Coexpression cluster:C529

Full id: C529_testis_temporal_amygdala_occipital_insula_brain_putamen

Phase1 CAGE Peaks

Hg19::chr11:125774362..125774414,+	p1@DDX25
Hg19::chr12:124457511..124457524,-	p6@CCDC92
Hg19::chr12:124457526..124457542,-	p7@CCDC92
Hg19::chr12:124457547..124457562,-	p8@CCDC92
Hg19::chr12:31882027..31882048,-	p3@AMN1
Hg19::chr13:37006421..37006487,+	p2@CCNA1
Hg19::chr13:50510622..50510649,-	p4@SPRYD7
Hg19::chr14:105940901..105940956,+	p2@CRIP2
Hg19::chr15:91446123..91446133,+	p14@MAN2A2
Hg19::chr15:91446139..91446156,+	p11@MAN2A2
Hg19::chr1:145516574..145516603,+	p2@PEX11B
Hg19::chr1:244615425..244615441,-	p9@ADSS
Hg19::chr6:43478068..43478103,-	p1@LRRC73
Hg19::chr9:90589429..90589488,-	p1@CDK20
Hg19::chr9:99212366..99212385,+	p2@HABP4
Hg19::chrX:71289516..71289537,+	p@chrX:71289516..71289537 +

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:0006167	AMP biosynthetic process	0.0180732803962082
GO:0033391	chromatoid body	0.0180732803962082
GO:0046033	AMP metabolic process	0.0180732803962082
GO:0004572	mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity	0.0180732803962082
GO:0004019	adenylosuccinate synthase activity	0.0180732803962082
GO:0007141	male meiosis I	0.0180732803962082
GO:0005737	cytoplasm	0.0180732803962082
GO:0007283	spermatogenesis	0.0180732803962082
GO:0048232	male gamete generation	0.0180732803962082
GO:0007276	gamete generation	0.022917850838468
GO:0016559	peroxisome fission	0.022917850838468
GO:0007140	male meiosis	0.0245072039266199
GO:0048285	organelle fission	0.0254315348049321
GO:0019953	sexual reproduction	0.0254315348049321
GO:0004559	alpha-mannosidase activity	0.0280008139512107
GO:0006013	mannose metabolic process	0.0373146430493189
GO:0005779	integral to peroxisomal membrane	0.0373146430493189
GO:0031231	intrinsic to peroxisomal membrane	0.0373146430493189
GO:0004004	ATP-dependent RNA helicase activity	0.0374514524468862
GO:0006406	mRNA export from nucleus	0.0374514524468862
GO:0008186	RNA-dependent ATPase activity	0.0374514524468862
GO:0007286	spermatid development	0.0374514524468862
GO:0015924	mannosyl-oligosaccharide mannosidase activity	0.0374514524468862
GO:0009167	purine ribonucleoside monophosphate metabolic process	0.0374514524468862
GO:0048515	spermatid differentiation	0.0374514524468862
GO:0009168	purine ribonucleoside monophosphate biosynthetic process	0.0374514524468862
GO:0009127	purine nucleoside monophosphate biosynthetic process	0.0374514524468862
GO:0009126	purine nucleoside monophosphate metabolic process	0.0374514524468862
GO:0007031	peroxisome organization and biogenesis	0.0405746259930195
GO:0006405	RNA export from nucleus	0.0405746259930195
GO:0003724	RNA helicase activity	0.0405746259930195
GO:0009161	ribonucleoside monophosphate metabolic process	0.0419160099579801
GO:0009156	ribonucleoside monophosphate biosynthetic process	0.0419160099579801
GO:0015923	mannosidase activity	0.0431412155542507
GO:0009124	nucleoside monophosphate biosynthetic process	0.0442251507911105
GO:0009123	nucleoside monophosphate metabolic process	0.0442251507911105
GO:0051168	nuclear export	0.0479907101573285
GO:0031903	microbody membrane	0.0479907101573285
GO:0005778	peroxisomal membrane	0.0479907101573285
GO:0044439	peroxisomal part	0.0479907101573285
GO:0044438	microbody part	0.0479907101573285
GO:0000079	regulation of cyclin-dependent protein kinase activity	0.0488329871421061

