Coexpression cluster:C3571

Full id: C3571_Neutrophils_Mast_CD14_Eosinophils_Dendritic_thyroid_Prostate

Phase1 CAGE Peaks

Hg19::chr16:55542958..55542972,+	p3@LPCAT2
Hg19::chr16:55542976..55543003,+	p1@LPCAT2
Hg19::chr16:55543013..55543047,+	p2@LPCAT2

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	3.21e-28	76
myeloid cell	3.65e-28	112
common myeloid progenitor	3.65e-28	112
granulocyte monocyte progenitor cell	3.22e-24	71
myeloid lineage restricted progenitor cell	2.86e-23	70
macrophage dendritic cell progenitor	3.02e-21	65
monopoietic cell	8.46e-21	63
monocyte	8.46e-21	63
monoblast	8.46e-21	63
promonocyte	8.46e-21	63
CD14-positive, CD16-negative classical monocyte	5.84e-19	42
classical monocyte	3.51e-16	45

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	1.65e-23	216
bone marrow	6.58e-20	80
hematopoietic system	2.56e-19	102
blood island	2.56e-19	102
hemolymphoid system	8.31e-19	112
anatomical system	6.06e-17	625
anatomical group	1.33e-16	626
bone element	3.66e-16	86
skeletal element	4.79e-14	101
skeletal system	4.79e-14	101
multi-cellular organism	5.99e-14	659
immune system	2.12e-12	115
musculoskeletal system	8.29e-11	167
embryonic structure	1.43e-10	605
developing anatomical structure	1.43e-10	605
germ layer	1.75e-10	604
embryonic tissue	1.75e-10	604
presumptive structure	1.75e-10	604
epiblast (generic)	1.75e-10	604
embryo	4.93e-10	612
organ	1.42e-09	511
mesoderm	4.50e-09	448
mesoderm-derived structure	4.50e-09	448
presumptive mesoderm	4.50e-09	448
cardiovascular system	1.40e-07	110
splanchnic layer of lateral plate mesoderm	1.84e-07	84
circulatory system	2.38e-07	113
artery	4.13e-07	42
arterial blood vessel	4.13e-07	42
arterial system	4.13e-07	42
blood vessel	5.64e-07	60
epithelial tube open at both ends	5.64e-07	60
blood vasculature	5.64e-07	60
vascular cord	5.64e-07	60

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
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461458366495508
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127882100062719
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470624379217369
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00614688198368211
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000646110573628335

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.