Coexpression cluster:C652

Full id: C652_cerebellum_occipital_pineal_pituitary_medial_parietal_amygdala

Phase1 CAGE Peaks

Hg19::chr11:105948040..105948082,-	p1@KBTBD3
Hg19::chr11:8190534..8190595,-	p1@RIC3
Hg19::chr17:40897043..40897087,-	p1@EZH1
Hg19::chr17:5095296..5095308,+	p2@LOC100130950
Hg19::chr19:38085739..38085762,+	p3@ZNF540
Hg19::chr19:38085768..38085821,+	p1@ZNF540
Hg19::chr1:244998602..244998646,+	p3@FAM36A
Hg19::chr3:108308331..108308389,+	p2@DZIP3
Hg19::chr4:149363637..149363651,-	p4@NR3C2
Hg19::chr4:149363662..149363688,-	p6@NR3C2
Hg19::chr6:117002339..117002400,+	p1@KPNA5
Hg19::chr6:27342978..27343050,-	p1@ZNF204P
Hg19::chr8:119634141..119634223,-	p1@SAMD12

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:0031593	polyubiquitin binding	0.0282241442524776
GO:0055078	sodium ion homeostasis	0.0282241442524776
GO:0006883	cellular sodium ion homeostasis	0.0282241442524776
GO:0012505	endomembrane system	0.0302301958653872
GO:0000209	protein polyubiquitination	0.0398664843190308
GO:0006607	NLS-bearing substrate import into nucleus	0.0398664843190308
GO:0031090	organelle membrane	0.0398664843190308
GO:0030004	cellular monovalent inorganic cation homeostasis	0.0398664843190308
GO:0055067	monovalent inorganic cation homeostasis	0.0398664843190308
GO:0043130	ubiquitin binding	0.0398664843190308
GO:0032182	small conjugating protein binding	0.0398664843190308
GO:0005789	endoplasmic reticulum membrane	0.0398664843190308
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.0398664843190308
GO:0044432	endoplasmic reticulum part	0.0456690194223664

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
lymphoid lineage restricted progenitor cell	1.60e-10	52
lymphocyte	2.18e-10	53
common lymphoid progenitor	2.18e-10	53
mature alpha-beta T cell	1.03e-08	18
alpha-beta T cell	1.03e-08	18
immature T cell	1.03e-08	18
mature T cell	1.03e-08	18
immature alpha-beta T cell	1.03e-08	18

Uber Anatomy

Ontology term	p-value	n
adult organism	4.02e-53	115
neural tube	3.68e-29	57
neural rod	3.68e-29	57
future spinal cord	3.68e-29	57
neural keel	3.68e-29	57
central nervous system	2.96e-28	82
regional part of nervous system	8.63e-28	94
nervous system	8.63e-28	94
anterior neural tube	1.29e-24	42
regional part of forebrain	2.19e-24	41
forebrain	2.19e-24	41
future forebrain	2.19e-24	41
regional part of brain	4.16e-24	59
brain	6.78e-24	69
future brain	6.78e-24	69
telencephalon	7.02e-20	34
gray matter	7.33e-20	34
brain grey matter	7.33e-20	34
neurectoderm	1.19e-19	90
neural plate	2.46e-19	86
presumptive neural plate	2.46e-19	86
regional part of telencephalon	3.11e-19	33
cerebral hemisphere	9.18e-19	32
regional part of cerebral cortex	1.87e-15	22
pre-chordal neural plate	9.99e-15	61
cerebral cortex	1.87e-14	25
pallium	1.87e-14	25
anterior region of body	2.04e-14	129
craniocervical region	2.04e-14	129
neocortex	3.17e-14	20
ectoderm	6.31e-14	173
presumptive ectoderm	6.31e-14	173
ectoderm-derived structure	1.69e-13	169
head	5.69e-13	123
basal ganglion	5.05e-07	9
nuclear complex of neuraxis	5.05e-07	9
aggregate regional part of brain	5.05e-07	9
collection of basal ganglia	5.05e-07	9
cerebral subcortex	5.05e-07	9
nucleus of brain	6.71e-07	9
neural nucleus	6.71e-07	9

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
CHD2#1106	7	5.56985844913985	7.97823784692744e-05	0.00122157921491754
E2F1#1869	7	2.64244034647348	0.00779501640558097	0.0320235905271997
EGR1#1958	8	3.06964867372932	0.00126568416933679	0.0084925659467629
ELF1#1997	9	2.94791397148214	0.000603403467917953	0.00503949258583632
ETS1#2113	6	4.49019734870877	0.00106508682285967	0.00752462982430093
HDAC2#3066	4	4.12788314973116	0.0127681960324703	0.0460382401324068
HEY1#23462	11	3.41855549801252	9.95779509504428e-06	0.000261039699279952
IRF1#3659	9	5.28726721400578	4.89873907841973e-06	0.000151411485827487
IRF3#3661	3	10.8419889718822	0.00234831973571704	0.0133103313187101
JUND#3727	6	3.22830643470971	0.0059186599284079	0.0265466576879103
MAX#4149	6	2.97810254261867	0.00885876695823828	0.0336143279447554
MYC#4609	9	3.6154259111142	0.000116372921993874	0.00158129997399405
NRF1#4899	8	7.51401812166825	1.78371877765449e-06	6.69866254654647e-05
PAX5#5079	6	3.07826101438977	0.00751515295554873	0.0309872106883238
POLR2A#5430	13	2.14745317655807	4.83928878402115e-05	0.000840669463264112
POU2F2#5452	6	4.20282648818886	0.00151318059670815	0.00965689387959685
SETDB1#9869	4	12.4061619009263	0.000225772565725305	0.00250179957472521
SIX5#147912	4	5.25745087860277	0.00546626873738978	0.0247567927434627
SP2#6668	4	8.0472401519522	0.00115644787909033	0.0079069237344887
TAF1#6872	12	3.0858888791495	4.82574043270037e-06	0.000149509197582555
TBP#6908	11	3.13649827369694	2.43452380190334e-05	0.000528056555237762
TRIM28#10155	4	5.72016155238847	0.00403993547839026	0.0193411332306945
USF1#7391	6	2.9360765894806	0.00950376317872054	0.0357990161805668
YY1#7528	9	3.40004128836036	0.00019190138529349	0.00231485201878803
ZEB1#6935	7	9.09377108636977	3.17961465987139e-06	0.000107086673802744
ZNF143#7702	7	7.26970275889195	1.40394872054989e-05	0.000338630485971155

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.