Coexpression cluster:C2798

Full id: C2798_seminal_ductus_hippocampus_putamen_parietal_amygdala_caudate

Phase1 CAGE Peaks

Hg19::chr4:95917409..95917421,+	p11@BMPR1B
Hg19::chr5:131317011..131317016,-	p@chr5:131317011..131317016 -
Hg19::chr5:131335358..131335378,-	p3@ACSL6
Hg19::chr5:131335380..131335396,-	p4@ACSL6

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:0001550	ovarian cumulus expansion	0.00532783868959813
GO:0048165	fused antrum stage, oogenesis	0.00532783868959813
GO:0001547	antral ovarian follicle growth	0.00532783868959813
GO:0022605	oogenesis stage	0.00532783868959813
GO:0000287	magnesium ion binding	0.00625347626226086
GO:0005025	transforming growth factor beta receptor activity, type I	0.0106550500303272
GO:0015645	fatty-acid ligase activity	0.0112798249239386
GO:0004467	long-chain-fatty-acid-CoA ligase activity	0.0112798249239386
GO:0001502	cartilage condensation	0.0112798249239386
GO:0046332	SMAD binding	0.0112798249239386
GO:0006637	acyl-CoA metabolic process	0.0112798249239386
GO:0048477	oogenesis	0.0112798249239386
GO:0007405	neuroblast proliferation	0.0112798249239386
GO:0030509	BMP signaling pathway	0.0112798249239386
GO:0004675	transmembrane receptor protein serine/threonine kinase activity	0.0112798249239386
GO:0005024	transforming growth factor beta receptor activity	0.0112798249239386
GO:0001541	ovarian follicle development	0.0112798249239386
GO:0022601	menstrual cycle phase	0.0118754373208547
GO:0022602	menstrual cycle process	0.0118754373208547
GO:0008585	female gonad development	0.0118754373208547
GO:0009953	dorsal/ventral pattern formation	0.0118754373208547
GO:0016877	ligase activity, forming carbon-sulfur bonds	0.0118754373208547
GO:0046545	development of primary female sexual characteristics	0.0118754373208547
GO:0046660	female sex differentiation	0.0118754373208547
GO:0042698	menstrual cycle	0.0118754373208547
GO:0043010	camera-type eye development	0.0118754373208547
GO:0007292	female gamete generation	0.0118754373208547
GO:0051216	cartilage development	0.0118754373208547
GO:0060173	limb development	0.0118754373208547
GO:0035107	appendage morphogenesis	0.0118754373208547
GO:0035108	limb morphogenesis	0.0118754373208547
GO:0048589	developmental growth	0.0118754373208547
GO:0048736	appendage development	0.0118754373208547
GO:0048731	system development	0.0118754373208547
GO:0031903	microbody membrane	0.0122269174325372
GO:0005778	peroxisomal membrane	0.0122269174325372
GO:0044439	peroxisomal part	0.0122269174325372
GO:0044438	microbody part	0.0122269174325372
GO:0045597	positive regulation of cell differentiation	0.0122269174325372
GO:0001654	eye development	0.0122269174325372
GO:0048869	cellular developmental process	0.0122269174325372
GO:0030154	cell differentiation	0.0122269174325372
GO:0008406	gonad development	0.0125838056125745
GO:0048608	reproductive structure development	0.0125838056125745
GO:0048856	anatomical structure development	0.0135298304788747
GO:0045137	development of primary sexual characteristics	0.0135298304788747
GO:0048609	reproductive process in a multicellular organism	0.0135298304788747
GO:0032504	multicellular organism reproduction	0.0135298304788747
GO:0051094	positive regulation of developmental process	0.0147731056398816
GO:0007178	transmembrane receptor protein serine/threonine kinase signaling pathway	0.0159343656977792
GO:0004702	receptor signaling protein serine/threonine kinase activity	0.0159343656977792
GO:0007275	multicellular organismal development	0.0159343656977792
GO:0007548	sex differentiation	0.0161617906101618
GO:0005741	mitochondrial outer membrane	0.0161617906101618
GO:0007423	sensory organ development	0.0162435810661104
GO:0003002	regionalization	0.0162435810661104
GO:0003006	reproductive developmental process	0.0162435810661104
GO:0031968	organelle outer membrane	0.0170629428085416
GO:0019867	outer membrane	0.0173140632093917
GO:0042579	microbody	0.0174431267736113
GO:0005777	peroxisome	0.0174431267736113
GO:0043235	receptor complex	0.0188751820253275
GO:0007389	pattern specification process	0.0209354184380529
GO:0019199	transmembrane receptor protein kinase activity	0.0211059568177126
GO:0045595	regulation of cell differentiation	0.0235570851566974
GO:0030145	manganese ion binding	0.0236824483250839
GO:0005792	microsome	0.0257037987277299
GO:0032502	developmental process	0.0258298488267971
GO:0042598	vesicular fraction	0.02603453710581
GO:0005057	receptor signaling protein activity	0.0268742409044643
GO:0006631	fatty acid metabolic process	0.0285855311650691
GO:0001501	skeletal development	0.0308368239405674
GO:0005886	plasma membrane	0.0309517442921071
GO:0032501	multicellular organismal process	0.0309517442921071
GO:0050793	regulation of developmental process	0.0334143824400436
GO:0048699	generation of neurons	0.0338100634234986
GO:0022008	neurogenesis	0.0359262911726028
GO:0007276	gamete generation	0.0359262911726028
GO:0032787	monocarboxylic acid metabolic process	0.0381186699285198
GO:0006732	coenzyme metabolic process	0.0381186699285198
GO:0006954	inflammatory response	0.0381186699285198
GO:0007167	enzyme linked receptor protein signaling pathway	0.0385177082049996
GO:0009888	tissue development	0.0385177082049996
GO:0022414	reproductive process	0.0385177082049996
GO:0019953	sexual reproduction	0.0393067648118722
GO:0051186	cofactor metabolic process	0.0422844170472928
GO:0016337	cell-cell adhesion	0.0422844170472928
GO:0031966	mitochondrial membrane	0.0491083704470924

