Coexpression cluster:C1038

Full id: C1038_Hepatocyte_liver_hippocampus_amygdala_caudate_corpus_thalamus

Phase1 CAGE Peaks

Hg19::chr14:74551096..74551171,-	p1@ALDH6A1
Hg19::chr16:8768441..8768452,+	p5@ABAT
Hg19::chr8:27468842..27468878,-	p12@CLU
Hg19::chr8:27468880..27468910,-	p11@CLU
Hg19::chr8:27468913..27468922,-	p35@CLU
Hg19::chr8:27468927..27468936,-	p37@CLU
Hg19::chr8:27468945..27468948,-	p48@CLU
Hg19::chr8:27468954..27468973,-	p21@CLU

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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p.value	FDR	nGenes	nPathway	Name
6.95890409625456e-06	0.00220249314646457	2	44	Valine, leucine and isoleucine degradation (KEGG):00280
3.64966676839917e-06	0.00220249314646457	2	32	Propanoate metabolism (KEGG):00640

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:0006725	aromatic compound metabolic process	0.00209725369783426
GO:0003867	4-aminobutyrate transaminase activity	0.00209725369783426
GO:0019859	thymine metabolic process	0.00209725369783426
GO:0018478	malonate-semialdehyde dehydrogenase (acetylating) activity	0.00209725369783426
GO:0047298	(S)-3-amino-2-methylpropionate transaminase activity	0.00209725369783426
GO:0032145	succinate-semialdehyde dehydrogenase binding	0.00209725369783426
GO:0004491	methylmalonate-semialdehyde dehydrogenase (acylating) activity	0.00209725369783426
GO:0032144	4-aminobutyrate transaminase complex	0.00209725369783426
GO:0009448	gamma-aminobutyric acid metabolic process	0.00209725369783426
GO:0048148	behavioral response to cocaine	0.00209725369783426
GO:0019626	short-chain fatty acid catabolic process	0.00209725369783426
GO:0046359	butyrate catabolic process	0.00209725369783426
GO:0006573	valine metabolic process	0.00209725369783426
GO:0019605	butyrate metabolic process	0.00209725369783426
GO:0016235	aggresome	0.00209725369783426
GO:0009450	gamma-aminobutyric acid catabolic process	0.00209725369783426
GO:0042220	response to cocaine	0.00279625594751804
GO:0014073	response to tropane	0.00279625594751804
GO:0046459	short-chain fatty acid metabolic process	0.00353200879941799
GO:0009062	fatty acid catabolic process	0.0041941369797639
GO:0048037	cofactor binding	0.00424254131842541
GO:0016234	inclusion body	0.00437636192623535
GO:0031018	endocrine pancreas development	0.00437636192623535
GO:0042135	neurotransmitter catabolic process	0.00536802122965575
GO:0043279	response to alkaloid	0.00536802122965575
GO:0006519	amino acid and derivative metabolic process	0.0056332784920928
GO:0046395	carboxylic acid catabolic process	0.00563617767666475
GO:0031016	pancreas development	0.00563617767666475
GO:0016054	organic acid catabolic process	0.00563617767666475
GO:0042221	response to chemical stimulus	0.00563617767666475
GO:0014070	response to organic cyclic substance	0.00595191720609126
GO:0009308	amine metabolic process	0.00615585991956573
GO:0006206	pyrimidine base metabolic process	0.00657937560058684
GO:0006807	nitrogen compound metabolic process	0.00657937560058684
GO:0042219	amino acid derivative catabolic process	0.00670884138064908
GO:0009081	branched chain family amino acid metabolic process	0.00745382928836276
GO:0019752	carboxylic acid metabolic process	0.00813738920926449
GO:0006082	organic acid metabolic process	0.00813738920926449
GO:0000062	acyl-CoA binding	0.00859955944077925
GO:0019439	aromatic compound catabolic process	0.0088035397728746
GO:0009112	nucleobase metabolic process	0.00940624816327905
GO:0006629	lipid metabolic process	0.0103180539925961
GO:0030534	adult behavior	0.0104316746465184
GO:0044444	cytoplasmic part	0.0104316746465184
GO:0006958	complement activation, classical pathway	0.0104316746465184
GO:0005739	mitochondrion	0.0105162913588557
GO:0002455	humoral immune response mediated by circulating immunoglobulin	0.0107005558179499
GO:0005504	fatty acid binding	0.0108265630239047
GO:0042133	neurotransmitter metabolic process	0.0109474069369195
GO:0035270	endocrine system development	0.0110633973551524
GO:0006956	complement activation	0.0125698213712117
