Coexpression cluster:C486

Full id: C486_acute_Neural_chronic_neuroectodermal_caudate_Astrocyte_myelodysplastic

Phase1 CAGE Peaks

Hg19::chr10:105793289..105793301,-	p@chr10:105793289..105793301 -
Hg19::chr10:105793325..105793341,-	p@chr10:105793325..105793341 -
Hg19::chr10:105793354..105793360,-	p@chr10:105793354..105793360 -
Hg19::chr14:23588242..23588262,-	p1@CEBPE
Hg19::chr14:23588275..23588288,-	p1@CU690200
Hg19::chr14:23588458..23588473,-	p2@CEBPE
Hg19::chr16:1537839..1537851,-	p@chr16:1537839..1537851 -
Hg19::chr16:1537876..1537921,+	p@chr16:1537876..1537921 +
Hg19::chr17:56359033..56359070,-	p@chr17:56359033..56359070 -
Hg19::chr22:50523663..50523686,-	p7@MLC1
Hg19::chr22:50523689..50523719,-	p5@MLC1
Hg19::chr7:2119411..2119445,-	p15@MAD1L1
Hg19::chr8:130559296..130559308,+	p@chr8:130559296..130559308 +
Hg19::chr8:130695974..130696000,+	p@chr8:130695974..130696000 +
Hg19::chr9:100947946..100947962,-	p@chr9:100947946..100947962 -
Hg19::chr9:100947965..100947975,-	p@chr9:100947965..100947975 -
Hg19::chr9:127148331..127148341,-	p@chr9:127148331..127148341 -
Hg19::chr9:127149681..127149698,-	p@chr9:127149681..127149698 -
Hg19::chr9:127149714..127149721,-	p@chr9:127149714..127149721 -

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:0000093	mitotic telophase	0.00551925114800423
GO:0051326	telophase	0.00551925114800423
GO:0000089	mitotic metaphase	0.00827838931830998
GO:0051323	metaphase	0.00827838931830998
GO:0051322	anaphase	0.0091976688152717
GO:0000090	mitotic anaphase	0.0091976688152717
GO:0000299	integral to membrane of membrane fraction	0.0126128318365972
GO:0030225	macrophage differentiation	0.0151734731405287
GO:0007093	mitotic cell cycle checkpoint	0.0330872449633977
GO:0002573	myeloid leukocyte differentiation	0.0330872449633977
GO:0006909	phagocytosis	0.0410950816486348
GO:0000075	cell cycle checkpoint	0.0477251694968636
GO:0042089	cytokine biosynthetic process	0.0477251694968636
GO:0007088	regulation of mitosis	0.0477251694968636
GO:0042107	cytokine metabolic process	0.0477251694968636
GO:0009059	macromolecule biosynthetic process	0.0477251694968636
GO:0030099	myeloid cell differentiation	0.0477251694968636
GO:0005819	spindle	0.0477251694968636

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	1.15e-26	112
common myeloid progenitor	1.15e-26	112
hematopoietic stem cell	6.08e-16	172
angioblastic mesenchymal cell	6.08e-16	172
CD14-positive, CD16-negative classical monocyte	1.19e-15	42
hematopoietic oligopotent progenitor cell	1.08e-14	165
hematopoietic multipotent progenitor cell	1.08e-14	165
hematopoietic cell	5.54e-14	182
classical monocyte	9.13e-14	45
myeloid leukocyte	3.86e-13	76
monopoietic cell	3.28e-12	63
monocyte	3.28e-12	63
monoblast	3.28e-12	63
promonocyte	3.28e-12	63
macrophage dendritic cell progenitor	4.15e-12	65
myeloid lineage restricted progenitor cell	1.06e-11	70
granulocyte monocyte progenitor cell	3.03e-11	71

Uber Anatomy

Ontology term	p-value	n
central nervous system	2.99e-35	82
neural tube	9.14e-35	57
neural rod	9.14e-35	57
future spinal cord	9.14e-35	57
neural keel	9.14e-35	57
adult organism	2.37e-34	115
regional part of nervous system	4.75e-31	94
nervous system	4.75e-31	94
brain	2.92e-30	69
future brain	2.92e-30	69
regional part of brain	6.19e-29	59
regional part of forebrain	4.89e-27	41
forebrain	4.89e-27	41
future forebrain	4.89e-27	41
anterior neural tube	5.26e-26	42
telencephalon	7.98e-26	34
gray matter	1.17e-25	34
brain grey matter	1.17e-25	34
regional part of telencephalon	4.09e-25	33
cerebral hemisphere	2.59e-24	32
neurectoderm	1.81e-22	90
neural plate	1.41e-20	86
presumptive neural plate	1.41e-20	86
cerebral cortex	8.76e-19	25
pallium	8.76e-19	25
regional part of cerebral cortex	1.54e-16	22
hematopoietic system	2.98e-15	102
blood island	2.98e-15	102
neocortex	6.39e-15	20
pre-chordal neural plate	1.72e-14	61
hemolymphoid system	4.90e-13	112
anterior region of body	4.09e-12	129
craniocervical region	4.09e-12	129
ectoderm	1.47e-11	173
presumptive ectoderm	1.47e-11	173
head	4.51e-11	123
ectoderm-derived structure	2.52e-10	169
posterior neural tube	9.01e-10	15
chordal neural plate	9.01e-10	15
bone marrow	3.06e-09	80
basal ganglion	1.00e-08	9
nuclear complex of neuraxis	1.00e-08	9
aggregate regional part of brain	1.00e-08	9
collection of basal ganglia	1.00e-08	9
cerebral subcortex	1.00e-08	9
nucleus of brain	2.55e-08	9
neural nucleus	2.55e-08	9
bone element	2.92e-08	86
segmental subdivision of nervous system	4.17e-08	13
immune system	6.35e-08	115
segmental subdivision of hindbrain	1.26e-07	12
hindbrain	1.26e-07	12
presumptive hindbrain	1.26e-07	12
telencephalic nucleus	5.48e-07	7

Disease

Ontology term	p-value	n
myeloid leukemia	4.36e-19	31
leukemia	3.66e-18	39
hematologic cancer	1.09e-11	51
immune system cancer	1.09e-11	51

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
SPI1#6688	7	3.02264550313995	0.00528452342160744	0.0244749597174838

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.