Coexpression cluster:C806

Full id: C806_Melanocyte_CD14_Monocytederived_Macrophage_granulocyte_Mast_Eosinophils

Phase1 CAGE Peaks

Hg19::chr11:68816311..68816323,+	p3@TPCN2
Hg19::chr11:68816334..68816353,+	p2@TPCN2
Hg19::chr11:68816356..68816464,+	p1@TPCN2
Hg19::chr14:93651358..93651412,+	p1@C14orf109
Hg19::chr16:1524969..1525015,-	p2@CLCN7
Hg19::chr1:2487325..2487330,+	p15@TNFRSF14
Hg19::chr1:2487402..2487416,+	p5@TNFRSF14
Hg19::chr1:2487548..2487559,+	p11@TNFRSF14
Hg19::chr1:2487562..2487573,+	p8@TNFRSF14
Hg19::chr4:3387396..3387446,+	p4@RGS12

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:0022832	voltage-gated channel activity	0.0291262085968781
GO:0005244	voltage-gated ion channel activity	0.0291262085968781
GO:0005031	tumor necrosis factor receptor activity	0.0291262085968781
GO:0043120	tumor necrosis factor binding	0.0291262085968781
GO:0005035	death receptor activity	0.0291262085968781
GO:0022836	gated channel activity	0.0353237716946849
GO:0005216	ion channel activity	0.0400503140713481
GO:0022838	substrate specific channel activity	0.0400503140713481
GO:0022803	passive transmembrane transporter activity	0.0400503140713481
GO:0015267	channel activity	0.0400503140713481
GO:0000794	condensed nuclear chromosome	0.0401184445550083
GO:0008277	regulation of G-protein coupled receptor protein signaling pathway	0.0401184445550083
GO:0005247	voltage-gated chloride channel activity	0.0401184445550083
GO:0022844	voltage-gated anion channel activity	0.0401184445550083
GO:0016021	integral to membrane	0.0401184445550083
GO:0031224	intrinsic to membrane	0.0401184445550083
GO:0000793	condensed chromosome	0.0444359502873847
GO:0043168	anion binding	0.0458535690852464
GO:0031404	chloride ion binding	0.0458535690852464

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
myeloid leukocyte	1.17e-44	72
granulocyte monocyte progenitor cell	1.06e-40	67
macrophage dendritic cell progenitor	2.01e-39	61
myeloid lineage restricted progenitor cell	4.30e-39	66
monopoietic cell	1.07e-38	59
monocyte	1.07e-38	59
monoblast	1.07e-38	59
promonocyte	1.07e-38	59
defensive cell	1.80e-38	48
phagocyte	1.80e-38	48
classical monocyte	1.15e-33	42
CD14-positive, CD16-negative classical monocyte	1.15e-33	42
leukocyte	2.38e-32	136
myeloid cell	3.39e-31	108
common myeloid progenitor	3.39e-31	108
hematopoietic lineage restricted progenitor cell	1.32e-26	120
hematopoietic stem cell	6.19e-26	168
angioblastic mesenchymal cell	6.19e-26	168
hematopoietic cell	7.61e-26	177
nongranular leukocyte	8.17e-26	115
stuff accumulating cell	1.43e-25	87
hematopoietic oligopotent progenitor cell	3.26e-24	161
hematopoietic multipotent progenitor cell	3.26e-24	161
intermediate monocyte	7.15e-08	9
CD14-positive, CD16-positive monocyte	7.15e-08	9

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	7.38e-37	108
hematopoietic system	9.19e-37	98
blood island	9.19e-37	98
immune system	1.32e-35	93
bone marrow	4.81e-35	76
bone element	3.26e-32	82
skeletal element	4.35e-27	90
skeletal system	6.73e-21	100
lateral plate mesoderm	7.40e-14	203
adult organism	5.35e-09	114

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
BATF#10538	4	9.74312071692145	0.000488289084255501	0.00436650600826786
BCL11A#53335	3	8.51083653108212	0.00435985480765636	0.020670913213039
BHLHE40#8553	3	13.4615440640932	0.00118010821523276	0.0080073623889484
CCNT2#905	5	3.16810078848132	0.0122715766979429	0.0444794613297863
E2F6#1876	6	3.01029343901843	0.00625579584731478	0.0276047432185951
FOS#2353	8	7.19836424711553	8.49742894810215e-07	3.69160974172563e-05
HMGN3#9324	5	4.0892738616753	0.00403802327158728	0.0193337510870263
MAFK#7975	3	8.13021994134897	0.00495756569707518	0.0231619935509007
MAX#4149	5	3.22627775450356	0.0113549221837195	0.0416294000051069
NFE2#4778	5	38.6021303258145	8.66761903293144e-08	5.14339468284276e-06
NFKB1#4790	6	3.2928380545163	0.0039127525205927	0.0190687802378992
NRF1#4899	4	4.88411177908436	0.0063093473218055	0.0278269393978904
PAX5#5079	5	3.33478276558891	0.00985362449367583	0.0370300704722756
POLR2A#5430	10	2.14745317655807	0.000479337749163792	0.00436418404541167
USF1#7391	6	3.81689956632477	0.00178092866379164	0.0109275840854084
USF2#7392	5	6.4960986925348	0.000489096753205606	0.00437335409315413

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.