Coexpression cluster:C986

Full id: C986_cerebellum_CD4_granulocyte_Mast_pineal_non_pituitary

Phase1 CAGE Peaks

Hg19::chr11:107328527..107328569,-	p1@CWF19L2
Hg19::chr13:107220455..107220517,-	p1@ARGLU1
Hg19::chr1:155826967..155827018,-	p1@GON4L
Hg19::chr1:53018743..53018777,-	p1@ZCCHC11
Hg19::chr4:68411245..68411267,-	p3@CENPC1
Hg19::chr5:70751463..70751503,+	p1@BDP1
Hg19::chr6:99873145..99873196,-	p1@PNISR
Hg19::chrX:77041685..77041716,-	p1@ATRX

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:0003676	nucleic acid binding	0.0204835785567552
GO:0003677	DNA binding	0.0228631337756485
GO:0005720	nuclear heterochromatin	0.0330563092809218
GO:0044427	chromosomal part	0.0330563092809218
GO:0005694	chromosome	0.0330563092809218
GO:0000792	heterochromatin	0.0330563092809218
GO:0000790	nuclear chromatin	0.0330563092809218
GO:0006306	DNA methylation	0.0330563092809218
GO:0006305	DNA alkylation	0.0330563092809218
GO:0006304	DNA modification	0.0333998818179596
GO:0005634	nucleus	0.0333998818179596
GO:0000776	kinetochore	0.0333998818179596
GO:0043414	biopolymer methylation	0.0447173103598427
GO:0003678	DNA helicase activity	0.0452035226043505

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
hematopoietic stem cell	1.37e-19	172
angioblastic mesenchymal cell	1.37e-19	172
leukocyte	4.34e-18	140
hematopoietic oligopotent progenitor cell	3.94e-17	165
hematopoietic multipotent progenitor cell	3.94e-17	165
hematopoietic cell	7.39e-17	182
lymphocyte	1.36e-14	53
common lymphoid progenitor	1.36e-14	53
lymphoid lineage restricted progenitor cell	1.77e-14	52
hematopoietic lineage restricted progenitor cell	1.63e-13	124
nongranular leukocyte	7.50e-13	119
mature alpha-beta T cell	7.69e-10	18
alpha-beta T cell	7.69e-10	18
immature T cell	7.69e-10	18
mature T cell	7.69e-10	18
immature alpha-beta T cell	7.69e-10	18
T cell	1.26e-07	25
pro-T cell	1.26e-07	25
B cell	3.59e-07	14
CD8-positive, alpha-beta T cell	5.39e-07	11

Uber Anatomy

Ontology term	p-value	n
adult organism	7.25e-25	115
neural tube	9.86e-17	57
neural rod	9.86e-17	57
future spinal cord	9.86e-17	57
neural keel	9.86e-17	57
regional part of forebrain	5.58e-15	41
forebrain	5.58e-15	41
future forebrain	5.58e-15	41
anterior neural tube	7.08e-15	42
central nervous system	1.16e-14	82
regional part of nervous system	2.35e-14	94
nervous system	2.35e-14	94
regional part of brain	6.15e-13	59
brain	6.81e-13	69
future brain	6.81e-13	69
gray matter	3.24e-12	34
brain grey matter	3.24e-12	34
telencephalon	1.32e-11	34
regional part of telencephalon	1.89e-11	33
cerebral hemisphere	4.58e-11	32
neurectoderm	4.74e-10	90
neural plate	1.26e-09	86
presumptive neural plate	1.26e-09	86
regional part of cerebral cortex	1.34e-08	22
cerebral cortex	2.58e-08	25
pallium	2.58e-08	25
neocortex	9.02e-08	20
pre-chordal neural plate	2.84e-07	61

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
ATF3#467	3	8.42369044725328	0.00417116638960993	0.0198719298679168
E2F1#1869	6	3.68054191115949	0.00136649155081914	0.00899388776632215
ELF1#1997	8	4.25809795880754	9.24826870984006e-06	0.000246712627276369
FOXA1#3169	5	6.92588734336591	0.000265089107894171	0.00283838849080986
FOXA2#3170	3	9.23642390724947	0.00321193954839541	0.016844175470493
GABPB1#2553	5	4.41730239761386	0.00218222865485036	0.0125882230590399
HEY1#23462	8	4.04011104310571	1.4081650274634e-05	0.000339490644744346
IRF1#3659	5	4.77322734597744	0.00152554848029467	0.0097150462032619
MXI1#4601	4	4.98078581437965	0.00509441532042917	0.0236974720136425
MYC#4609	5	3.26392616975588	0.00858363949794343	0.0327046341076836
NFKB1#4790	6	4.11604756814538	0.000729985658978431	0.00581754843479957
POLR2A#5430	8	2.14745317655807	0.00221072578897191	0.0127308111311445
POU2F2#5452	5	5.69132753608908	0.00067095477352849	0.00541612657230963
RFX5#5993	4	6.02395541359755	0.0025264968061986	0.0139921942911536
SIN3A#25942	6	4.05666354511135	0.00079220890752307	0.00612870415502236
SIX5#147912	4	8.5433576777295	0.00067799930596263	0.00547003240752654
SP1#6667	5	3.56148836133806	0.00581376186659607	0.0261356523581882
SRF#6722	4	6.8985891310839	0.00152207190456878	0.00970118806549854
TAF1#6872	8	3.34304628574529	6.40776711117462e-05	0.00104451504498824
TAF7#6879	6	8.57480205369294	1.07203127640034e-05	0.000278097055330291
TBP#6908	8	3.70677068709639	2.80450451364125e-05	0.000592674315864383
THAP1#55145	3	11.7634292260692	0.00160737792430693	0.0101231950212079
YY1#7528	8	4.91117074985386	2.95299276601526e-06	0.000101117249668809

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.