Coexpression cluster:C3640

Full id: C3640_Eosinophils_Basophils_CD8_Dendritic_Natural_CD34_immature

Phase1 CAGE Peaks

Hg19::chr17:43302954..43302970,+	p@chr17:43302954..43302970 +
Hg19::chr17:74722536..74722639,-	p1@JMJD6
Hg19::chr20:23331500..23331522,+	p2@NXT1

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:0033749	histone demethylase activity (H4-R3 specific)	0.0024726245143059
GO:0033746	histone demethylase activity (H3-R2 specific)	0.0024726245143059
GO:0032452	histone demethylase activity	0.00618119735410036
GO:0032451	demethylase activity	0.00618119735410036
GO:0008536	Ran GTPase binding	0.0108779465636226
GO:0006611	protein export from nucleus	0.0115367065479968
GO:0006405	RNA export from nucleus	0.021184878106964
GO:0051168	nuclear export	0.0228100652115979
GO:0017016	Ras GTPase binding	0.0228100652115979
GO:0051213	dioxygenase activity	0.0228100652115979
GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	0.0228100652115979
GO:0016701	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen	0.0228100652115979
GO:0031267	small GTPase binding	0.0228100652115979
GO:0005643	nuclear pore	0.0228100652115979
GO:0050658	RNA transport	0.0228100652115979
GO:0051236	establishment of RNA localization	0.0228100652115979
GO:0050657	nucleic acid transport	0.0228100652115979
GO:0006403	RNA localization	0.0228100652115979
GO:0007507	heart development	0.0228100652115979
GO:0051020	GTPase binding	0.0228100652115979
GO:0046930	pore complex	0.0228100652115979
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0233421005353548
GO:0044453	nuclear membrane part	0.0238275617848449
GO:0031965	nuclear membrane	0.0292470614675695
GO:0006913	nucleocytoplasmic transport	0.0292470614675695
GO:0051169	nuclear transport	0.0292470614675695
GO:0001568	blood vessel development	0.0292470614675695
GO:0001944	vasculature development	0.0292470614675695
GO:0005635	nuclear envelope	0.032988036057757
GO:0006605	protein targeting	0.0358207019324699
GO:0019899	enzyme binding	0.0484371679013504

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	9.12e-44	140
hematopoietic stem cell	6.55e-40	172
angioblastic mesenchymal cell	6.55e-40	172
hematopoietic cell	5.04e-39	182
hematopoietic oligopotent progenitor cell	1.42e-36	165
hematopoietic multipotent progenitor cell	1.42e-36	165
hematopoietic lineage restricted progenitor cell	1.03e-33	124
nongranular leukocyte	2.65e-32	119
myeloid leukocyte	1.85e-24	76
CD14-positive, CD16-negative classical monocyte	2.75e-24	42
mesenchymal cell	6.21e-24	358
myeloid cell	2.54e-22	112
common myeloid progenitor	2.54e-22	112
granulocyte monocyte progenitor cell	3.36e-21	71
connective tissue cell	3.43e-21	365
classical monocyte	3.56e-21	45
motile cell	3.87e-21	390
multi fate stem cell	8.64e-20	430
somatic stem cell	9.67e-20	436
stem cell	1.36e-19	444
myeloid lineage restricted progenitor cell	9.05e-19	70
macrophage dendritic cell progenitor	1.38e-18	65
monopoietic cell	2.05e-17	63
monocyte	2.05e-17	63
monoblast	2.05e-17	63
promonocyte	2.05e-17	63
native cell	4.53e-17	722
animal cell	1.64e-13	679
eukaryotic cell	1.64e-13	679
somatic cell	2.25e-13	591
lymphoid lineage restricted progenitor cell	2.36e-13	52
lymphocyte	5.09e-13	53
common lymphoid progenitor	5.09e-13	53
lymphocyte of B lineage	5.11e-07	24
pro-B cell	5.11e-07	24
granulocyte	8.21e-07	8

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.78e-20	102
blood island	4.78e-20	102
connective tissue	1.09e-19	375
bone marrow	7.62e-19	80
bone element	1.24e-18	86
hemolymphoid system	2.63e-18	112
lateral plate mesoderm	3.66e-16	216
immune system	3.20e-15	115
skeletal element	9.70e-12	101
skeletal system	9.70e-12	101
musculoskeletal system	8.05e-08	167

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
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0324694697354547
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381215783149284
PPARGC1A#10891	1	116.683712121212	0.00854576321178668	0.0325650733052063
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370712835850152
SP2#6668	2	17.4356869958964	0.00427356848176974	0.0203134543358615

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.