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
neural cell	1.24e-08	25

Uber Anatomy

Ontology term	p-value	n
nervous system	1.06e-60	89
neural tube	3.48e-60	56
neural rod	3.48e-60	56
future spinal cord	3.48e-60	56
neural keel	3.48e-60	56
central nervous system	3.96e-59	81
regional part of nervous system	5.80e-57	53
regional part of brain	5.80e-57	53
neurectoderm	2.34e-53	86
brain	1.13e-51	68
future brain	1.13e-51	68
neural plate	8.19e-50	82
presumptive neural plate	8.19e-50	82
regional part of forebrain	3.79e-44	41
forebrain	3.79e-44	41
anterior neural tube	3.79e-44	41
future forebrain	3.79e-44	41
pre-chordal neural plate	5.70e-40	61
adult organism	1.17e-39	114
ectoderm-derived structure	5.45e-38	171
ectoderm	5.45e-38	171
presumptive ectoderm	5.45e-38	171
ecto-epithelium	4.95e-37	104
telencephalon	1.47e-36	34
brain grey matter	1.80e-36	34
gray matter	1.80e-36	34
cerebral hemisphere	1.60e-34	32
regional part of telencephalon	3.04e-34	32
structure with developmental contribution from neural crest	4.13e-31	132
cerebral cortex	3.20e-26	25
pallium	3.20e-26	25
regional part of cerebral cortex	3.42e-26	22
organ system subdivision	4.61e-24	223
neocortex	8.77e-24	20
posterior neural tube	1.60e-16	15
chordal neural plate	1.60e-16	15
anatomical cluster	2.29e-15	373
segmental subdivision of hindbrain	1.44e-13	12
hindbrain	1.44e-13	12
presumptive hindbrain	1.44e-13	12
segmental subdivision of nervous system	3.18e-12	13
tube	4.72e-12	192
basal ganglion	5.21e-12	9
nuclear complex of neuraxis	5.21e-12	9
aggregate regional part of brain	5.21e-12	9
collection of basal ganglia	5.21e-12	9
cerebral subcortex	5.21e-12	9
neural nucleus	1.24e-11	9
nucleus of brain	1.24e-11	9
organ part	6.94e-11	218
regional part of metencephalon	1.91e-10	9
metencephalon	1.91e-10	9
future metencephalon	1.91e-10	9
embryo	1.95e-10	592
cell layer	7.10e-10	309
epithelium	7.82e-10	306
developing anatomical structure	1.47e-09	581
telencephalic nucleus	1.74e-09	7
embryonic structure	2.69e-09	564
germ layer	3.63e-09	560
germ layer / neural crest	3.63e-09	560
embryonic tissue	3.63e-09	560
presumptive structure	3.63e-09	560
germ layer / neural crest derived structure	3.63e-09	560
epiblast (generic)	3.63e-09	560
diencephalon	7.23e-09	7
future diencephalon	7.23e-09	7
gyrus	9.58e-09	6
multi-cellular organism	1.12e-08	656
multi-tissue structure	1.43e-08	342
brainstem	5.15e-08	6
limbic system	8.19e-08	5
organ	8.45e-08	503
anatomical conduit	8.79e-08	240
temporal lobe	1.71e-07	6
parietal lobe	1.78e-07	5
anatomical system	2.32e-07	624
occipital lobe	2.35e-07	5
anatomical group	2.76e-07	625
cerebellum	3.42e-07	6
rhombic lip	3.42e-07	6

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
CCNT2#905	10	3.72717739821331	6.33214862336528e-05	0.00103299479861863
CTCFL#140690	5	5.80778657616893	0.00123224332028407	0.00828735012731975
E2F1#1869	12	3.46403944579717	1.12150247414086e-05	0.000287009548877228
E2F6#1876	8	2.36101446197524	0.0107042805720474	0.0395172979379306
EGR1#1958	9	2.64080069725243	0.00262508258343361	0.0145127838616919
ELF1#1997	9	2.25428715466281	0.00807668348299441	0.0319418640669666
HEY1#23462	9	2.13888231693832	0.0115734531098334	0.0422910279324688
HMGN3#9324	11	5.29200146805038	5.5376987114284e-07	2.56247991015893e-05
MAX#4149	10	3.79562088765125	5.38997370122769e-05	0.000913985165420553
MXI1#4601	9	5.27377321522551	1.18160458251851e-05	0.000299092586024359
MYC#4609	8	2.45754441016913	0.00836194648630699	0.0329204361083917
NRF1#4899	9	6.4642655899646	2.18388258131197e-06	7.84058139943764e-05
PAX5#5079	7	2.74629168930852	0.0082571252608217	0.0325371983517566
POLR2A#5430	14	1.76849085128312	0.0027921942926151	0.0152909642769875
RFX5#5993	5	3.54350318446915	0.0104239688604285	0.0386848441409387
SIN3A#25942	9	2.8635272083139	0.00144693709318507	0.00927722162656733
TAF1#6872	10	1.96649781514429	0.012416800069541	0.0449496770351054
TCF12#6938	6	3.75334055371285	0.00342470150881989	0.0174516906991774
THAP1#55145	4	7.3809752006709	0.00175939848493061	0.0108126290671807
USF2#7392	5	3.82123452502047	0.00761212062526408	0.0313684606211314
ZNF143#7702	6	4.7650152537275	0.000997952415924964	0.00715389885145084
ZNF263#10127	6	2.90182646012142	0.0121295164888246	0.0439828682930475

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.