Coexpression cluster:C291

Full id: C291_spinal_substantia_retina_medulla_tongue_skeletal_trachea

Phase1 CAGE Peaks

Hg19::chr10:104184955..104184965,-	p4@CUEDC2
Hg19::chr10:60936793..60936819,-	p@chr10:60936793..60936819 -
Hg19::chr11:125366211..125366212,-	p14@FEZ1
Hg19::chr17:42984119..42984130,-	p43@GFAP
Hg19::chr17:42984138..42984151,-	p38@GFAP
Hg19::chr17:42984459..42984521,+	p@chr17:42984459..42984521 +
Hg19::chr17:42984550..42984567,+	p@chr17:42984550..42984567 +
Hg19::chr17:42984604..42984618,+	p@chr17:42984604..42984618 +
Hg19::chr17:42989173..42989181,-	p40@GFAP
Hg19::chr17:73504580..73504588,-	p@chr17:73504580..73504588 -
Hg19::chr19:1452223..1452232,+	p@chr19:1452223..1452232 +
Hg19::chr19:40919278..40919294,-	p2@PRX
Hg19::chr1:156404868..156404881,+	p@chr1:156404868..156404881 +
Hg19::chr1:156404895..156404923,+	p@chr1:156404895..156404923 +
Hg19::chr1:156404975..156404990,+	p@chr1:156404975..156404990 +
Hg19::chr1:161275051..161275059,-	p@chr1:161275051..161275059 -
Hg19::chr1:161275062..161275086,-	p@chr1:161275062..161275086 -
Hg19::chr1:161275096..161275109,-	p@chr1:161275096..161275109 -
Hg19::chr1:161275111..161275127,-	p@chr1:161275111..161275127 -
Hg19::chr1:161275189..161275203,-	p@chr1:161275189..161275203 -
Hg19::chr1:161275238..161275250,-	p@chr1:161275238..161275250 -
Hg19::chr1:161275265..161275277,-	p@chr1:161275265..161275277 -
Hg19::chr1:161275395..161275412,-	p@chr1:161275395..161275412 -
Hg19::chr1:161275623..161275644,-	p@chr1:161275623..161275644 -
Hg19::chr1:161276191..161276202,-	p6@MPZ
Hg19::chr1:161276686..161276694,-	p11@MPZ
Hg19::chr1:161279749..161279764,-	p1@MPZ
Hg19::chr1:44991346..44991355,+	p@chr1:44991346..44991355 +
Hg19::chr20:52573198..52573199,-	p@chr20:52573198..52573199 -
Hg19::chr2:128403624..128403631,+	p4@GPR17
Hg19::chr2:128403720..128403732,+	p1@GPR17
Hg19::chr2:241521605..241521654,-	p@chr2:241521605..241521654 -
Hg19::chr3:44062980..44062993,+	p@chr3:44062980..44062993 +
Hg19::chr4:115519490..115519496,+	p11@UGT8
Hg19::chr5:123774243..123774262,-	p@chr5:123774243..123774262 -
Hg19::chr5:123774265..123774292,-	p@chr5:123774265..123774292 -
Hg19::chr5:123774307..123774326,-	p@chr5:123774307..123774326 -
Hg19::chr5:146435694..146435705,-	p23@PPP2R2B
Hg19::chr6:133424178..133424190,-	p@chr6:133424178..133424190 -
Hg19::chr7:29966288..29966313,-	p@chr7:29966288..29966313 -
Hg19::chr7:33842781..33842787,-	p1@ENST00000440034
Hg19::chr7:4998664..4998674,-	p2@MMD2
Hg19::chr7:99531868..99531881,-	p@chr7:99531868..99531881 -
Hg19::chr9:90113407..90113437,+	p11@DAPK1

