Coexpression cluster:C3284

Full id: C3284_Neurons_Neural_brain_duodenum_occipital_temporal_parietal

Phase1 CAGE Peaks

Hg19::chr12:49582837..49582875,-	p1@TUBA1A
Hg19::chr16:89989741..89989759,+	p1@TUBB3
Hg19::chr5:43233373..43233374,-	p1@ENST00000501221

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
2.96743344876993e-05	0.00626128457690455	2	156	Phagosome (KEGG):04145
9.83008350895251e-06	0.00311122143058347	2	90	Gap junction (KEGG):04540
4.05721049695343e-06	0.00256821424457152	2	58	Pathogenic Escherichia coli infection (KEGG):05130
0.000107161409738044	0.0169582930910455	2	296	Metabolism of proteins (Reactome):REACT_17015
0.00014649401603791	0.0185461424303994	2	346	{CDC2,351} (Static Module):NA

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:0051258	protein polymerization	0.000564821943157806
GO:0007018	microtubule-based movement	0.000772748234088321
GO:0030705	cytoskeleton-dependent intracellular transport	0.000772748234088321
GO:0003924	GTPase activity	0.000999902247954942
GO:0005874	microtubule	0.000999902247954942
GO:0007017	microtubule-based process	0.000999902247954942
GO:0015630	microtubule cytoskeleton	0.00231158995183011
GO:0007010	cytoskeleton organization and biogenesis	0.00323121690947206
GO:0005525	GTP binding	0.00323121690947206
GO:0032561	guanyl ribonucleotide binding	0.00323121690947206
GO:0019001	guanyl nucleotide binding	0.00323121690947206
GO:0046907	intracellular transport	0.0039276904959845
GO:0044430	cytoskeletal part	0.0039276904959845
GO:0017111	nucleoside-triphosphatase activity	0.00398252561133767
GO:0016462	pyrophosphatase activity	0.00398252561133767
GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.00398252561133767
GO:0016817	hydrolase activity, acting on acid anhydrides	0.00398252561133767
GO:0051649	establishment of cellular localization	0.0040439511919829
GO:0051641	cellular localization	0.0040439511919829
GO:0005856	cytoskeleton	0.00608515578786366
GO:0006996	organelle organization and biogenesis	0.00672161565731717
GO:0005200	structural constituent of cytoskeleton	0.0159025179172436
GO:0043234	protein complex	0.0200923685812479
GO:0043232	intracellular non-membrane-bound organelle	0.0200923685812479
GO:0043228	non-membrane-bound organelle	0.0200923685812479
GO:0019904	protein domain specific binding	0.0200923685812479
GO:0016043	cellular component organization and biogenesis	0.024117104410547
GO:0032553	ribonucleotide binding	0.0257609028649648
GO:0032555	purine ribonucleotide binding	0.0257609028649648
GO:0017076	purine nucleotide binding	0.0259211692716775
GO:0030182	neuron differentiation	0.0259211692716775
GO:0032991	macromolecular complex	0.0259211692716775
GO:0016787	hydrolase activity	0.0259211692716775
GO:0007067	mitosis	0.0259211692716775
GO:0006810	transport	0.0259211692716775
GO:0048699	generation of neurons	0.0259211692716775
GO:0000087	M phase of mitotic cell cycle	0.0259211692716775
GO:0044446	intracellular organelle part	0.0259211692716775
GO:0044422	organelle part	0.0259211692716775
GO:0051234	establishment of localization	0.0259211692716775
GO:0022008	neurogenesis	0.0262332920829515
GO:0000166	nucleotide binding	0.026251361438029
GO:0051179	localization	0.0283173817486308
GO:0000279	M phase	0.0285313078467313
GO:0000278	mitotic cell cycle	0.029711842062198
GO:0022403	cell cycle phase	0.0328788603232456
GO:0044267	cellular protein metabolic process	0.0402331255801294
GO:0044260	cellular macromolecule metabolic process	0.0404174924579409
GO:0019538	protein metabolic process	0.0424714515947361

