Coexpression cluster:C503

Full id: C503_occipital_spinal_thalamus_locus_optic_globus_pineal

Phase1 CAGE Peaks

Hg19::chr14:95623976..95624057,+	p1@DICER1-AS
Hg19::chr18:46065393..46065444,+	p1@CTIF
Hg19::chr1:10436775..10436792,+	p@chr1:10436775..10436792 +
Hg19::chr1:66999791..66999798,+	p3@SGIP1
Hg19::chr1:67125565..67125577,+	p@chr1:67125565..67125577 +
Hg19::chr1:6997068..6997095,+	p@chr1:6997068..6997095 +
Hg19::chr3:133380806..133380856,+	p1@TFP1
Hg19::chr3:185080917..185080987,+	p2@MAP3K13
Hg19::chr4:118006697..118006741,-	p1@TRAM1L1
Hg19::chr4:134070293..134070304,-	p2@ENST00000509715
Hg19::chr4:71587632..71587646,+	p3@RUFY3
Hg19::chr4:71587669..71587752,+	p1@RUFY3
Hg19::chr4:71588022..71588055,+	p12@RUFY3
Hg19::chr4:85887859..85888004,+	p1@WDFY3-AS2
Hg19::chr5:133706714..133706743,-	p1@CDKL3
Hg19::chr5:81574463..81574494,+	p@chr5:81574463..81574494 +
Hg19::chr7:86781858..86781879,+	p3@DMTF1
Hg19::chrX:100740401..100740449,+	p1@ARMCX4
Hg19::chrX:102585134..102585176,+	p1@TCEAL7

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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No GOStat results

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
nervous system	8.31e-44	89
central nervous system	1.28e-41	81
adult organism	1.33e-39	114
neural tube	2.95e-36	56
neural rod	2.95e-36	56
future spinal cord	2.95e-36	56
neural keel	2.95e-36	56
neurectoderm	5.94e-35	86
brain	8.57e-35	68
future brain	8.57e-35	68
regional part of nervous system	4.56e-34	53
regional part of brain	4.56e-34	53
neural plate	2.96e-33	82
presumptive neural plate	2.96e-33	82
ectoderm-derived structure	3.78e-31	171
ectoderm	3.78e-31	171
presumptive ectoderm	3.78e-31	171
regional part of forebrain	1.41e-28	41
forebrain	1.41e-28	41
anterior neural tube	1.41e-28	41
future forebrain	1.41e-28	41
pre-chordal neural plate	7.65e-25	61
structure with developmental contribution from neural crest	1.93e-24	132
brain grey matter	9.08e-24	34
gray matter	9.08e-24	34
ecto-epithelium	1.09e-23	104
telencephalon	1.16e-23	34
cerebral hemisphere	2.16e-22	32
regional part of telencephalon	2.34e-22	32
organ system subdivision	9.17e-20	223
cerebral cortex	1.18e-17	25
pallium	1.18e-17	25
regional part of cerebral cortex	7.50e-17	22
neocortex	2.05e-15	20
multi-cellular organism	9.72e-14	656
anatomical cluster	4.21e-12	373
multi-tissue structure	1.55e-11	342
anatomical system	6.37e-09	624
posterior neural tube	8.29e-09	15
chordal neural plate	8.29e-09	15
anatomical group	1.23e-08	625
organ	4.97e-08	503
basal ganglion	1.38e-07	9
nuclear complex of neuraxis	1.38e-07	9
aggregate regional part of brain	1.38e-07	9
collection of basal ganglia	1.38e-07	9
cerebral subcortex	1.38e-07	9
neural nucleus	1.47e-07	9
nucleus of brain	1.47e-07	9
embryo	1.48e-07	592
segmental subdivision of nervous system	1.63e-07	13
germ layer	1.73e-07	560
germ layer / neural crest	1.73e-07	560
embryonic tissue	1.73e-07	560
presumptive structure	1.73e-07	560
germ layer / neural crest derived structure	1.73e-07	560
epiblast (generic)	1.73e-07	560
embryonic structure	2.58e-07	564
organ part	3.37e-07	218
cell layer	5.02e-07	309
epithelium	7.80e-07	306
segmental subdivision of hindbrain	8.09e-07	12
hindbrain	8.09e-07	12
presumptive hindbrain	8.09e-07	12
developing anatomical structure	9.99e-07	581

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
POLR2A#5430	15	1.6953577709669	0.00416073088978701	0.0198276406916621
SRF#6722	5	3.630836384781	0.00982851932453297	0.036941041844564
TRIM28#10155	5	4.89224343296382	0.00277009792540522	0.0151763236233224
USF1#7391	12	4.01778901718397	3.83675826695491e-06	0.00012537772110216
USF2#7392	5	3.41899931186042	0.0125738661207166	0.0454709835104403
YY1#7528	12	3.10179205253928	5.99478432712854e-05	0.000985967370615712

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.