Coexpression cluster:C310

Full id: C310_caudate_medulla_spinal_thalamus_locus_globus_hippocampus

Phase1 CAGE Peaks

Hg19::chr11:10715319..10715330,-	p14@MRVI1
Hg19::chr11:121975826..121975852,-	p1@ENST00000534195
Hg19::chr11:56998629..56998644,+	p@chr11:56998629..56998644 +
Hg19::chr12:22063787..22063800,-	p@chr12:22063787..22063800 -
Hg19::chr15:68871022..68871041,+	p10@CORO2B
Hg19::chr16:9459384..9459398,+	p@chr16:9459384..9459398 +
Hg19::chr17:42984560..42984585,-	p12@GFAP
Hg19::chr17:42991062..42991079,-	p@chr17:42991062..42991079 -
Hg19::chr17:72809329..72809358,-	p@chr17:72809329..72809358 -
Hg19::chr18:24445257..24445287,+	p1@CHST9-AS1
Hg19::chr1:110565860..110565886,+	p@chr1:110565860..110565886 +
Hg19::chr1:234667532..234667549,-	p1@LOC100506795
Hg19::chr1:39570480..39570491,+	p@chr1:39570480..39570491 +
Hg19::chr1:39570495..39570532,+	p@chr1:39570495..39570532 +
Hg19::chr20:50348989..50349013,-	p7@ATP9A
Hg19::chr20:50349144..50349177,-	p13@ATP9A
Hg19::chr2:115219171..115219200,+	p4@DPP10
Hg19::chr2:115588636..115588637,+	p@chr2:115588636..115588637 +
Hg19::chr2:115865026..115865030,+	p@chr2:115865026..115865030 +
Hg19::chr3:125899546..125899551,-	p9@ALDH1L1
Hg19::chr4:95917070..95917084,+	p9@BMPR1B
Hg19::chr5:112074029..112074040,+	p9@APC
Hg19::chr5:11385338..11385350,-	p27@CTNND2
Hg19::chr5:7802309..7802315,+	p@chr5:7802309..7802315 +
Hg19::chr5:81147871..81147905,+	p1@ENST00000512859
Hg19::chr6:164348133..164348161,+	p@chr6:164348133..164348161 +
Hg19::chr6:168240693..168240704,+	p@chr6:168240693..168240704 +
Hg19::chr6:3247609..3247615,-	p@chr6:3247609..3247615 -
Hg19::chr6:56716896..56716928,-	p8@DST
Hg19::chr7:229611..229617,+	p@chr7:229611..229617 +
Hg19::chr8:104153713..104153716,-	p1@C8orf56
Hg19::chr8:104184250..104184260,-	p1@ENST00000521102
Hg19::chr8:104184325..104184341,-	p1@LOC100499183
Hg19::chr8:104184361..104184375,-	p2@LOC100499183
Hg19::chr8:145033682..145033707,-	p@chr8:145033682..145033707 -
Hg19::chr9:130854016..130854029,+	p9@SLC25A25
Hg19::chr9:71939697..71939715,+	p@chr9:71939697..71939715 +
Hg19::chr9:71939727..71939735,+	p@chr9:71939727..71939735 +
Hg19::chr9:71939745..71939754,+	p@chr9:71939745..71939754 +

