Coexpression cluster:C1246

Full id: C1246_Neutrophils_Eosinophils_CD14_migratory_Macrophage_Dendritic_Mast

Phase1 CAGE Peaks

Hg19::chr1:113162400..113162411,+	p2@CAPZA1
Hg19::chr1:113162434..113162462,+	p1@CAPZA1
Hg19::chr1:183604794..183604908,-	p1@ARPC5
Hg19::chr2:114647617..114647739,+	p1@ACTR3
Hg19::chr2:65454926..65454991,+	p1@ACTR2
Hg19::chr2:74405929..74406028,-	p1@MOB1A
Hg19::chr3:32544275..32544350,-	p1@CMTM6

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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p.value	FDR	nGenes	nPathway	Name
1.74638393235245e-06	0.0011054610291791	3	161	B Cell Receptor Signaling Pathway (Wikipathways):WP23
1.00120440508419e-05	0.00316881194209147	3	288	{ACTB,297} (Static Module):NA

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:0005885	Arp2/3 protein complex	4.82014492712258e-09
GO:0015629	actin cytoskeleton	1.26213686987012e-06
GO:0051674	localization of cell	1.77346057312997e-06
GO:0006928	cell motility	1.77346057312997e-06
GO:0003779	actin binding	2.4283099190298e-06
GO:0008092	cytoskeletal protein binding	7.26812926157398e-06
GO:0044430	cytoskeletal part	3.33261028016598e-05
GO:0042995	cell projection	8.59652002920549e-05
GO:0030027	lamellipodium	0.000120112910821792
GO:0005856	cytoskeleton	0.000120112910821792
GO:0008064	regulation of actin polymerization and/or depolymerization	0.000120112910821792
GO:0030832	regulation of actin filament length	0.000120112910821792
GO:0032535	regulation of cellular component size	0.000120112910821792
GO:0032956	regulation of actin cytoskeleton organization and biogenesis	0.000120112910821792
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.000149645091196196
GO:0033043	regulation of organelle organization and biogenesis	0.000149645091196196
GO:0008154	actin polymerization and/or depolymerization	0.000167315413004414
GO:0031252	leading edge	0.000220567027407585
GO:0051128	regulation of cellular component organization and biogenesis	0.000404005243817653
GO:0043234	protein complex	0.00103781835649468
GO:0043232	intracellular non-membrane-bound organelle	0.00103781835649468
GO:0043228	non-membrane-bound organelle	0.00103781835649468
GO:0030036	actin cytoskeleton organization and biogenesis	0.00203067940918858
GO:0030029	actin filament-based process	0.00215508979634188
GO:0032991	macromolecular complex	0.00278776736494061
GO:0044446	intracellular organelle part	0.00328257180343258
GO:0044422	organelle part	0.00328257180343258
GO:0005515	protein binding	0.00419695336488923
GO:0051179	localization	0.00419695336488923
GO:0051246	regulation of protein metabolic process	0.00450519677872128
GO:0008290	F-actin capping protein complex	0.00768364925082847
GO:0030833	regulation of actin filament polymerization	0.00785660237095375
GO:0051693	actin filament capping	0.00817185007384652
GO:0051016	barbed-end actin filament capping	0.00817185007384652
GO:0030835	negative regulation of actin filament depolymerization	0.00822346760366912
GO:0030834	regulation of actin filament depolymerization	0.00822346760366912
GO:0030042	actin filament depolymerization	0.00822346760366912
GO:0007010	cytoskeleton organization and biogenesis	0.00926117514738054
GO:0030041	actin filament polymerization	0.0105104523203369
GO:0051261	protein depolymerization	0.0151928279867193
GO:0065008	regulation of biological quality	0.0163106517320554
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0163508907983883
GO:0005200	structural constituent of cytoskeleton	0.0260551783294516
GO:0051258	protein polymerization	0.0290372716261605
GO:0051248	negative regulation of protein metabolic process	0.0304283631416647
GO:0006996	organelle organization and biogenesis	0.0360306094662073
GO:0042330	taxis	0.0394054466876717
GO:0006935	chemotaxis	0.0394054466876717
GO:0007626	locomotory behavior	0.0484140530797965

