Coexpression cluster:C899

Full id: C899_pituitary_cerebellum_occipital_parietal_testicular_brain_temporal

Phase1 CAGE Peaks

Hg19::chr13:26042960..26043015,+	p2@ATP8A2
Hg19::chr14:74185796..74185825,-	p1@AK308604
Hg19::chr16:2136434..2136445,+	p@chr16:2136434..2136445 +
Hg19::chr16:87369953..87369959,-	p@chr16:87369953..87369959 -
Hg19::chr2:203735519..203735539,-	p8@ICA1L
Hg19::chr2:203735586..203735600,-	p14@ICA1L
Hg19::chr9:14662234..14662273,-	p@chr9:14662234..14662273 -
Hg19::chr9:74061853..74061893,-	p7@TRPM3
Hg19::chr9:74061895..74061905,-	p14@TRPM3

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:0004012	phospholipid-translocating ATPase activity	0.0218266084661406
GO:0015247	aminophospholipid transporter activity	0.0218266084661406
GO:0015914	phospholipid transport	0.0218266084661406
GO:0015075	ion transmembrane transporter activity	0.0218266084661406
GO:0005548	phospholipid transporter activity	0.0218266084661406
GO:0022891	substrate-specific transmembrane transporter activity	0.0218266084661406
GO:0022857	transmembrane transporter activity	0.0218266084661406
GO:0022892	substrate-specific transporter activity	0.0222822945446405
GO:0005319	lipid transporter activity	0.0413879448357098
GO:0005262	calcium channel activity	0.0461577732564526
GO:0006869	lipid transport	0.0468509204505933
GO:0015662	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism	0.0468509204505933
GO:0006816	calcium ion transport	0.0488370558464889
GO:0042625	ATPase activity, coupled to transmembrane movement of ions	0.0488370558464889
GO:0008285	negative regulation of cell proliferation	0.0488370558464889
GO:0006810	transport	0.0488370558464889
GO:0015674	di-, tri-valent inorganic cation transport	0.0488370558464889
GO:0051234	establishment of localization	0.0488370558464889
GO:0042626	ATPase activity, coupled to transmembrane movement of substances	0.0488370558464889
GO:0043492	ATPase activity, coupled to movement of substances	0.0488370558464889
GO:0016820	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	0.0488370558464889
GO:0051179	localization	0.0488370558464889
GO:0015405	P-P-bond-hydrolysis-driven transmembrane transporter activity	0.0488370558464889
GO:0015399	primary active transmembrane transporter activity	0.0488370558464889

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
regional part of nervous system	3.42e-84	53
regional part of brain	3.42e-84	53
neural tube	1.79e-79	56
neural rod	1.79e-79	56
future spinal cord	1.79e-79	56
neural keel	1.79e-79	56
brain	1.77e-68	68
future brain	1.77e-68	68
central nervous system	5.36e-61	81
brain grey matter	7.64e-61	34
gray matter	7.64e-61	34
cerebral hemisphere	3.46e-58	32
regional part of forebrain	9.88e-56	41
forebrain	9.88e-56	41
anterior neural tube	9.88e-56	41
future forebrain	9.88e-56	41
telencephalon	1.24e-54	34
nervous system	1.79e-54	89
neural plate	7.52e-53	82
presumptive neural plate	7.52e-53	82
regional part of telencephalon	5.93e-52	32
neurectoderm	3.65e-50	86
regional part of cerebral cortex	6.73e-46	22
neocortex	2.74e-43	20
ecto-epithelium	1.32e-40	104
cerebral cortex	2.84e-40	25
pallium	2.84e-40	25
adult organism	7.19e-40	114
pre-chordal neural plate	2.54e-36	61
structure with developmental contribution from neural crest	2.31e-33	132
segmental subdivision of hindbrain	4.50e-30	12
hindbrain	4.50e-30	12
presumptive hindbrain	4.50e-30	12
segmental subdivision of nervous system	1.14e-27	13
ectoderm-derived structure	4.52e-26	171
ectoderm	4.52e-26	171
presumptive ectoderm	4.52e-26	171
posterior neural tube	7.94e-24	15
chordal neural plate	7.94e-24	15
brainstem	1.35e-23	6
gyrus	1.71e-23	6
regional part of metencephalon	2.57e-23	9
metencephalon	2.57e-23	9
future metencephalon	2.57e-23	9
neural nucleus	3.57e-22	9
nucleus of brain	3.57e-22	9
organ system subdivision	8.21e-22	223
tube	1.68e-19	192
pons	6.73e-18	3
basal ganglion	1.25e-15	9
nuclear complex of neuraxis	1.25e-15	9
aggregate regional part of brain	1.25e-15	9
collection of basal ganglia	1.25e-15	9
cerebral subcortex	1.25e-15	9
anatomical conduit	1.81e-14	240
organ part	1.13e-13	218
temporal lobe	1.36e-13	6
pituitary gland	2.43e-13	2
corpus striatum	3.01e-13	4
striatum	3.01e-13	4
ventral part of telencephalon	3.01e-13	4
future corpus striatum	3.01e-13	4
telencephalic nucleus	5.63e-13	7
locus ceruleus	1.01e-12	2
brainstem nucleus	1.01e-12	2
hindbrain nucleus	1.01e-12	2
middle temporal gyrus	2.29e-12	2
limbic system	2.11e-11	5
occipital lobe	8.93e-11	5
anatomical cluster	1.11e-10	373
parietal lobe	2.00e-10	5
multi-tissue structure	2.93e-10	342
epithelium	4.15e-10	306
cell layer	5.93e-10	309
cerebellum	8.33e-10	6
rhombic lip	8.33e-10	6
frontal cortex	8.09e-09	3
medulla oblongata	1.96e-08	3
myelencephalon	1.96e-08	3
future myelencephalon	1.96e-08	3
caudate-putamen	2.96e-08	3
dorsal striatum	2.96e-08	3
insula	2.52e-07	1
nucleus accumbens	3.01e-07	1
ventral striatum	3.01e-07	1
paracentral gyrus	3.40e-07	1
olfactory region	3.60e-07	1
primary subdivision of skull	3.60e-07	1
cranium	3.60e-07	1
neurocranium	3.60e-07	1
chondrocranium	3.60e-07	1
cartilaginous neurocranium	3.60e-07	1
head paraxial mesoderm	3.60e-07	1
gland of diencephalon	4.44e-07	4
neuroendocrine gland	4.44e-07	4
occipital pole	5.78e-07	1
pole of cerebral hemisphere	5.78e-07	1
putamen	7.73e-07	1
postcentral gyrus	9.73e-07	1

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
RAD21#5885	4	4.60223728686948	0.00735124290019625	0.0303965657317917

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.