Coexpression cluster:C3217

Full id: C3217_Mast_Macrophage_acute_Reticulocytes_CD14_granulocyte_Monocytederived

Phase1 CAGE Peaks

Hg19::chr12:102224578..102224667,-	p1@GNPTAB
Hg19::chr4:79697495..79697538,+	p1@BMP2K
Hg19::chr4:79697539..79697550,+	p2@BMP2K

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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GO ID	GO name	FDR corrected p-value
GO:0003976	UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity	0.00659356832303857
GO:0016780	phosphotransferase activity, for other substituted phosphate groups	0.0346065531136793

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>

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Cell Type

Ontology term	p-value	n
myeloid cell	8.17e-33	108
common myeloid progenitor	8.17e-33	108
hematopoietic stem cell	5.37e-27	168
angioblastic mesenchymal cell	5.37e-27	168
hematopoietic oligopotent progenitor cell	1.10e-26	161
hematopoietic multipotent progenitor cell	1.10e-26	161
granulocyte monocyte progenitor cell	1.08e-23	67
myeloid lineage restricted progenitor cell	1.85e-23	66
hematopoietic cell	1.83e-22	177
myeloid leukocyte	1.95e-20	72
macrophage dendritic cell progenitor	7.44e-20	61
monopoietic cell	5.29e-19	59
monocyte	5.29e-19	59
monoblast	5.29e-19	59
promonocyte	5.29e-19	59
leukocyte	6.98e-18	136
hematopoietic lineage restricted progenitor cell	1.06e-17	120
defensive cell	6.29e-17	48
phagocyte	6.29e-17	48
nongranular leukocyte	8.70e-14	115
classical monocyte	2.39e-13	42
CD14-positive, CD16-negative classical monocyte	2.39e-13	42
mesenchymal cell	1.38e-12	354
connective tissue cell	1.40e-10	361
multi fate stem cell	3.06e-08	427
motile cell	3.24e-08	386
stem cell	8.55e-08	441
somatic stem cell	1.69e-07	433
lymphocyte of B lineage	2.44e-07	24
pro-B cell	2.44e-07	24

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	3.06e-24	108
hematopoietic system	5.74e-23	98
blood island	5.74e-23	98
immune system	1.39e-21	93
bone marrow	2.64e-19	76
bone element	3.67e-17	82
adult organism	1.18e-15	114
skeletal element	1.54e-13	90
skeletal system	2.25e-13	100
connective tissue	1.22e-09	371
lateral plate mesoderm	6.94e-09	203

Disease

Ontology term	p-value	n
myeloid leukemia	7.37e-09	31
leukemia	6.33e-07	39

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189312244862923
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171277850054008
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323885514305734
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.031929704181094
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108392568095332
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174425784646849
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.0046973793578751
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275620644010799
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247488504779226
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00613320299402923
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328153485611223

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.