Coexpression cluster:C3494

Full id: C3494_CD14_Dendritic_Eosinophils_Mast_Whole_Neutrophils_CD4

Phase1 CAGE Peaks

Hg19::chr15:45879429..45879438,+	p6@PLDN
Hg19::chr15:45879534..45879558,+	p3@PLDN
Hg19::chr15:45879564..45879584,+	p1@PLDN

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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No GOStat results

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	6.91e-36	136
hematopoietic stem cell	2.12e-34	168
angioblastic mesenchymal cell	2.12e-34	168
hematopoietic cell	1.91e-32	177
hematopoietic oligopotent progenitor cell	6.10e-32	161
hematopoietic multipotent progenitor cell	6.10e-32	161
hematopoietic lineage restricted progenitor cell	3.14e-30	120
myeloid leukocyte	5.41e-29	72
nongranular leukocyte	3.72e-27	115
myeloid cell	1.88e-26	108
common myeloid progenitor	1.88e-26	108
granulocyte monocyte progenitor cell	2.66e-26	67
myeloid lineage restricted progenitor cell	6.65e-26	66
macrophage dendritic cell progenitor	4.89e-23	61
monopoietic cell	3.47e-22	59
monocyte	3.47e-22	59
monoblast	3.47e-22	59
promonocyte	3.47e-22	59
defensive cell	3.92e-21	48
phagocyte	3.92e-21	48
classical monocyte	4.43e-21	42
CD14-positive, CD16-negative classical monocyte	4.43e-21	42
mesenchymal cell	3.81e-16	354
connective tissue cell	1.40e-15	361
multi fate stem cell	5.35e-15	427
somatic stem cell	1.12e-13	433
stem cell	1.37e-13	441
motile cell	1.41e-13	386
stuff accumulating cell	1.84e-12	87

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.72e-29	98
blood island	1.72e-29	98
hemolymphoid system	1.32e-25	108
bone marrow	8.02e-24	76
bone element	2.90e-23	82
skeletal element	4.54e-22	90
skeletal system	9.47e-21	100
immune system	1.47e-18	93
connective tissue	2.91e-15	371
musculoskeletal system	2.56e-13	167
blood	7.37e-09	15
haemolymphatic fluid	7.37e-09	15
organism substance	7.37e-09	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
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139073986277762
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164082450118777
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189653332248567
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00659585227537599
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324515919456605
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321394717483778
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319867540231967
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461206624742843
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255443508212915
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153858764771792
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00387382314191947
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000850224902814258
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000626949700503757
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.0043326818842608
JUND#3727	3	6.99466394187103	0.00292184504273499	0.01564654537344
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186209800688314
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.0071935288974158
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293934859699249
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269179577966528
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.0019926895212584
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245372136673448
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172645586479936
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00881024963741664
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276012576336034
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239393891567697
SREBF1#6720	3	47.0058494404883	9.62099323994382e-06	0.000254445913645605
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00374525734036313
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00612654292768034
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189953319313364
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421097770292922
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328655043594823
ZBTB33#10009	3	31.6647250299812	3.14815888737575e-05	0.000633507834371168
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139873986476485
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00388389279204083
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109162414909467

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.