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:0005856	cytoskeleton	0.0148251947762522
GO:0022610	biological adhesion	0.0151374665443906
GO:0007155	cell adhesion	0.0151374665443906
GO:0051983	regulation of chromosome segregation	0.0151374665443906
GO:0051988	regulation of attachment of spindle microtubules to kinetochore	0.0151374665443906
GO:0008608	attachment of spindle microtubules to kinetochore	0.0151374665443906
GO:0005200	structural constituent of cytoskeleton	0.0151374665443906
GO:0007050	cell cycle arrest	0.0157391534528605
GO:0005737	cytoplasm	0.0157391534528605
GO:0001550	ovarian cumulus expansion	0.0157391534528605
GO:0048165	fused antrum stage, oogenesis	0.0157391534528605
GO:0022605	oogenesis stage	0.0157391534528605
GO:0001547	antral ovarian follicle growth	0.0157391534528605
GO:0008092	cytoskeletal protein binding	0.0180510776937678
GO:0009397	folic acid and derivative catabolic process	0.0180510776937678
GO:0009258	10-formyltetrahydrofolate catabolic process	0.0180510776937678
GO:0009256	10-formyltetrahydrofolate metabolic process	0.0180510776937678
GO:0007010	cytoskeleton organization and biogenesis	0.0208843123068426
GO:0030877	beta-catenin destruction complex	0.0208843123068426
GO:0043232	intracellular non-membrane-bound organelle	0.0208843123068426
GO:0043228	non-membrane-bound organelle	0.0208843123068426
GO:0060070	Wnt receptor signaling pathway through beta-catenin	0.0222302899749747
GO:0016155	formyltetrahydrofolate dehydrogenase activity	0.0222302899749747
GO:0005025	transforming growth factor beta receptor activity, type I	0.0255610711707634
GO:0007158	neuron adhesion	0.028065349005499
GO:0045786	negative regulation of progression through cell cycle	0.028065349005499
GO:0016328	lateral plasma membrane	0.029204055500909
GO:0008605	protein kinase CK2 regulator activity	0.029204055500909
GO:0045736	negative regulation of cyclin-dependent protein kinase activity	0.0306597459072613
GO:0008013	beta-catenin binding	0.0306597459072613
GO:0016020	membrane	0.032026848311643
GO:0001502	cartilage condensation	0.0340563595119381
GO:0016742	hydroxymethyl-, formyl- and related transferase activity	0.0340563595119381
GO:0004274	dipeptidyl-peptidase IV activity	0.0360543689207515
GO:0044425	membrane part	0.0387702042148781
GO:0045104	intermediate filament cytoskeleton organization and biogenesis	0.038778576974243
GO:0045103	intermediate filament-based process	0.038778576974243
GO:0046332	SMAD binding	0.038778576974243
GO:0016337	cell-cell adhesion	0.038778576974243
GO:0048477	oogenesis	0.038778576974243
GO:0000074	regulation of progression through cell cycle	0.038778576974243
GO:0051726	regulation of cell cycle	0.038778576974243
GO:0004675	transmembrane receptor protein serine/threonine kinase activity	0.038778576974243
GO:0001541	ovarian follicle development	0.038778576974243
GO:0030509	BMP signaling pathway	0.038778576974243
GO:0005024	transforming growth factor beta receptor activity	0.038778576974243
GO:0004012	phospholipid-translocating ATPase activity	0.038778576974243
GO:0015247	aminophospholipid transporter activity	0.038778576974243
GO:0008239	dipeptidyl-peptidase activity	0.038778576974243
GO:0016806	dipeptidyl-peptidase and tripeptidyl-peptidase activity	0.038778576974243
GO:0015914	phospholipid transport	0.0423412243388375
GO:0031114	regulation of microtubule depolymerization	0.0423412243388375
GO:0007026	negative regulation of microtubule depolymerization	0.0423412243388375
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.04264988463264
GO:0007019	microtubule depolymerization	0.04264988463264
GO:0022601	menstrual cycle phase	0.0432029043855401
GO:0016528	sarcoplasm	0.0432029043855401
GO:0022602	menstrual cycle process	0.0432029043855401
GO:0016529	sarcoplasmic reticulum	0.0432029043855401
GO:0003779	actin binding	0.0441054878504274
GO:0008585	female gonad development	0.0441054878504274
GO:0000287	magnesium ion binding	0.0441054878504274
GO:0004372	glycine hydroxymethyltransferase activity	0.0441054878504274
GO:0009953	dorsal/ventral pattern formation	0.0441054878504274
GO:0031110	regulation of microtubule polymerization or depolymerization	0.0441054878504274
GO:0046660	female sex differentiation	0.0441054878504274
GO:0046545	development of primary female sexual characteristics	0.0441054878504274
GO:0044464	cell part	0.0457671947271353
GO:0000776	kinetochore	0.0457671947271353
GO:0031109	microtubule polymerization or depolymerization	0.0459059997980458
GO:0005548	phospholipid transporter activity	0.0459059997980458
GO:0042698	menstrual cycle	0.0459247048038725
GO:0043010	camera-type eye development	0.0459247048038725
GO:0016646	oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor	0.0459247048038725
GO:0007292	female gamete generation	0.0459247048038725
GO:0006996	organelle organization and biogenesis	0.0459247048038725
GO:0051216	cartilage development	0.0459247048038725
GO:0060173	limb development	0.0459247048038725
GO:0035107	appendage morphogenesis	0.0459247048038725
GO:0035108	limb morphogenesis	0.0459247048038725
GO:0048589	developmental growth	0.0459247048038725
GO:0048736	appendage development	0.0459247048038725

