Coexpression cluster:C1474

Full id: C1474_Mast_CD34_immature_CD14_CD133_pleomorphic_granulocyte

Phase1 CAGE Peaks

Hg19::chr1:28764653..28764670,+	p2@PHACTR4
Hg19::chr3:15839437..15839503,-	p1@ANKRD28
Hg19::chr3:15839515..15839526,-	p11@ANKRD28
Hg19::chr3:15839528..15839539,-	p14@ANKRD28
Hg19::chr3:15839573..15839583,-	p15@ANKRD28
Hg19::chr3:15839586..15839603,-	p7@ANKRD28

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:0004864	protein phosphatase inhibitor activity	0.0164759143109795
GO:0019212	phosphatase inhibitor activity	0.0164759143109795
GO:0019888	protein phosphatase regulator activity	0.0192869987391987
GO:0019208	phosphatase regulator activity	0.0192869987391987

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>

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Cell Type

Ontology term	p-value	n
connective tissue cell	3.36e-18	365
multi fate stem cell	3.86e-18	430
mesenchymal cell	2.23e-17	358
somatic stem cell	3.20e-16	436
stem cell	1.84e-15	444
motile cell	6.90e-14	390
myeloid cell	1.43e-12	112
common myeloid progenitor	1.43e-12	112
granulocyte monocyte progenitor cell	3.58e-12	71
CD14-positive, CD16-negative classical monocyte	1.59e-11	42
somatic cell	8.02e-11	591
classical monocyte	2.66e-10	45
myeloid leukocyte	3.18e-10	76
myeloid lineage restricted progenitor cell	9.55e-10	70
macrophage dendritic cell progenitor	2.62e-09	65
monopoietic cell	2.11e-08	63
monocyte	2.11e-08	63
monoblast	2.11e-08	63
promonocyte	2.11e-08	63
animal cell	4.21e-08	679
eukaryotic cell	4.21e-08	679
fibroblast	1.31e-07	75
skin fibroblast	5.98e-07	23

Uber Anatomy

Ontology term	p-value	n
connective tissue	8.38e-18	375
skeletal element	8.60e-15	101
skeletal system	8.60e-15	101
bone element	2.94e-14	86
bone marrow	7.52e-14	80
musculoskeletal system	3.76e-13	167
hemolymphoid system	1.42e-11	112
hematopoietic system	4.86e-11	102
blood island	4.86e-11	102
immune system	5.08e-09	115
mesoderm	2.34e-07	448
mesoderm-derived structure	2.34e-07	448
presumptive mesoderm	2.34e-07	448

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
CTCF#10664	5	4.46688031089586	0.00114484834617236	0.0078358225588764
EP300#2033	6	6.7739417262232	1.03454107484288e-05	0.000269778864707904
FOS#2353	6	8.9979553088944	1.88302066097805e-06	6.9442371049395e-05
FOXA1#3169	6	11.0814197493855	5.39600313513231e-07	2.50579444833296e-05
FOXA2#3170	5	20.5253864605544	6.3869668268396e-07	2.91287523331135e-05
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.0025327212763711
JUN#3725	5	10.4273576602803	1.82465747415735e-05	0.000415356150705142
JUND#3727	6	6.99466394187103	8.53468650061654e-06	0.000232304957893638
MAFK#7975	5	22.5839442815249	3.97263246201883e-07	1.92527963666257e-05
NR3C1#2908	6	14.973023331173	8.86442195171695e-08	5.24527685107857e-06
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380445681933176
RAD21#5885	5	8.62919491288027	4.63176377415657e-05	0.000812866370037201
STAT3#6774	6	10.5194649971542	7.37398960627247e-07	3.26881197151736e-05
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00573387744759359
TBP#6908	6	3.70677068709639	0.00038541647290796	0.00377922364229034
USF1#7391	5	5.3012493976733	0.000500332754985889	0.00441262055378916

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.