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:0007638	mechanosensory behavior	0.000225625857182879
GO:0032502	developmental process	0.000680714741513836
GO:0009612	response to mechanical stimulus	0.000680714741513836
GO:0007422	peripheral nervous system development	0.00103494969512009
GO:0007399	nervous system development	0.00143356170058839
GO:0008489	UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity	0.00754747717880883
GO:0003851	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity	0.00754747717880883
GO:0048468	cell development	0.00754747717880883
GO:0048731	system development	0.0170389325473447
GO:0045217	intercellular junction maintenance	0.0170389325473447
GO:0009628	response to abiotic stimulus	0.0180450614628599
GO:0048869	cellular developmental process	0.0193185416021582
GO:0030154	cell differentiation	0.0193185416021582
GO:0048856	anatomical structure development	0.0239334495934795
GO:0008219	cell death	0.0239334495934795
GO:0016265	death	0.0239334495934795
GO:0043015	gamma-tubulin binding	0.0267100411830768
GO:0006688	glycosphingolipid biosynthetic process	0.0309604441808687
GO:0007275	multicellular organismal development	0.0309604441808687
GO:0007610	behavior	0.0309604441808687
GO:0019226	transmission of nerve impulse	0.0369535581590065
GO:0009247	glycolipid biosynthetic process	0.038663346172115
GO:0019835	cytolysis	0.0394425961671539
GO:0035250	UDP-galactosyltransferase activity	0.0401562837425331
GO:0045216	intercellular junction assembly and maintenance	0.0408122765299571
GO:0006687	glycosphingolipid metabolic process	0.0414172317562238
GO:0030148	sphingolipid biosynthetic process	0.0440698256137007
GO:0005856	cytoskeleton	0.0468734084861649
GO:0007028	cytoplasm organization and biogenesis	0.0468734084861649

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	8.60e-100	56
neural rod	8.60e-100	56
future spinal cord	8.60e-100	56
neural keel	8.60e-100	56
regional part of nervous system	7.10e-87	53
regional part of brain	7.10e-87	53
central nervous system	3.58e-79	81
brain	1.14e-74	68
future brain	1.14e-74	68
nervous system	9.89e-71	89
neural plate	2.41e-70	82
presumptive neural plate	2.41e-70	82
neurectoderm	8.68e-67	86
brain grey matter	2.35e-62	34
gray matter	2.35e-62	34
telencephalon	3.01e-62	34
regional part of forebrain	1.53e-61	41
forebrain	1.53e-61	41
anterior neural tube	1.53e-61	41
future forebrain	1.53e-61	41
regional part of telencephalon	3.57e-54	32
ecto-epithelium	3.96e-54	104
cerebral hemisphere	6.63e-54	32
adult organism	2.20e-52	114
regional part of cerebral cortex	4.67e-44	22
structure with developmental contribution from neural crest	6.07e-44	132
pre-chordal neural plate	1.85e-43	61
neocortex	4.18e-42	20
posterior neural tube	2.46e-39	15
chordal neural plate	2.46e-39	15
cerebral cortex	1.36e-38	25
pallium	1.36e-38	25
ectoderm-derived structure	4.64e-36	171
ectoderm	4.64e-36	171
presumptive ectoderm	4.64e-36	171
brainstem	6.70e-31	6
neural nucleus	3.72e-26	9
nucleus of brain	3.72e-26	9
organ system subdivision	5.09e-26	223
segmental subdivision of hindbrain	6.37e-26	12
hindbrain	6.37e-26	12
presumptive hindbrain	6.37e-26	12
tube	1.66e-24	192
segmental subdivision of nervous system	7.84e-24	13
gyrus	8.98e-20	6
basal ganglion	3.73e-19	9
nuclear complex of neuraxis	3.73e-19	9
aggregate regional part of brain	3.73e-19	9
collection of basal ganglia	3.73e-19	9
cerebral subcortex	3.73e-19	9
anatomical conduit	3.42e-18	240
telencephalic nucleus	2.50e-17	7
spinal cord	1.18e-16	3
dorsal region element	1.18e-16	3
dorsum	1.18e-16	3
medulla oblongata	1.61e-16	3
myelencephalon	1.61e-16	3
future myelencephalon	1.61e-16	3
pons	3.64e-16	3
occipital lobe	1.19e-15	5
epithelium	9.56e-14	306
regional part of metencephalon	1.16e-13	9
metencephalon	1.16e-13	9
future metencephalon	1.16e-13	9
organ part	1.16e-13	218
anatomical cluster	1.21e-13	373
cell layer	1.53e-13	309
temporal lobe	2.56e-11	6
locus ceruleus	2.59e-11	2
brainstem nucleus	2.59e-11	2
hindbrain nucleus	2.59e-11	2
corpus striatum	3.17e-11	4
striatum	3.17e-11	4
ventral part of telencephalon	3.17e-11	4
future corpus striatum	3.17e-11	4
middle temporal gyrus	2.66e-10	2
multi-tissue structure	1.51e-09	342
limbic system	1.62e-09	5
parietal lobe	1.83e-09	5
frontal cortex	1.93e-07	3
organ	2.23e-07	503
caudate-putamen	4.05e-07	3
dorsal striatum	4.05e-07	3

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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