Coexpression cluster:C654

Full id: C654_Eosinophils_Neutrophils_Natural_CD8_CD4_CD14_CD34

Phase1 CAGE Peaks

Hg19::chr11:269478..269491,-	p@chr11:269478..269491 -
Hg19::chr17:40440375..40440398,-	p@chr17:40440375..40440398 -
Hg19::chr17:47817223..47817245,+	p@chr17:47817223..47817245 +
Hg19::chr17:7747301..7747312,-	p@chr17:7747301..7747312 -
Hg19::chr19:13948014..13948028,+	p@chr19:13948014..13948028 +
Hg19::chr2:43386231..43386235,+	p@chr2:43386231..43386235 +
Hg19::chr2:70313762..70313774,-	p18@PCBP1-AS1
Hg19::chr3:196438771..196438791,-	p@chr3:196438771..196438791 -
Hg19::chr4:123073610..123073629,+	p2@KIAA1109
Hg19::chr5:131763102..131763114,-	p@chr5:131763102..131763114 -
Hg19::chr9:117135390..117135416,-	p@chr9:117135390..117135416 -
Hg19::chr9:117145466..117145492,+	p@chr9:117145466..117145492 +
Hg19::chr9:117147710..117147721,-	p@chr9:117147710..117147721 -

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:0004190	aspartic-type endopeptidase activity	0.0275226657247145

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	3.63e-67	136
hematopoietic stem cell	3.81e-52	168
angioblastic mesenchymal cell	3.81e-52	168
hematopoietic lineage restricted progenitor cell	4.68e-50	120
hematopoietic cell	5.15e-50	177
nongranular leukocyte	1.62e-49	115
hematopoietic oligopotent progenitor cell	7.12e-48	161
hematopoietic multipotent progenitor cell	7.12e-48	161
myeloid leukocyte	4.96e-39	72
classical monocyte	7.38e-36	42
CD14-positive, CD16-negative classical monocyte	7.38e-36	42
defensive cell	3.23e-30	48
phagocyte	3.23e-30	48
granulocyte monocyte progenitor cell	1.35e-28	67
macrophage dendritic cell progenitor	1.27e-26	61
myeloid cell	4.93e-26	108
common myeloid progenitor	4.93e-26	108
myeloid lineage restricted progenitor cell	1.77e-25	66
mature alpha-beta T cell	1.89e-24	18
alpha-beta T cell	1.89e-24	18
immature T cell	1.89e-24	18
mature T cell	1.89e-24	18
immature alpha-beta T cell	1.89e-24	18
monopoietic cell	4.74e-24	59
monocyte	4.74e-24	59
monoblast	4.74e-24	59
promonocyte	4.74e-24	59
lymphoid lineage restricted progenitor cell	1.39e-20	52
lymphocyte	4.77e-20	53
common lymphoid progenitor	4.77e-20	53
nucleate cell	4.90e-19	55
T cell	1.78e-18	25
pro-T cell	1.78e-18	25
granulocyte	3.82e-18	8
intermediate monocyte	1.14e-16	9
CD14-positive, CD16-positive monocyte	1.14e-16	9
blood cell	1.45e-15	11
CD8-positive, alpha-beta T cell	1.56e-14	11
mesenchymal cell	2.34e-14	354
connective tissue cell	1.03e-13	361
CD4-positive, alpha-beta T cell	1.13e-13	6
stuff accumulating cell	8.72e-13	87
motile cell	1.86e-11	386
multi fate stem cell	9.38e-09	427
stem cell	1.84e-08	441
somatic stem cell	2.18e-08	433
neutrophil	4.27e-08	3
natural killer cell	4.36e-08	3
pro-NK cell	4.36e-08	3
naive T cell	1.49e-07	3
basophil	1.81e-07	3
single nucleate cell	2.15e-07	3
mononuclear cell	2.15e-07	3

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	7.40e-38	98
blood island	7.40e-38	98
hemolymphoid system	1.58e-34	108
bone marrow	5.26e-24	76
immune system	5.90e-23	93
bone element	1.64e-21	82
skeletal element	1.03e-18	90
skeletal system	7.29e-16	100
blood	8.10e-15	15
haemolymphatic fluid	8.10e-15	15
organism substance	8.10e-15	15
connective tissue	7.78e-13	371
lateral plate mesoderm	2.70e-11	203

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
BCL11A#53335	6	13.0935946632033	2.65123192532282e-06	9.29167822311376e-05
CTCF#10664	7	2.88629189319425	0.00467512780428698	0.022060528294941
EBF1#1879	10	6.85112834351462	6.58271412928801e-08	4.02512927955919e-06
ELF1#1997	9	2.94791397148214	0.000603403467917953	0.00503989561627344
GABPB1#2553	6	3.26200792439177	0.00561630441383157	0.0253944591166402
IRF4#3662	5	8.42865872567082	0.000186792261757661	0.00225974713607186
MAX#4149	6	2.97810254261867	0.00885876695823828	0.0336155492624877
NFKB1#4790	11	4.64374597431786	3.97495193507342e-07	1.92551022795516e-05
PAX5#5079	6	3.07826101438977	0.00751515295554873	0.0309884341252588
POLR2A#5430	13	2.14745317655807	4.83928878402115e-05	0.000840809318440167
POU2F2#5452	5	3.50235540682405	0.00961613860265682	0.0361896832374644
SP1#6667	7	3.06835920361433	0.00326017741207416	0.0168860180886537
SPI1#6688	7	4.41771265843531	0.000349608792469154	0.00352951113356076
SRF#6722	5	5.3066070239107	0.00156826497609789	0.00994764809223732
TAF1#6872	10	2.57157406595792	0.000635041234822482	0.0052112101456451
TBP#6908	11	3.13649827369694	2.43452380190334e-05	0.000528166247085547
TCF12#6938	8	6.54428609365318	5.08413564000193e-06	0.000156724333561441
USF1#7391	6	2.9360765894806	0.00950376317872054	0.0358003073984633
USF2#7392	4	3.99759919540603	0.0142546073921536	0.049996203157777

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.