Coexpression cluster:C3005

Full id: C3005_Macrophage_CD14_Adipocyte_Osteoblast_Neutrophils_Eosinophils_Monocytederived

Phase1 CAGE Peaks

Hg19::chr10:20105324..20105339,+	p2@PLXDC2
Hg19::chr10:20105340..20105382,+	p1@PLXDC2
Hg19::chr10:20105389..20105394,+	p6@PLXDC2

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

---

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

---

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>

---

Cell Type

Ontology term	p-value	n
myeloid leukocyte	6.77e-31	76
macrophage dendritic cell progenitor	1.07e-27	65
granulocyte monocyte progenitor cell	1.50e-27	71
monopoietic cell	3.67e-27	63
monocyte	3.67e-27	63
monoblast	3.67e-27	63
promonocyte	3.67e-27	63
CD14-positive, CD16-negative classical monocyte	6.16e-26	42
myeloid lineage restricted progenitor cell	1.06e-25	70
classical monocyte	8.56e-22	45
myeloid cell	1.32e-17	112
common myeloid progenitor	1.32e-17	112
leukocyte	9.20e-07	140

Uber Anatomy

Ontology term	p-value	n
adult organism	7.83e-29	115
bone marrow	1.16e-23	80
hematopoietic system	2.90e-23	102
blood island	2.90e-23	102
bone element	9.17e-22	86
hemolymphoid system	4.94e-19	112
skeletal element	8.78e-18	101
skeletal system	8.78e-18	101
immune system	1.77e-15	115
neural tube	3.84e-12	57
neural rod	3.84e-12	57
future spinal cord	3.84e-12	57
neural keel	3.84e-12	57
neurectoderm	7.53e-12	90
musculoskeletal system	3.15e-11	167
neural plate	4.32e-11	86
presumptive neural plate	4.32e-11	86
regional part of brain	5.23e-11	59
embryo	5.57e-11	612
central nervous system	7.70e-11	82
organ	3.30e-10	511
brain	4.07e-10	69
future brain	4.07e-10	69
embryonic structure	4.63e-10	605
developing anatomical structure	4.63e-10	605
anterior neural tube	6.28e-10	42
germ layer	7.69e-10	604
embryonic tissue	7.69e-10	604
presumptive structure	7.69e-10	604
epiblast (generic)	7.69e-10	604
regional part of nervous system	1.02e-09	94
nervous system	1.02e-09	94
regional part of forebrain	1.89e-09	41
forebrain	1.89e-09	41
future forebrain	1.89e-09	41
multi-cellular organism	3.64e-09	659
gray matter	3.50e-08	34
brain grey matter	3.50e-08	34
telencephalon	4.05e-08	34
regional part of telencephalon	6.58e-08	33
pre-chordal neural plate	1.21e-07	61
lateral plate mesoderm	1.49e-07	216
cerebral hemisphere	2.80e-07	32

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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00641342563217305
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327763088126668
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0108877758904893

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

---

This analysis result is provided for C0 - C305 clusters.