Coexpression cluster:C3449

Full id: C3449_Eosinophils_CD14_Neutrophils_CD34_granulocyte_Basophils_Mast

Phase1 CAGE Peaks

Hg19::chr14:74225423..74225445,+	p1@MIR4505
Hg19::chr14:74226747..74226779,-	p3@C14orf43
Hg19::chr14:74226783..74226819,-	p4@C14orf43

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
CD14-positive, CD16-negative classical monocyte	8.71e-25	42
myeloid leukocyte	2.99e-23	76
classical monocyte	4.06e-22	45
granulocyte monocyte progenitor cell	1.07e-19	71
macrophage dendritic cell progenitor	3.10e-18	65
monopoietic cell	1.11e-17	63
monocyte	1.11e-17	63
monoblast	1.11e-17	63
promonocyte	1.11e-17	63
myeloid lineage restricted progenitor cell	1.03e-16	70
myeloid cell	9.72e-16	112
common myeloid progenitor	9.72e-16	112
somatic cell	9.27e-07	591

Uber Anatomy

Ontology term	p-value	n
bone marrow	6.48e-19	80
bone element	1.71e-16	86
hematopoietic system	8.91e-16	102
blood island	8.91e-16	102
skeletal element	5.36e-15	101
skeletal system	5.36e-15	101
hemolymphoid system	4.99e-14	112
immune system	6.69e-12	115
musculoskeletal system	2.20e-11	167
lateral plate mesoderm	3.37e-09	216
anatomical system	1.53e-07	625
anatomical group	2.30e-07	626
mesoderm	8.42e-07	448
mesoderm-derived structure	8.42e-07	448
presumptive mesoderm	8.42e-07	448
organ	9.15e-07	511

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
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461096574075635
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0401849957060791
ESR1#2099	2	20.5124021974363	0.00309974157709518	0.0163057273380801
FOSL1#8061	2	26.4757198109153	0.00186983370259098	0.0110236275509398
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376658477862162
GATA3#2625	2	18.1576775714707	0.00394454681927962	0.018943510611061
HNF4G#3174	2	19.1689483509645	0.00354398661128422	0.0179701130114052
JUNB#3726	2	20.4070884398808	0.00313146219943874	0.016446081698038
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186156294687446
MEF2A#4205	2	12.495487273096	0.00823502947802974	0.0324819942463913
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293875957278564
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269110783935442
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00308309972882063
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172620186217102
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00662905485339465
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.0298213869530997
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027596640880633
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.032975743659883
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308496499726549
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00374455181953043
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.0061418592751826
USF1#7391	3	6.36149927720796	0.0038840405729056	0.018990885458506
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109143391543523

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.