Coexpression cluster:C4686

Full id: C4686_Monocytederived_CD14_Macrophage_smallcell_squamous_Basophils_signet

Phase1 CAGE Peaks

Hg19::chr7:36320649..36320687,+	p4@EEPD1
Hg19::chr7:36320699..36320726,+	p2@EEPD1
Hg19::chr7:36320733..36320746,+	p9@EEPD1

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
monopoietic cell	3.54e-21	63
monocyte	3.54e-21	63
monoblast	3.54e-21	63
promonocyte	3.54e-21	63
macrophage dendritic cell progenitor	4.71e-21	65
classical monocyte	3.01e-19	45
CD14-positive, CD16-negative classical monocyte	3.82e-19	42
granulocyte monocyte progenitor cell	5.88e-18	71
myeloid leukocyte	7.84e-18	76
myeloid lineage restricted progenitor cell	2.50e-17	70
myeloid cell	1.37e-08	112
common myeloid progenitor	1.37e-08	112
nongranular leukocyte	3.08e-07	119

Uber Anatomy

Ontology term	p-value	n
bone marrow	5.29e-16	80
bone element	2.59e-14	86
hematopoietic system	1.14e-11	102
blood island	1.14e-11	102
skeletal element	3.81e-10	101
skeletal system	3.81e-10	101
neural tube	5.79e-10	57
neural rod	5.79e-10	57
future spinal cord	5.79e-10	57
neural keel	5.79e-10	57
regional part of nervous system	6.93e-10	94
nervous system	6.93e-10	94
hemolymphoid system	7.59e-10	112
organ	9.41e-10	511
central nervous system	1.67e-09	82
brain	1.27e-08	69
future brain	1.27e-08	69
gray matter	4.25e-08	34
brain grey matter	4.25e-08	34
telencephalon	4.47e-08	34
regional part of forebrain	7.82e-08	41
forebrain	7.82e-08	41
future forebrain	7.82e-08	41
regional part of brain	9.04e-08	59
regional part of telencephalon	1.10e-07	33
immune system	1.29e-07	115
anterior neural tube	2.47e-07	42
cerebral hemisphere	3.61e-07	32
neural plate	3.73e-07	86
presumptive neural plate	3.73e-07	86

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0281310642984456
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327717270686966
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00919188446009032
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00901978678026507
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00244113075415465
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157678176209476
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00723441801524113
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00310216347502456
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.0066856046921952
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00204083415281672
SMARCC1#6599	3	43.6633593196315	1.20046018043203e-05	0.000302618539184506

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.