Coexpression cluster:C2178

Full id: C2178_acute_CD14_Macrophage_Dendritic_anaplastic_chronic_mesothelioma

Phase1 CAGE Peaks

Hg19::chr12:104995242..104995271,+	p8@CHST11
Hg19::chr12:104995275..104995304,+	p9@CHST11
Hg19::chr12:104995308..104995320,+	p15@CHST11
Hg19::chr14:76071877..76071891,+	p3@FLVCR2

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

---

GO ID	GO name	FDR corrected p-value
GO:0047756	chondroitin 4-sulfotransferase activity	0.00485636911762825
GO:0001537	N-acetylgalactosamine 4-O-sulfotransferase activity	0.00485636911762825
GO:0030206	chondroitin sulfate biosynthetic process	0.00485636911762825
GO:0030204	chondroitin sulfate metabolic process	0.00485636911762825
GO:0050650	chondroitin sulfate proteoglycan biosynthetic process	0.00485636911762825
GO:0050654	chondroitin sulfate proteoglycan metabolic process	0.00485636911762825
GO:0006024	glycosaminoglycan biosynthetic process	0.00755301754465224
GO:0030166	proteoglycan biosynthetic process	0.00755301754465224
GO:0006023	aminoglycan biosynthetic process	0.00755301754465224
GO:0006029	proteoglycan metabolic process	0.0093862161464397
GO:0044272	sulfur compound biosynthetic process	0.0120176833395542
GO:0030203	glycosaminoglycan metabolic process	0.0120176833395542
GO:0006022	aminoglycan metabolic process	0.0120176833395542
GO:0008146	sulfotransferase activity	0.0120176833395542
GO:0016782	transferase activity, transferring sulfur-containing groups	0.013371554684495
GO:0006790	sulfur metabolic process	0.0173822650001481
GO:0016051	carbohydrate biosynthetic process	0.0262316209486302

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
defensive cell	6.22e-31	48
phagocyte	6.22e-31	48
monopoietic cell	1.10e-28	59
monocyte	1.10e-28	59
monoblast	1.10e-28	59
promonocyte	1.10e-28	59
myeloid lineage restricted progenitor cell	7.72e-28	66
macrophage dendritic cell progenitor	2.14e-27	61
myeloid cell	2.82e-27	108
common myeloid progenitor	2.82e-27	108
classical monocyte	1.55e-26	42
CD14-positive, CD16-negative classical monocyte	1.55e-26	42
granulocyte monocyte progenitor cell	5.38e-24	67
myeloid leukocyte	1.33e-21	72
hematopoietic oligopotent progenitor cell	2.14e-15	161
hematopoietic multipotent progenitor cell	2.14e-15	161
hematopoietic stem cell	3.58e-14	168
angioblastic mesenchymal cell	3.58e-14	168
stuff accumulating cell	1.25e-13	87
hematopoietic cell	9.34e-13	177
hematopoietic lineage restricted progenitor cell	3.02e-12	120
nongranular leukocyte	1.65e-11	115
leukocyte	2.48e-10	136
conventional dendritic cell	3.17e-07	8

Uber Anatomy

Ontology term	p-value	n
bone marrow	6.42e-20	76
immune system	6.21e-19	93
bone element	1.04e-17	82
hematopoietic system	2.93e-16	98
blood island	2.93e-16	98
skeletal element	3.05e-15	90
hemolymphoid system	9.31e-15	108
skeletal system	1.04e-14	100
musculoskeletal system	4.99e-07	167

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
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319923796613181
STAT1#6772	3	15.5299406228994	0.00043408865517555	0.00404856090890152
STAT2#6773	3	48.9478283898305	1.42094046481278e-05	0.000340214583229211

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.