Coexpression cluster:C613

Full id: C613_CD4_CD19_CD8_Natural_CD14_immature_Peripheral

Phase1 CAGE Peaks

Hg19::chr10:120514851..120514864,+	p@chr10:120514851..120514864 +
Hg19::chr11:66445589..66445601,+	p@chr11:66445589..66445601 +
Hg19::chr12:16035195..16035237,-	p5@EPS8
Hg19::chr15:63796007..63796022,-	p@chr15:63796007..63796022 -
Hg19::chr17:7386814..7386828,+	p@chr17:7386814..7386828 +
Hg19::chr19:14116676..14116682,+	p@chr19:14116676..14116682 +
Hg19::chr1:176176478..176176481,+	p2@ENST00000456125
Hg19::chr1:179335173..179335190,+	p4@AXDND1
Hg19::chr2:157198321..157198340,+	p@chr2:157198321..157198340 +
Hg19::chr2:157198353..157198377,+	p@chr2:157198353..157198377 +
Hg19::chr2:198318580..198318624,-	p1@AK096309
Hg19::chr3:185655763..185655783,-	p1@TRA2B
Hg19::chr5:40679504..40679537,+	p3@PTGER4
Hg19::chr6:43192303..43192348,+	p@chr6:43192303..43192348 +

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:0004957	prostaglandin E receptor activity	0.0246190848913119
GO:0030278	regulation of ossification	0.0246190848913119
GO:0004955	prostaglandin receptor activity	0.0246190848913119
GO:0046850	regulation of bone remodeling	0.0246190848913119
GO:0004954	prostanoid receptor activity	0.0246190848913119
GO:0004953	icosanoid receptor activity	0.0246190848913119
GO:0007173	epidermal growth factor receptor signaling pathway	0.0257868660157688
GO:0005070	SH3/SH2 adaptor activity	0.0334876079256093
GO:0060090	molecular adaptor activity	0.0349427208736638
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0349427208736638
GO:0019933	cAMP-mediated signaling	0.0349427208736638
GO:0001503	ossification	0.0349427208736638
GO:0031214	biomineral formation	0.0349427208736638
GO:0030674	protein binding, bridging	0.0349427208736638
GO:0046849	bone remodeling	0.0349427208736638
GO:0048771	tissue remodeling	0.0358204378027972
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0369769702662953
GO:0019935	cyclic-nucleotide-mediated signaling	0.0369769702662953
GO:0007166	cell surface receptor linked signal transduction	0.0477975200649953

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	1.69e-54	136
hematopoietic stem cell	7.30e-50	168
angioblastic mesenchymal cell	7.30e-50	168
hematopoietic cell	3.27e-47	177
hematopoietic oligopotent progenitor cell	5.81e-45	161
hematopoietic multipotent progenitor cell	5.81e-45	161
nongranular leukocyte	2.06e-43	115
hematopoietic lineage restricted progenitor cell	8.25e-43	120
classical monocyte	2.14e-32	42
CD14-positive, CD16-negative classical monocyte	2.14e-32	42
defensive cell	1.66e-25	48
phagocyte	1.66e-25	48
myeloid leukocyte	3.38e-25	72
granulocyte monocyte progenitor cell	3.47e-23	67
myeloid cell	4.72e-23	108
common myeloid progenitor	4.72e-23	108
macrophage dendritic cell progenitor	3.98e-21	61
lymphocyte	1.03e-20	53
common lymphoid progenitor	1.03e-20	53
lymphoid lineage restricted progenitor cell	2.46e-20	52
myeloid lineage restricted progenitor cell	3.04e-20	66
monopoietic cell	9.36e-20	59
monocyte	9.36e-20	59
monoblast	9.36e-20	59
promonocyte	9.36e-20	59
nucleate cell	1.91e-19	55
mesenchymal cell	2.41e-17	354
connective tissue cell	1.34e-16	361
motile cell	2.38e-15	386
stem cell	6.19e-11	441
multi fate stem cell	2.01e-10	427
somatic stem cell	4.64e-10	433
T cell	8.47e-10	25
pro-T cell	8.47e-10	25
stuff accumulating cell	1.21e-09	87
lymphocyte of B lineage	1.77e-09	24
pro-B cell	1.77e-09	24
native cell	2.38e-08	722
mature alpha-beta T cell	3.43e-08	18
alpha-beta T cell	3.43e-08	18
immature T cell	3.43e-08	18
mature T cell	3.43e-08	18
immature alpha-beta T cell	3.43e-08	18
B cell	4.66e-08	14
intermediate monocyte	1.64e-07	9
CD14-positive, CD16-positive monocyte	1.64e-07	9