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
non-terminally differentiated cell	5.17e-35	180
mesodermal cell	6.71e-22	119
embryonic cell	1.07e-20	248
contractile cell	1.08e-19	59
electrically responsive cell	1.61e-19	60
electrically active cell	1.61e-19	60
muscle precursor cell	1.60e-18	57
myoblast	1.60e-18	57
multi-potent skeletal muscle stem cell	1.60e-18	57
muscle cell	1.21e-17	54
smooth muscle cell	8.97e-17	42
smooth muscle myoblast	8.97e-17	42
vascular associated smooth muscle cell	2.17e-13	32
neurectodermal cell	4.67e-10	59
fibroblast	6.35e-10	75
ectodermal cell	8.29e-10	71
somatic cell	4.57e-08	591
neural cell	7.93e-08	25
migratory neural crest cell	1.22e-07	41
epithelial cell of nephron	1.52e-07	16
kidney tubule cell	6.47e-07	12
nephron tubule epithelial cell	6.47e-07	12
kidney cell	8.10e-07	18
kidney epithelial cell	8.10e-07	18

Uber Anatomy

Ontology term	p-value	n
cell layer	3.11e-32	312
epithelium	2.62e-31	309
organism subdivision	2.35e-25	365
tube	1.01e-22	194
regional part of nervous system	2.16e-20	94
nervous system	2.16e-20	94
vasculature	5.15e-20	79
vascular system	5.15e-20	79
central nervous system	5.96e-20	82
somite	3.78e-19	83
paraxial mesoderm	3.78e-19	83
presomitic mesoderm	3.78e-19	83
presumptive segmental plate	3.78e-19	83
trunk paraxial mesoderm	3.78e-19	83
presumptive paraxial mesoderm	3.78e-19	83
multi-cellular organism	3.38e-18	659
anatomical conduit	4.65e-18	241
ectoderm-derived structure	1.36e-16	169
dermomyotome	1.58e-16	70
neural plate	1.98e-16	86
presumptive neural plate	1.98e-16	86
multilaminar epithelium	3.26e-16	82
brain	4.82e-16	69
future brain	4.82e-16	69
ectoderm	5.70e-16	173
presumptive ectoderm	5.70e-16	173
anatomical system	6.81e-16	625
vessel	7.87e-16	69
head	9.25e-16	123
anatomical group	1.03e-15	626
skeletal muscle tissue	1.21e-15	61
striated muscle tissue	1.21e-15	61
myotome	1.21e-15	61
anatomical cluster	2.05e-15	286
neurectoderm	2.20e-15	90
blood vessel	2.23e-15	60
epithelial tube open at both ends	2.23e-15	60
blood vasculature	2.23e-15	60
vascular cord	2.23e-15	60
artery	4.82e-15	42
arterial blood vessel	4.82e-15	42
arterial system	4.82e-15	42
muscle tissue	1.26e-14	63
musculature	1.26e-14	63
musculature of body	1.26e-14	63
embryo	3.03e-14	612
neural tube	3.67e-14	57
neural rod	3.67e-14	57
future spinal cord	3.67e-14	57
neural keel	3.67e-14	57
regional part of brain	3.68e-14	59
anterior region of body	6.24e-14	129
craniocervical region	6.24e-14	129
trunk mesenchyme	1.25e-13	143
cardiovascular system	1.57e-13	110
germ layer	1.74e-13	604
embryonic tissue	1.74e-13	604
presumptive structure	1.74e-13	604
epiblast (generic)	1.74e-13	604
embryonic structure	1.80e-13	605
developing anatomical structure	1.80e-13	605
pre-chordal neural plate	3.65e-13	61
multi-tissue structure	1.32e-12	347
splanchnic layer of lateral plate mesoderm	2.35e-12	84
circulatory system	2.59e-12	113
epithelial tube	3.89e-12	118
systemic artery	5.79e-11	33
systemic arterial system	5.79e-11	33
telencephalon	1.57e-10	34
gray matter	2.04e-10	34
brain grey matter	2.04e-10	34
cerebral hemisphere	3.73e-10	32

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.