Coexpression cluster:C3037

Full id: C3037_Mast_acute_osteosarcoma_hepatoblastoma_lung_Myoblast_salivary

Phase1 CAGE Peaks

Hg19::chr10:70480963..70481010,+	p1@CCAR1
Hg19::chr5:134094461..134094489,+	p1@DDX46
Hg19::chr6:4021554..4021656,+	p1@PRPF4B

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:0008380	RNA splicing	0.00739210564264424
GO:0006397	mRNA processing	0.00739210564264424
GO:0016071	mRNA metabolic process	0.00772919383390072
GO:0006396	RNA processing	0.013624874723357
GO:0044428	nuclear part	0.0480363006905583

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>disease_data<br>

---

Cell Type

Ontology term	p-value	n
hematopoietic stem cell	4.78e-10	172
angioblastic mesenchymal cell	4.78e-10	172
hematopoietic oligopotent progenitor cell	7.80e-10	165
hematopoietic multipotent progenitor cell	7.80e-10	165
myeloid cell	1.75e-09	112
common myeloid progenitor	1.75e-09	112
hematopoietic cell	1.27e-08	182

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.49e-07	94
nervous system	1.49e-07	94
central nervous system	6.41e-07	82

Disease

Ontology term	p-value	n
cancer	7.43e-29	235
disease of cellular proliferation	1.24e-27	239
cell type cancer	3.81e-17	143
organ system cancer	3.13e-15	137
hematologic cancer	1.17e-12	51
immune system cancer	1.17e-12	51
leukemia	7.22e-12	39
carcinoma	1.58e-11	106
myeloid leukemia	7.93e-11	31
germ cell and embryonal cancer	8.44e-08	22
germ cell cancer	8.44e-08	22

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
BCLAF1#9774	2	14.4350984067479	0.00620114743554613	0.0273716933781751
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189085534054281
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323446869941557
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320299209286135
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0318958136686956
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0459889473942911
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0401694162836434
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185649517115701
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293112368486467
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268481806665493
SRF#6722	3	13.7971782621678	0.000380661502580019	0.0037389172075571
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00540425335302375
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189456500580864
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327811837005694
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0108909314017027

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.