Uber Anatomy

Ontology term	p-value	n
bone marrow	5.49e-21	76
hematopoietic system	6.30e-21	98
blood island	6.30e-21	98
bone element	6.78e-19	82
immune system	2.74e-17	93
hemolymphoid system	1.05e-16	108
connective tissue	4.09e-16	371
skeletal element	9.78e-15	90
skeletal system	7.62e-12	100

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
CCNT2#905	7	3.16810078848132	0.00298309793757347	0.0158792948777898
E2F1#1869	8	2.80422240850247	0.00271661961112939	0.0149216911521375
E2F4#1874	6	5.42916870655047	0.000415844926371784	0.00391229873573036
E2F6#1876	10	3.58368266549813	4.45981311345876e-05	0.000790392706187883
EGR1#1958	9	3.20668656094937	0.000388926705764649	0.00380506943544301
ELF1#1997	10	3.04149854200538	0.000196088323365343	0.00235773295002913
ELK4#2005	4	4.63876618813372	0.00873391381785387	0.0331815651226934
ETS1#2113	9	6.25420344998722	1.57751348151719e-06	6.00415198601216e-05
FOSL2#2355	4	4.83720017273191	0.00754162287399241	0.0310889895929305
GABPB1#2553	8	4.03867647781838	0.000216036814387084	0.0024775083845144
GTF2B#2959	3	6.84510641449805	0.00861410984863984	0.0328147438897759
GTF2F1#2962	6	5.45985466146756	0.000403313355276991	0.00388039092692526
HEY1#23462	12	3.46295232266204	2.86301377032512e-06	9.8423401961483e-05
HMGN3#9324	8	4.67345584191462	7.53694136401289e-05	0.00116684052640994
IRF1#3659	8	4.36409357346509	0.000123814325023423	0.00165084186022231
JUN#3725	5	4.46886756869155	0.0035274588508083	0.0179089142443035
JUNB#3726	3	6.55942128424739	0.00967931304671205	0.0364221861028845
JUND#3727	6	2.99771311794473	0.00911646392082055	0.0344943980663205
MAX#4149	9	4.14807139864744	4.88080712048191e-05	0.000847177355585857
MXI1#4601	8	5.69232664500531	1.76881691091529e-05	0.000403700763459532
MYC#4609	12	4.47624160423663	1.49722896143429e-07	8.42960083575398e-06
NRF1#4899	7	6.10513972385545	5.0447325218961e-05	0.000859629335706162
POLR2A#5430	14	2.14745317655807	2.25331953374171e-05	0.000492640650584991
POU2F2#5452	5	3.25218716347947	0.0136235155601946	0.0480700814754269
REST#5978	6	4.13572659262629	0.00177616132713793	0.0109085864654489
RFX5#5993	5	4.30282529542682	0.00416022449376229	0.0198261321425526
SIN3A#25942	10	3.86348909058224	2.23981931004689e-05	0.000490099494913026
SMARCB1#6598	4	5.21506165175926	0.00578175973782598	0.0259985019055717
SP1#6667	7	2.84919068907045	0.00553793111322891	0.0250704806040102
TAF1#6872	13	3.10425726533491	1.55079831716319e-06	5.91108851993454e-05
TBP#6908	14	3.70677068709639	1.08014255397772e-08	8.13330989148374e-07
TCF12#6938	7	5.31723245109321	0.000122552626457257	0.001651519194138
TFAP2C#7022	5	3.8604387892358	0.00663727318202302	0.0283038738253768
YY1#7528	8	2.80638328563077	0.00270263965483941	0.0148660126882484
ZBTB7A#51341	8	4.20109103307194	0.000162864413547647	0.00202637556427242
ZNF263#10127	6	3.52364641586172	0.00406102910510794	0.0194260898048078

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.