Coexpression cluster:C275

Full id: C275_pons_medulla_cerebellum_locus_thalamus_diencephalon_spinal

Phase1 CAGE Peaks

Hg19::chr10:17045960..17045970,-	p@chr10:17045960..17045970 -
Hg19::chr10:61043434..61043446,-	p13@FAM13C
Hg19::chr10:61043452..61043467,-	p16@FAM13C
Hg19::chr11:22359520..22359556,+	p3@SLC17A6
Hg19::chr11:22359562..22359575,+	p6@SLC17A6
Hg19::chr11:22359879..22359909,+	p2@SLC17A6
Hg19::chr11:3224761..3224787,-	p@chr11:3224761..3224787 -
Hg19::chr11:3224982..3224985,-	p@chr11:3224982..3224985 -
Hg19::chr11:3224990..3225000,-	p@chr11:3224990..3225000 -
Hg19::chr11:3253592..3253608,-	p2@MRGPRE
Hg19::chr11:3253635..3253658,-	p1@MRGPRE
Hg19::chr11:3253663..3253670,-	p4@MRGPRE
Hg19::chr11:3253872..3253882,-	p3@MRGPRE
Hg19::chr12:33592574..33592584,-	p6@SYT10
Hg19::chr13:93587956..93587973,+	p@chr13:93587956..93587973 +
Hg19::chr16:47920709..47920716,-	p4@uc002eex.1
Hg19::chr16:49669972..49669983,-	p@chr16:49669972..49669983 -
Hg19::chr16:49670005..49670020,-	p@chr16:49670005..49670020 -
Hg19::chr16:67237164..67237171,+	p@chr16:67237164..67237171 +
Hg19::chr17:68101117..68101162,+	p2@KCNJ16
Hg19::chr1:205313500..205313511,-	p11@KLHDC8A
Hg19::chr1:216692584..216692595,-	p@chr1:216692584..216692595 -
Hg19::chr1:216692717..216692725,-	p@chr1:216692717..216692725 -
Hg19::chr1:216692728..216692741,-	p@chr1:216692728..216692741 -
Hg19::chr1:218222373..218222381,-	p@chr1:218222373..218222381 -
Hg19::chr1:218222386..218222394,-	p@chr1:218222386..218222394 -
Hg19::chr21:31312092..31312103,-	p7@GRIK1
Hg19::chr2:17381145..17381164,-	p@chr2:17381145..17381164 -
Hg19::chr2:72381655..72381673,-	p@chr2:72381655..72381673 -
Hg19::chr4:117675601..117675614,+	p@chr4:117675601..117675614 +
Hg19::chr4:117675642..117675654,+	p@chr4:117675642..117675654 +
Hg19::chr4:186661365..186661384,-	p46@SORBS2
Hg19::chr4:82965824..82965835,-	p6@ENST00000508294 p6@ENST00000510780 p6@ENST00000512343 p6@ENST00000512716 p6@ENST00000514050
Hg19::chr5:126959224..126959239,+	p@chr5:126959224..126959239 +
Hg19::chr5:126959900..126959932,+	p@chr5:126959900..126959932 +
Hg19::chr5:126959946..126959960,+	p@chr5:126959946..126959960 +
Hg19::chr6:140415977..140415987,-	p@chr6:140415977..140415987 -
Hg19::chr6:140415989..140415997,-	p@chr6:140415989..140415997 -
Hg19::chr6:140416018..140416025,-	p@chr6:140416018..140416025 -
Hg19::chr6:71665623..71665630,-	p13@B3GAT2
Hg19::chr7:31569075..31569083,+	p3@CCDC129
Hg19::chr7:31569365..31569379,+	p1@CCDC129
Hg19::chr9:135457530..135457541,+	p2@BARHL1
Hg19::chr9:135457972..135457978,+	p8@BARHL1
Hg19::chr9:135458021..135458030,+	p6@BARHL1
Hg19::chr9:135458288..135458301,+	p3@BARHL1
Hg19::chr9:135458306..135458314,+	p9@BARHL1

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:0051966	regulation of synaptic transmission, glutamatergic	0.0414160162571539
GO:0035249	synaptic transmission, glutamatergic	0.0414160162571539
GO:0016021	integral to membrane	0.0414160162571539
GO:0031224	intrinsic to membrane	0.0414160162571539
GO:0051179	localization	0.0414160162571539
GO:0015018	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity	0.0414160162571539
GO:0015277	kainate selective glutamate receptor activity	0.0414160162571539
GO:0044425	membrane part	0.04833425076599

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	3.33e-49	94
nervous system	3.33e-49	94
adult organism	4.26e-48	115
central nervous system	1.33e-47	82
neural tube	1.66e-45	57
neural rod	1.66e-45	57
future spinal cord	1.66e-45	57
neural keel	1.66e-45	57
regional part of brain	2.13e-41	59
brain	2.39e-39	69
future brain	2.39e-39	69
neurectoderm	8.93e-39	90
neural plate	1.98e-37	86
presumptive neural plate	1.98e-37	86
ectoderm	2.48e-33	173
presumptive ectoderm	2.48e-33	173
anterior neural tube	2.18e-32	42
ectoderm-derived structure	6.37e-32	169
regional part of forebrain	6.99e-32	41
forebrain	6.99e-32	41
future forebrain	6.99e-32	41
gray matter	6.75e-26	34
brain grey matter	6.75e-26	34
telencephalon	8.22e-26	34
regional part of telencephalon	7.54e-25	33
cerebral hemisphere	4.33e-24	32
pre-chordal neural plate	1.03e-23	61
anterior region of body	6.63e-23	129
craniocervical region	6.63e-23	129
head	5.83e-22	123
regional part of cerebral cortex	2.76e-19	22
cerebral cortex	1.53e-18	25
pallium	1.53e-18	25
neocortex	1.23e-17	20
posterior neural tube	6.23e-14	15
chordal neural plate	6.23e-14	15
segmental subdivision of nervous system	7.68e-12	13
segmental subdivision of hindbrain	3.04e-11	12
hindbrain	3.04e-11	12
presumptive hindbrain	3.04e-11	12
organ part	7.98e-11	219
nucleus of brain	7.75e-09	9
neural nucleus	7.75e-09	9
brainstem	1.11e-08	8
basal ganglion	1.16e-08	9
nuclear complex of neuraxis	1.16e-08	9
aggregate regional part of brain	1.16e-08	9
collection of basal ganglia	1.16e-08	9
cerebral subcortex	1.16e-08	9
regional part of metencephalon	2.36e-08	9
metencephalon	2.36e-08	9
future metencephalon	2.36e-08	9
multi-cellular organism	3.32e-08	659
tube	5.04e-08	194
organ	7.93e-08	511
embryo	1.09e-07	612
diencephalon	1.74e-07	7
future diencephalon	1.74e-07	7
epithelium	2.96e-07	309
anatomical conduit	3.02e-07	241
telencephalic nucleus	6.44e-07	7
cell layer	6.47e-07	312
gyrus	6.53e-07	6
anatomical cluster	7.96e-07	286

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)
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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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