Coexpression cluster:C4333

Full id: C4333_CD14_Mesenchymal_Eosinophils_CD14CD16_Smooth_xeroderma_Monocytederived

Phase1 CAGE Peaks

Hg19::chr3:48507621..48507689,+	p1@TREX1
Hg19::chr6:37401042..37401063,+	p2@FTSJD2
Hg19::chr6:37401066..37401079,+	p4@FTSJD2

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:0008296	3'-5'-exodeoxyribonuclease activity	0.00191754554170662
GO:0008853	exodeoxyribonuclease III activity	0.00191754554170662
GO:0032405	MutLalpha complex binding	0.00191754554170662
GO:0032407	MutSalpha complex binding	0.00191754554170662
GO:0016895	exodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.00191754554170662
GO:0032404	mismatch repair complex binding	0.00191754554170662
GO:0004529	exodeoxyribonuclease activity	0.00191754554170662
GO:0016796	exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.00461409395973154
GO:0008408	3'-5' exonuclease activity	0.00503355704697986
GO:0004536	deoxyribonuclease activity	0.00838926174496644
GO:0003697	single-stranded DNA binding	0.00922818791946309
GO:0004527	exonuclease activity	0.00922818791946309
GO:0006298	mismatch repair	0.00922818791946309
GO:0045005	maintenance of fidelity during DNA-dependent DNA replication	0.00922818791946309
GO:0032403	protein complex binding	0.0112975391498881
GO:0042803	protein homodimerization activity	0.0153803131991051
GO:0043566	structure-specific DNA binding	0.0153803131991051
GO:0006261	DNA-dependent DNA replication	0.0153803131991051
GO:0005635	nuclear envelope	0.0165268456375839
GO:0006310	DNA recombination	0.0165268456375839
GO:0004518	nuclease activity	0.0196548418024928
GO:0006260	DNA replication	0.0255872483221476
GO:0042802	identical protein binding	0.0255872483221476
GO:0046983	protein dimerization activity	0.0255872483221476
GO:0006281	DNA repair	0.0263087248322147
GO:0000287	magnesium ion binding	0.0278399204573701
GO:0006974	response to DNA damage stimulus	0.0278399204573701
GO:0009719	response to endogenous stimulus	0.0316994247363375
GO:0031967	organelle envelope	0.0348993288590604
GO:0031975	envelope	0.0348993288590604

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	1.49e-57	140
nongranular leukocyte	3.03e-52	119
hematopoietic lineage restricted progenitor cell	1.50e-48	124
hematopoietic stem cell	1.65e-45	172
angioblastic mesenchymal cell	1.65e-45	172
hematopoietic cell	1.33e-44	182
hematopoietic oligopotent progenitor cell	4.32e-42	165
hematopoietic multipotent progenitor cell	4.32e-42	165
myeloid leukocyte	5.73e-32	76
macrophage dendritic cell progenitor	1.14e-30	65
monopoietic cell	1.14e-30	63
monocyte	1.14e-30	63
monoblast	1.14e-30	63
promonocyte	1.14e-30	63
granulocyte monocyte progenitor cell	2.51e-29	71
myeloid lineage restricted progenitor cell	1.39e-28	70
CD14-positive, CD16-negative classical monocyte	3.86e-26	42
classical monocyte	1.39e-25	45
myeloid cell	3.56e-22	112
common myeloid progenitor	3.56e-22	112
lymphocyte	9.09e-19	53
common lymphoid progenitor	9.09e-19	53
lymphoid lineage restricted progenitor cell	1.66e-18	52
mesenchymal cell	1.88e-15	358
connective tissue cell	1.59e-14	365
motile cell	3.24e-13	390
lymphocyte of B lineage	5.73e-12	24
pro-B cell	5.73e-12	24
multi fate stem cell	7.03e-11	430
somatic stem cell	2.27e-10	436
stem cell	1.47e-09	444
B cell	5.08e-08	14
T cell	6.15e-07	25
pro-T cell	6.15e-07	25
intermediate monocyte	9.91e-07	9
CD14-positive, CD16-positive monocyte	9.91e-07	9

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	4.01e-37	112
hematopoietic system	3.78e-36	102
blood island	3.78e-36	102
bone marrow	4.13e-28	80
bone element	5.32e-25	86
immune system	4.22e-22	115
skeletal element	4.65e-19	101
skeletal system	4.65e-19	101
connective tissue	4.63e-13	375
lateral plate mesoderm	5.49e-13	216
musculoskeletal system	1.88e-09	167
adult organism	2.01e-09	115

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	22.4631745260087	8.81932387510763e-05	0.00129931071546391
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.029637912952296
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323507088382307
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321726595258743
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463959152703921
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376888320789893
HNF4A#3172	2	15.4215269086358	0.00544421048668661	0.0246857942525534
IRF4#3662	3	21.9145126867441	9.49854535978121e-05	0.00137132786678213
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187124131775312
MEF2A#4205	2	12.495487273096	0.00823502947802974	0.0324954941495427
MEF2C#4208	2	27.5409029950827	0.00172911993836969	0.0106509912853667
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295474653854669
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270331345447451
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460613302964609
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173411085681
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.0088417932714359
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370859489133412
SP1#6667	3	5.6983813781409	0.00540396270171217	0.024737429787601
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109285408373603
STAT1#6772	2	13.8043916647995	0.00677093170844408	0.0287599372335363
STAT2#6773	2	43.5091807909604	0.000696899089886823	0.00560994635799984
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00630679256201579
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190882929459173
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330490761149765
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.0378227804718644

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.