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	5.21e-131	56
neural rod	5.21e-131	56
future spinal cord	5.21e-131	56
neural keel	5.21e-131	56
regional part of nervous system	3.67e-119	53
regional part of brain	3.67e-119	53
central nervous system	3.33e-100	81
brain	1.67e-99	68
future brain	1.67e-99	68
regional part of forebrain	2.21e-98	41
forebrain	2.21e-98	41
anterior neural tube	2.21e-98	41
future forebrain	2.21e-98	41
nervous system	1.69e-89	89
neural plate	3.96e-87	82
presumptive neural plate	3.96e-87	82
brain grey matter	8.90e-86	34
gray matter	8.90e-86	34
telencephalon	4.48e-85	34
neurectoderm	1.05e-82	86
regional part of telencephalon	7.34e-78	32
cerebral hemisphere	1.23e-77	32
adult organism	4.41e-67	114
ecto-epithelium	5.87e-67	104
pre-chordal neural plate	4.05e-64	61
regional part of cerebral cortex	2.53e-59	22
structure with developmental contribution from neural crest	1.37e-53	132
cerebral cortex	6.21e-52	25
pallium	6.21e-52	25
neocortex	8.79e-52	20
ectoderm-derived structure	6.46e-43	171
ectoderm	6.46e-43	171
presumptive ectoderm	6.46e-43	171
neural nucleus	8.66e-37	9
nucleus of brain	8.66e-37	9
basal ganglion	1.37e-36	9
nuclear complex of neuraxis	1.37e-36	9
aggregate regional part of brain	1.37e-36	9
collection of basal ganglia	1.37e-36	9
cerebral subcortex	1.37e-36	9
organ system subdivision	2.34e-32	223
tube	3.29e-32	192
posterior neural tube	1.26e-31	15
chordal neural plate	1.26e-31	15
telencephalic nucleus	1.05e-28	7
brainstem	2.46e-25	6
anatomical conduit	6.23e-24	240
gyrus	9.07e-24	6
segmental subdivision of hindbrain	5.10e-21	12
hindbrain	5.10e-21	12
presumptive hindbrain	5.10e-21	12
limbic system	6.34e-21	5
segmental subdivision of nervous system	2.68e-19	13
corpus striatum	4.90e-17	4
striatum	4.90e-17	4
ventral part of telencephalon	4.90e-17	4
future corpus striatum	4.90e-17	4
epithelium	9.17e-17	306
cell layer	1.64e-16	309
regional part of diencephalon	1.67e-16	4
anatomical cluster	1.23e-15	373
organ part	6.58e-15	218
temporal lobe	1.43e-14	6
diencephalon	2.68e-14	7
future diencephalon	2.68e-14	7
medulla oblongata	1.05e-13	3
myelencephalon	1.05e-13	3
future myelencephalon	1.05e-13	3
spinal cord	1.67e-13	3
dorsal region element	1.67e-13	3
dorsum	1.67e-13	3
caudate-putamen	1.90e-13	3
dorsal striatum	1.90e-13	3
pons	2.15e-13	3
occipital lobe	2.60e-13	5
parietal lobe	3.47e-13	5
frontal cortex	8.35e-13	3
multi-tissue structure	5.50e-12	342
regional part of metencephalon	3.89e-11	9
metencephalon	3.89e-11	9
future metencephalon	3.89e-11	9
dorsal plus ventral thalamus	8.13e-10	2
locus ceruleus	8.13e-10	2
brainstem nucleus	8.13e-10	2
hindbrain nucleus	8.13e-10	2
thalamic complex	8.13e-10	2
globus pallidus	1.19e-09	2
pallidum	1.19e-09	2
caudate nucleus	1.24e-09	2
future caudate nucleus	1.24e-09	2
amygdala	1.30e-09	2
Ammon's horn	1.89e-09	2
lobe parts of cerebral cortex	1.89e-09	2
hippocampal formation	1.89e-09	2
limbic lobe	1.89e-09	2
middle frontal gyrus	2.06e-09	2
middle temporal gyrus	3.53e-09	2
organ	4.65e-09	503
pineal body	1.98e-08	2
regional part of epithalamus	1.98e-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

---

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.