Coexpression cluster:C1831

Full id: C1831_testis_Eosinophils_CD14_Neutrophils_Basophils_Whole_Natural

Phase1 CAGE Peaks

Hg19::chr1:113162293..113162342,-	p3@ST7L
Hg19::chr3:39194422..39194451,+	p@chr3:39194422..39194451 +
Hg19::chr5:142388947..142388964,+	p@chr5:142388947..142388964 +
Hg19::chr6:15248904..15248915,-	p2@uc003nbk.2
Hg19::chr8:23386338..23386357,+	p8@SLC25A37

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:0048250	mitochondrial iron ion transport	0.0016484163428706
GO:0005381	iron ion transmembrane transporter activity	0.00494524902861179
GO:0046915	transition metal ion transmembrane transporter activity	0.0156599552572707
GO:0006839	mitochondrial transport	0.0156599552572707
GO:0015082	di-, tri-valent inorganic cation transmembrane transporter activity	0.0156599552572707
GO:0006826	iron ion transport	0.0156599552572707
GO:0007005	mitochondrion organization and biogenesis	0.0209584363593548
GO:0000041	transition metal ion transport	0.0210173083716001
GO:0015674	di-, tri-valent inorganic cation transport	0.0451666077946544
GO:0022890	inorganic cation transmembrane transporter activity	0.0451666077946544
GO:0005743	mitochondrial inner membrane	0.045468817457514
GO:0019866	organelle inner membrane	0.045468817457514

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
leukocyte	5.45e-37	140
hematopoietic stem cell	2.42e-36	172
angioblastic mesenchymal cell	2.42e-36	172
hematopoietic cell	1.36e-34	182
hematopoietic oligopotent progenitor cell	5.79e-33	165
hematopoietic multipotent progenitor cell	5.79e-33	165
hematopoietic lineage restricted progenitor cell	2.82e-30	124
nongranular leukocyte	1.88e-28	119
CD14-positive, CD16-negative classical monocyte	4.13e-24	42
classical monocyte	7.01e-23	45
myeloid leukocyte	2.22e-20	76
myeloid cell	1.86e-19	112
common myeloid progenitor	1.86e-19	112
granulocyte monocyte progenitor cell	2.79e-17	71
myeloid lineage restricted progenitor cell	8.58e-17	70
macrophage dendritic cell progenitor	2.72e-15	65
monopoietic cell	2.00e-14	63
monocyte	2.00e-14	63
monoblast	2.00e-14	63
promonocyte	2.00e-14	63
lymphocyte	1.24e-12	53
common lymphoid progenitor	1.24e-12	53
lymphoid lineage restricted progenitor cell	2.19e-12	52

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	9.38e-21	102
blood island	9.38e-21	102
hemolymphoid system	2.61e-18	112
bone marrow	4.94e-14	80
bone element	2.54e-13	86
immune system	5.18e-09	115
skeletal element	3.20e-08	101
skeletal system	3.20e-08	101
blood	1.58e-07	15
haemolymphatic fluid	1.58e-07	15
organism substance	1.58e-07	15

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
BRCA1#672	3	12.1105383859343	0.00112717647012594	0.00772803672050697
CCNT2#905	4	5.06896126157011	0.00270999809128077	0.0148986413989194
CHD2#1106	3	6.20641370047011	0.00777455012627559	0.0319571095969024
CTCF#10664	5	5.36025637307503	0.000225927829993709	0.00249874792298135
E2F6#1876	4	4.01372458535791	0.00663211823393388	0.0283003798256924
FOS#2353	4	7.19836424711553	0.000694785845338251	0.00559681750106298
JUN#3725	4	10.0102633538691	0.000190853134780107	0.00230540256110335
JUND#3727	5	6.99466394187103	5.97069468343598e-05	0.0009844859204979
RAD21#5885	4	8.28402711636506	0.000401162263912245	0.00386717608277007
REST#5978	3	5.79001722967681	0.00946878869443394	0.0357033295710155
RFX5#5993	3	7.22874649631706	0.0050291827895866	0.0234671978090267
SMARCC1#6599	2	17.4653437278526	0.00500803738519939	0.0233779294896902
SMC3#9126	3	9.0269597069597	0.00265096444946755	0.0146403720658845
SPI1#6688	4	6.56345880681818	0.000995742963645402	0.00714198196416195
STAT3#6774	3	6.31167899829254	0.00741117212246054	0.030615275899757
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00919168132258515
USF1#7391	4	5.08919942176637	0.0026686777536004	0.0147202934355272
YY1#7528	4	3.92893659988308	0.00719386626991762	0.0298450861747806
ZEB1#6935	3	10.1330592105263	0.00189555692435707	0.0111639355790294

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.