GO:0002541	activation of plasma proteins during acute inflammatory response	0.0125698213712117
GO:0008483	transaminase activity	0.0145432100741649
GO:0045597	positive regulation of cell differentiation	0.0145837638527713
GO:0044242	cellular lipid catabolic process	0.014622825012576
GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	0.014959226279668
GO:0016064	immunoglobulin mediated immune response	0.014990277895566
GO:0019724	B cell mediated immunity	0.0150202417598716
GO:0016769	transferase activity, transferring nitrogenous groups	0.0173066933148615
GO:0010033	response to organic substance	0.0173066933148615
GO:0048471	perinuclear region of cytoplasm	0.0175710701776496
GO:0051094	positive regulation of developmental process	0.0182656147218351
GO:0006220	pyrimidine nucleotide metabolic process	0.0182656147218351
GO:0002253	activation of immune response	0.0182656147218351
GO:0016903	oxidoreductase activity, acting on the aldehyde or oxo group of donors	0.0182656147218351
GO:0002449	lymphocyte mediated immunity	0.0182656147218351
GO:0006959	humoral immune response	0.0183675305377231
GO:0002250	adaptive immune response	0.0183675305377231
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0183675305377231
GO:0002443	leukocyte mediated immunity	0.0183675305377231
GO:0001505	regulation of neurotransmitter levels	0.0183675305377231
GO:0002526	acute inflammatory response	0.0183675305377231
GO:0050778	positive regulation of immune response	0.0194506153245901
GO:0002684	positive regulation of immune system process	0.0194506153245901
GO:0006575	amino acid derivative metabolic process	0.0200815244420623
GO:0050776	regulation of immune response	0.0215737452949274
GO:0002682	regulation of immune system process	0.0217268489507706
GO:0051240	positive regulation of multicellular organismal process	0.0225173967991115
GO:0002252	immune effector process	0.0232876191353746
GO:0045087	innate immune response	0.023829951962537
GO:0030170	pyridoxal phosphate binding	0.0238719907821851
GO:0048667	neuron morphogenesis during differentiation	0.0238719907821851
GO:0006979	response to oxidative stress	0.0238719907821851
GO:0048812	neurite morphogenesis	0.0238719907821851
GO:0005737	cytoplasm	0.0238719907821851
GO:0000904	cellular morphogenesis during differentiation	0.0244921440189288
GO:0046483	heterocycle metabolic process	0.0249762716353216
GO:0031175	neurite development	0.0256383812428713
GO:0045595	regulation of cell differentiation	0.0270331574805088
GO:0016042	lipid catabolic process	0.0271024798592471
GO:0048666	neuron development	0.0282667311209228
GO:0042803	protein homodimerization activity	0.0286823217678161
GO:0006916	anti-apoptosis	0.030518090645957
GO:0031980	mitochondrial lumen	0.032147883579936
GO:0005759	mitochondrial matrix	0.032147883579936
GO:0006631	fatty acid metabolic process	0.0331959097229849
GO:0032990	cell part morphogenesis	0.0343677338044235
GO:0048858	cell projection morphogenesis	0.0343677338044235
GO:0030030	cell projection organization and biogenesis	0.0343677338044235
GO:0030182	neuron differentiation	0.0350185658761542
GO:0043066	negative regulation of apoptosis	0.0374598251978158
GO:0043069	negative regulation of programmed cell death	0.0375794559595029
GO:0008284	positive regulation of cell proliferation	0.0376966780617515
GO:0050793	regulation of developmental process	0.0378115609926719
GO:0048699	generation of neurons	0.0383968082218322
GO:0019842	vitamin binding	0.0385026686984877
GO:0022008	neurogenesis	0.0407690182779484
GO:0051239	regulation of multicellular organismal process	0.0426851176233368
GO:0032787	monocarboxylic acid metabolic process	0.0432231044820223
GO:0050662	coenzyme binding	0.0432231044820223
GO:0007268	synaptic transmission	0.0432231044820223
GO:0006954	inflammatory response	0.0432231044820223
GO:0007610	behavior	0.0432784217108178
GO:0019899	enzyme binding	0.0444893924724475
GO:0019226	transmission of nerve impulse	0.0476822767761628
GO:0009117	nucleotide metabolic process	0.048689302116024