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	2.15e-103	56
neural rod	2.15e-103	56
future spinal cord	2.15e-103	56
neural keel	2.15e-103	56
regional part of nervous system	4.34e-96	53
regional part of brain	4.34e-96	53
regional part of forebrain	3.02e-80	41
forebrain	3.02e-80	41
anterior neural tube	3.02e-80	41
future forebrain	3.02e-80	41
central nervous system	1.18e-79	81
brain	2.53e-78	68
future brain	2.53e-78	68
adult organism	3.94e-74	114
nervous system	1.84e-70	89
neural plate	1.04e-69	82
presumptive neural plate	1.04e-69	82
brain grey matter	1.89e-68	34
gray matter	1.89e-68	34
telencephalon	2.83e-68	34
neurectoderm	7.14e-66	86
cerebral hemisphere	1.15e-63	32
regional part of telencephalon	1.88e-63	32
pre-chordal neural plate	8.56e-54	61
regional part of cerebral cortex	1.07e-52	22
ecto-epithelium	3.15e-52	104
neocortex	2.57e-47	20
cerebral cortex	7.45e-46	25
pallium	7.45e-46	25
structure with developmental contribution from neural crest	3.96e-42	132
ectoderm-derived structure	4.98e-32	171
ectoderm	4.98e-32	171
presumptive ectoderm	4.98e-32	171
organ system subdivision	8.42e-32	223
tube	5.81e-27	192
basal ganglion	1.61e-24	9
nuclear complex of neuraxis	1.61e-24	9
aggregate regional part of brain	1.61e-24	9
collection of basal ganglia	1.61e-24	9
cerebral subcortex	1.61e-24	9
neural nucleus	4.87e-24	9
nucleus of brain	4.87e-24	9
anatomical conduit	3.52e-23	240
posterior neural tube	4.83e-23	15
chordal neural plate	4.83e-23	15
telencephalic nucleus	3.56e-19	7
segmental subdivision of hindbrain	1.50e-16	12
hindbrain	1.50e-16	12
presumptive hindbrain	1.50e-16	12
anatomical cluster	2.87e-16	373
gyrus	4.49e-16	6
brainstem	5.54e-16	6
segmental subdivision of nervous system	3.92e-15	13
limbic system	6.00e-15	5
parietal lobe	6.93e-14	5
temporal lobe	7.04e-14	6
epithelium	2.47e-13	306
occipital lobe	4.02e-13	5
cell layer	4.50e-13	309
diencephalon	5.63e-13	7
future diencephalon	5.63e-13	7
multi-tissue structure	1.77e-12	342
corpus striatum	3.48e-12	4
striatum	3.48e-12	4
ventral part of telencephalon	3.48e-12	4
future corpus striatum	3.48e-12	4
regional part of diencephalon	8.41e-11	4
regional part of metencephalon	4.10e-10	9
metencephalon	4.10e-10	9
future metencephalon	4.10e-10	9
organ part	4.61e-10	218
caudate-putamen	1.32e-09	3
dorsal striatum	1.32e-09	3
frontal cortex	5.77e-09	3
medulla oblongata	7.54e-09	3
myelencephalon	7.54e-09	3
future myelencephalon	7.54e-09	3
pons	7.95e-09	3
spinal cord	1.57e-08	3
dorsal region element	1.57e-08	3
dorsum	1.57e-08	3
organ	5.16e-08	503
germ layer	1.19e-07	560
germ layer / neural crest	1.19e-07	560
embryonic tissue	1.19e-07	560
presumptive structure	1.19e-07	560
germ layer / neural crest derived structure	1.19e-07	560
epiblast (generic)	1.19e-07	560
embryonic structure	1.75e-07	564
amygdala	4.89e-07	2
Ammon's horn	5.33e-07	2
lobe parts of cerebral cortex	5.33e-07	2
hippocampal formation	5.33e-07	2
limbic lobe	5.33e-07	2
caudate nucleus	7.06e-07	2
future caudate nucleus	7.06e-07	2
developing anatomical structure	8.61e-07	581

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.