p32@CTNND2
Hg19::chr5:11385208..11385211,-	p31@CTNND2
Hg19::chr8:133460745..133460750,-	p@chr8:133460745..133460750 -
Hg19::chr9:138053475..138053498,-	p@chr9:138053475..138053498 -

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0007268	synaptic transmission	0.012004234792766
GO:0019226	transmission of nerve impulse	0.012004234792766
GO:0007158	neuron adhesion	0.012004234792766
GO:0005313	L-glutamate transmembrane transporter activity	0.012004234792766
GO:0015172	acidic amino acid transmembrane transporter activity	0.012004234792766
GO:0005246	calcium channel regulator activity	0.012004234792766
GO:0007267	cell-cell signaling	0.012004234792766
GO:0015813	L-glutamate transport	0.012004234792766
GO:0015800	acidic amino acid transport	0.012004234792766
GO:0017153	sodium:dicarboxylate symporter activity	0.012004234792766
GO:0032501	multicellular organismal process	0.012004234792766
GO:0005310	dicarboxylic acid transmembrane transporter activity	0.012004234792766
GO:0006835	dicarboxylic acid transport	0.012004234792766
GO:0007416	synaptogenesis	0.015263430192972
GO:0022610	biological adhesion	0.015263430192972
GO:0007155	cell adhesion	0.015263430192972
GO:0015179	L-amino acid transmembrane transporter activity	0.0166790804028058
GO:0016247	channel regulator activity	0.0166790804028058
GO:0005343	organic acid:sodium symporter activity	0.0166790804028058
GO:0015296	anion:cation symporter activity	0.0166790804028058
GO:0050808	synapse organization and biogenesis	0.0166790804028058
GO:0007269	neurotransmitter secretion	0.0166790804028058
GO:0050877	neurological system process	0.0184434811931709
GO:0007154	cell communication	0.0189883449215195
GO:0045055	regulated secretory pathway	0.0194403635047792
GO:0015171	amino acid transmembrane transporter activity	0.0221233606276199
GO:0003008	system process	0.0221233606276199
GO:0006865	amino acid transport	0.0221233606276199
GO:0003001	generation of a signal involved in cell-cell signaling	0.0221233606276199
GO:0001505	regulation of neurotransmitter levels	0.0238244046128343
GO:0015837	amine transport	0.0240492340692788
GO:0043062	extracellular structure organization and biogenesis	0.0240492340692788
GO:0015370	solute:sodium symporter activity	0.0244280890003623
GO:0046943	carboxylic acid transmembrane transporter activity	0.0245026736589769
GO:0046942	carboxylic acid transport	0.0245026736589769
GO:0015849	organic acid transport	0.0245026736589769
GO:0005342	organic acid transmembrane transporter activity	0.0245026736589769
GO:0015294	solute:cation symporter activity	0.0274605540620924
GO:0044425	membrane part	0.0313573386065829
GO:0007275	multicellular organismal development	0.0340974263283226
GO:0008509	anion transmembrane transporter activity	0.0465301057857495

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>

---

Uber Anatomy

Ontology term	p-value	n
neural tube	1.19e-104	56
neural rod	1.19e-104	56
future spinal cord	1.19e-104	56
neural keel	1.19e-104	56
regional part of nervous system	4.03e-99	53
regional part of brain	4.03e-99	53
regional part of forebrain	1.02e-89	41
forebrain	1.02e-89	41
anterior neural tube	1.02e-89	41
future forebrain	1.02e-89	41
telencephalon	6.55e-88	34
brain grey matter	1.67e-87	34
gray matter	1.67e-87	34
central nervous system	5.42e-86	81
brain	5.66e-84	68
future brain	5.66e-84	68
cerebral hemisphere	2.80e-80	32
regional part of telencephalon	8.63e-80	32
nervous system	8.99e-77	89
neural plate	3.28e-73	82
presumptive neural plate	3.28e-73	82
neurectoderm	1.79e-69	86
regional part of cerebral cortex	2.78e-67	22
pre-chordal neural plate	1.50e-62	61
cerebral cortex	5.58e-59	25
pallium	5.58e-59	25
neocortex	8.87e-59	20
ecto-epithelium	3.58e-56	104
adult organism	3.56e-51	114
structure with developmental contribution from neural crest	9.12e-48	132
ectoderm-derived structure	1.12e-38	171
ectoderm	1.12e-38	171
presumptive ectoderm	1.12e-38	171
neural nucleus	9.59e-30	9
nucleus of brain	9.59e-30	9
organ system subdivision	1.65e-29	223
tube	3.25e-25	192
basal ganglion	2.92e-23	9
nuclear complex of neuraxis	2.92e-23	9
aggregate regional part of brain	2.92e-23	9
collection of basal ganglia	2.92e-23	9
cerebral subcortex	2.92e-23	9
parietal lobe	2.18e-22	5
telencephalic nucleus	4.48e-22	7
gyrus	7.07e-19	6
anatomical conduit	1.46e-18	240
brainstem	2.05e-17	6
posterior neural tube	9.26e-17	15
chordal neural plate	9.26e-17	15
temporal lobe	4.47e-16	6
anatomical cluster	2.76e-15	373
limbic system	3.29e-15	5
occipital lobe	4.39e-15	5
organ part	1.05e-14	218
epithelium	8.94e-14	306
cell layer	1.46e-13	309
pons	2.38e-13	3
segmental subdivision of hindbrain	4.87e-12	12
hindbrain	4.87e-12	12
presumptive hindbrain	4.87e-12	12
multi-tissue structure	1.77e-11	342
segmental subdivision of nervous system	4.54e-11	13
corpus striatum	8.10e-11	4
striatum	8.10e-11	4
ventral part of telencephalon	8.10e-11	4
future corpus striatum	8.10e-11	4
Ammon's horn	2.02e-10	2
lobe parts of cerebral cortex	2.02e-10	2
hippocampal formation	2.02e-10	2
limbic lobe	2.02e-10	2
middle temporal gyrus	4.39e-10	2
globus pallidus	1.34e-09	2
pallidum	1.34e-09	2
locus ceruleus	1.66e-09	2
brainstem nucleus	1.66e-09	2
hindbrain nucleus	1.66e-09	2
meninx	2.80e-09	2
membrane organ	2.80e-09	2
meningeal cluster	2.80e-09	2
organ	2.77e-08	503
regional part of metencephalon	1.22e-07	9
metencephalon	1.22e-07	9
future metencephalon	1.22e-07	9
germ layer	3.39e-07	560
germ layer / neural crest	3.39e-07	560
embryonic tissue	3.39e-07	560
presumptive structure	3.39e-07	560
germ layer / neural crest derived structure	3.39e-07	560
epiblast (generic)	3.39e-07	560
embryonic structure	4.43e-07	564
frontal cortex	4.46e-07	3
caudate-putamen	6.01e-07	3
dorsal striatum	6.01e-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

---

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

---

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

---

This analysis result is provided for C0 - C305 clusters.