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	3.55e-69	56
neural rod	3.55e-69	56
future spinal cord	3.55e-69	56
neural keel	3.55e-69	56
adult organism	1.14e-65	114
regional part of nervous system	2.16e-64	53
regional part of brain	2.16e-64	53
central nervous system	2.10e-60	81
nervous system	2.58e-56	89
neural plate	1.76e-53	82
presumptive neural plate	1.76e-53	82
brain	2.38e-52	68
future brain	2.38e-52	68
neurectoderm	4.20e-50	86
regional part of forebrain	1.02e-49	41
forebrain	1.02e-49	41
anterior neural tube	1.02e-49	41
future forebrain	1.02e-49	41
brain grey matter	1.02e-45	34
gray matter	1.02e-45	34
telencephalon	1.10e-45	34
cerebral hemisphere	9.97e-43	32
regional part of telencephalon	1.31e-42	32
ecto-epithelium	9.02e-40	104
pre-chordal neural plate	8.15e-37	61
cerebral cortex	3.46e-32	25
pallium	3.46e-32	25
structure with developmental contribution from neural crest	4.18e-32	132
organ system subdivision	2.02e-31	223
ectoderm-derived structure	4.72e-29	171
ectoderm	4.72e-29	171
presumptive ectoderm	4.72e-29	171
regional part of cerebral cortex	1.87e-28	22
neocortex	1.90e-25	20
tube	2.18e-21	192
posterior neural tube	9.69e-20	15
chordal neural plate	9.69e-20	15
anatomical cluster	4.37e-19	373
anatomical conduit	5.36e-17	240
segmental subdivision of nervous system	1.34e-16	13
segmental subdivision of hindbrain	2.72e-15	12
hindbrain	2.72e-15	12
presumptive hindbrain	2.72e-15	12
neural nucleus	7.00e-15	9
nucleus of brain	7.00e-15	9
basal ganglion	8.10e-15	9
nuclear complex of neuraxis	8.10e-15	9
aggregate regional part of brain	8.10e-15	9
collection of basal ganglia	8.10e-15	9
cerebral subcortex	8.10e-15	9
multi-tissue structure	6.00e-13	342
telencephalic nucleus	7.24e-12	7
epithelium	8.58e-12	306
organ part	1.18e-11	218
cell layer	1.76e-11	309
regional part of metencephalon	8.26e-11	9
metencephalon	8.26e-11	9
future metencephalon	8.26e-11	9
brainstem	1.14e-10	6
gyrus	1.74e-10	6
organ	3.43e-10	503
limbic system	3.69e-09	5
germ layer	1.18e-08	560
germ layer / neural crest	1.18e-08	560
embryonic tissue	1.18e-08	560
presumptive structure	1.18e-08	560
germ layer / neural crest derived structure	1.18e-08	560
epiblast (generic)	1.18e-08	560
occipital lobe	1.26e-08	5
temporal lobe	1.49e-08	6
embryonic structure	2.14e-08	564
embryo	5.43e-08	592
corpus striatum	8.25e-08	4
striatum	8.25e-08	4
ventral part of telencephalon	8.25e-08	4
future corpus striatum	8.25e-08	4
developing anatomical structure	8.42e-08	581
anatomical system	2.59e-07	624
anatomical group	2.96e-07	625
multi-cellular organism	3.26e-07	656
regional part of diencephalon	5.31e-07	4

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CEBPB#1051	6	5.97836071936861	8.69217560109361e-05	0.0013016950496166
EP300#2033	8	6.7739417262232	2.25366016107097e-07	1.18993940122392e-05
STAT3#6774	6	7.88959874786568	1.7423325560997e-05	0.000398178270955136

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.