Coexpression cluster:C1025

Full id: C1025_Mast_lung_pineal_pituitary_cerebellum_Neutrophils_CD14

Phase1 CAGE Peaks

Hg19::chr13:33112899..33112948,-	p1@N4BP2L2
Hg19::chr1:104068562..104068632,+	p2@RNPC3
Hg19::chr22:38902300..38902322,-	p1@DDX17
Hg19::chr22:38902325..38902347,-	p2@DDX17
Hg19::chr2:135676381..135676435,+	p1@CCNT2
Hg19::chr3:50126345..50126401,+	p1@RBM5
Hg19::chr5:178054014..178054096,-	p1@CLK4
Hg19::chr6:170615819..170615877,+	p1@FAM120B

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:0006396	RNA processing	0.00680576209767547
GO:0003723	RNA binding	0.0213310656543628
GO:0005634	nucleus	0.0294399056100721
GO:0000074	regulation of progression through cell cycle	0.031184768323312
GO:0051726	regulation of cell cycle	0.031184768323312
GO:0016070	RNA metabolic process	0.0404000397154515
GO:0000166	nucleotide binding	0.0404000397154515
GO:0043283	biopolymer metabolic process	0.0404000397154515
GO:0008186	RNA-dependent ATPase activity	0.0410818184990109
GO:0022402	cell cycle process	0.0410818184990109
GO:0003724	RNA helicase activity	0.0410818184990109
GO:0043231	intracellular membrane-bound organelle	0.0410818184990109
GO:0043227	membrane-bound organelle	0.0410818184990109

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
leukocyte	4.75e-29	136
hematopoietic stem cell	7.75e-28	168
angioblastic mesenchymal cell	7.75e-28	168
hematopoietic oligopotent progenitor cell	2.55e-26	161
hematopoietic multipotent progenitor cell	2.55e-26	161
hematopoietic cell	9.60e-25	177
hematopoietic lineage restricted progenitor cell	1.02e-24	120
nongranular leukocyte	2.20e-22	115
myeloid leukocyte	8.64e-19	72
classical monocyte	8.72e-18	42
CD14-positive, CD16-negative classical monocyte	8.72e-18	42
myeloid cell	9.74e-18	108
common myeloid progenitor	9.74e-18	108
granulocyte monocyte progenitor cell	1.62e-16	67
myeloid lineage restricted progenitor cell	2.86e-16	66
defensive cell	2.22e-15	48
phagocyte	2.22e-15	48
macrophage dendritic cell progenitor	2.30e-14	61
monopoietic cell	5.31e-14	59
monocyte	5.31e-14	59
monoblast	5.31e-14	59
promonocyte	5.31e-14	59
nucleate cell	1.20e-08	55
lymphoid lineage restricted progenitor cell	1.41e-08	52
lymphocyte	2.83e-08	53
common lymphoid progenitor	2.83e-08	53
mature alpha-beta T cell	4.03e-07	18
alpha-beta T cell	4.03e-07	18
immature T cell	4.03e-07	18
mature T cell	4.03e-07	18
immature alpha-beta T cell	4.03e-07	18

Uber Anatomy

Ontology term	p-value	n
adult organism	6.93e-30	114
hematopoietic system	4.61e-19	98
blood island	4.61e-19	98
neural tube	2.54e-17	56
neural rod	2.54e-17	56
future spinal cord	2.54e-17	56
neural keel	2.54e-17	56
hemolymphoid system	5.60e-17	108
regional part of nervous system	6.31e-16	53
regional part of brain	6.31e-16	53
regional part of forebrain	1.43e-15	41
forebrain	1.43e-15	41
anterior neural tube	1.43e-15	41
future forebrain	1.43e-15	41
central nervous system	3.33e-14	81
nervous system	8.30e-14	89
brain	1.67e-13	68
future brain	1.67e-13	68
bone marrow	6.17e-13	76
immune system	1.30e-12	93
bone element	1.56e-12	82
telencephalon	3.53e-12	34
brain grey matter	4.95e-12	34
gray matter	4.95e-12	34
regional part of telencephalon	1.49e-11	32
cerebral hemisphere	3.80e-11	32
skeletal element	1.17e-09	90
neurectoderm	2.84e-09	86
neural plate	4.49e-09	82
presumptive neural plate	4.49e-09	82
regional part of cerebral cortex	5.86e-09	22
cerebral cortex	1.62e-08	25
pallium	1.62e-08	25
skeletal system	2.29e-08	100
neocortex	4.44e-08	20
pre-chordal neural plate	2.33e-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	0.01987102342583
CEBPB#1051	4	3.98557381291241	0.0113916368873439	0.0417420238887554
CHD2#1106	4	5.17201141705843	0.00443788460794178	0.0210036810879971
E2F1#1869	7	4.29396556301941	9.58670853279727e-05	0.00137022889346765
ETS1#2113	4	4.86438046110117	0.005553791515982	0.0251357441557308
GATA1#2623	4	6.78015407190022	0.00162430720984738	0.0101678866392502
GTF2F1#2962	4	6.36983043837883	0.00205190837519552	0.0119108080700892
HEY1#23462	8	4.04011104310571	1.4081650274634e-05	0.00033894295299205
HSF1#3297	2	41.0726666666667	0.00101154499084892	0.00717890373058377
IRF1#3659	4	3.81858187678195	0.0132613631682617	0.0469031632608651
MYC#4609	6	3.91671140370705	0.000964927056924644	0.00693858557547183
NFKB1#4790	7	4.80205549616961	4.48248622098168e-05	0.000793737501582071
NRF1#4899	4	6.10513972385545	0.00240374027777255	0.0135553040426721
POLR2A#5430	8	2.14745317655807	0.00221072578897191	0.012716086945775
POU2F2#5452	7	7.96785855052471	1.39153702916505e-06	5.41269034595787e-05
SETDB1#9869	3	15.1200098167539	0.000777510506788026	0.00609216143885022
SIN3A#25942	8	5.40888472681514	1.36410592556506e-06	5.3498257138599e-05
SIX5#147912	4	8.5433576777295	0.00067799930596263	0.00546918741912652
SPI1#6688	5	5.1277021928267	0.00109335443428073	0.0076431622330552
TAF1#6872	8	3.34304628574529	6.40776711117462e-05	0.00104321245412933
TBP#6908	8	3.70677068709639	2.80450451364125e-05	0.000591955632377078
TFAP2A#7020	3	6.19448788989186	0.00986148386238029	0.0370476083850048
USF1#7391	5	3.97593704825497	0.00353354209824939	0.0179380548874286
YY1#7528	7	4.29727440612212	9.53674534900876e-05	0.0013642078448228
ZNF143#7702	4	6.75043827611395	0.00165129218914978	0.0103256678806499

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.