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	4.07e-49	136
hematopoietic stem cell	9.53e-47	168
angioblastic mesenchymal cell	9.53e-47	168
hematopoietic oligopotent progenitor cell	4.16e-45	161
hematopoietic multipotent progenitor cell	4.16e-45	161
hematopoietic cell	6.51e-44	177
nongranular leukocyte	2.71e-41	115
hematopoietic lineage restricted progenitor cell	1.31e-38	120
myeloid leukocyte	8.65e-38	72
myeloid cell	1.40e-35	108
common myeloid progenitor	1.40e-35	108
multi fate stem cell	2.38e-35	427
macrophage dendritic cell progenitor	3.93e-35	61
mesenchymal cell	6.71e-35	354
somatic stem cell	1.51e-34	433
monopoietic cell	4.71e-34	59
monocyte	4.71e-34	59
monoblast	4.71e-34	59
promonocyte	4.71e-34	59
stem cell	2.70e-33	441
connective tissue cell	4.55e-33	361
granulocyte monocyte progenitor cell	6.54e-33	67
myeloid lineage restricted progenitor cell	1.61e-30	66
defensive cell	1.11e-29	48
phagocyte	1.11e-29	48
motile cell	3.58e-27	386
somatic cell	1.63e-26	588
classical monocyte	2.63e-26	42
CD14-positive, CD16-negative classical monocyte	2.63e-26	42
native cell	5.49e-26	722
animal cell	6.85e-21	679
eukaryotic cell	6.85e-21	679
stuff accumulating cell	3.11e-14	87
lymphocyte	5.07e-09	53
common lymphoid progenitor	5.07e-09	53
lymphoid lineage restricted progenitor cell	8.33e-09	52
nucleate cell	4.93e-08	55
lymphocyte of B lineage	1.98e-07	24
pro-B cell	1.98e-07	24

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.98e-38	98
blood island	2.98e-38	98
hemolymphoid system	1.21e-36	108
connective tissue	2.78e-32	371
bone marrow	1.09e-29	76
immune system	4.60e-29	93
bone element	1.54e-27	82
skeletal element	4.39e-27	90
skeletal system	3.42e-25	100
musculoskeletal system	7.52e-18	167
lateral plate mesoderm	4.33e-16	203
mesoderm	4.78e-12	315
mesoderm-derived structure	4.78e-12	315
presumptive mesoderm	4.78e-12	315
blood	2.00e-08	15
haemolymphatic fluid	2.00e-08	15
organism substance	2.00e-08	15

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
BRCA1#672	3	8.65038456138161	0.00365929333120223	0.0184749558260384
CCNT2#905	6	5.43102992311083	9.35028339706757e-05	0.00135856183598545
E2F1#1869	5	3.50527801062809	0.00509055358791505	0.0236900599843267
E2F4#1874	3	5.42916870655047	0.0135067508217614	0.0477048207329707
EGR1#1958	6	4.27558208126583	0.000376213061986645	0.00373704736359361
ELF1#1997	7	4.25809795880754	3.93848941900192e-05	0.000735572060856835
ELK4#2005	4	9.27753237626744	0.000432817858966577	0.00404320790452686
ETS1#2113	5	6.94911494443024	0.000201406263333039	0.00239383961946503
FOS#2353	4	5.14168874793966	0.00404209586567825	0.0193497020724926
GABPB1#2553	7	7.06768383618217	1.13438576906404e-06	4.65883269112383e-05
GTF2B#2959	5	22.8170213816602	5.978955273698e-07	2.74839837072951e-05
HDAC2#3066	4	7.66606870664358	0.000898637344705782	0.00668705277119538
HEY1#23462	7	4.04011104310571	5.68979821988558e-05	0.00095077893805861
HMGN3#9324	5	5.84181980239328	0.000462918719129959	0.00426375942386575
IRF1#3659	6	6.54614036019763	3.13027310449255e-05	0.000631856576652682
MYC#4609	5	3.73020133686386	0.00382194422230669	0.0188719224922457
NFKB1#4790	5	3.9200453029956	0.00303658142448461	0.016120445656064
PAX5#5079	6	5.71677045529528	6.92762487228137e-05	0.0010992315618903
PBX3#5090	3	9.39193400860463	0.00289381368834148	0.0156464592978202
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223481499505102
POU2F2#5452	4	5.20349946156716	0.00386671431017981	0.0190677452118074
REST#5978	5	6.89287765437716	0.000209438858484651	0.00243879863321201
SIN3A#25942	6	4.63618690869869	0.000235167814635783	0.00256642543288887
SMARCC1#6599	2	12.4752455198947	0.0102004731657184	0.037990414983042
SRF#6722	3	5.91307639807192	0.0106686813016745	0.0393970159983589
TAF1#6872	7	3.34304628574529	0.000214233631962245	0.00246685185099283
TAF7#6879	4	6.53318251709938	0.0016484941094751	0.0103124933392914
TBP#6908	6	3.17723201751119	0.00207411205185266	0.0120209871577935
TFAP2A#7020	4	9.43921964173997	0.000404983816888432	0.00389538633744805
TFAP2C#7022	4	6.17670206277727	0.00203675492806902	0.0118287631614636
YY1#7528	7	4.91117074985386	1.45048003565243e-05	0.000345544444442299
ZBTB7A#51341	5	5.25136379133993	0.000768769248321446	0.00603090900063423

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.