Coexpression cluster:C897

Full id: C897_melanoma_Melanocyte_CD14_Macrophage_retina_myxofibrosarcoma_Monocytederived

Phase1 CAGE Peaks

Hg19::chr12:56361058..56361072,+	p14@CDK2
Hg19::chr15:33446896..33446905,-	p@chr15:33446896..33446905 -
Hg19::chr15:33446939..33446959,-	p@chr15:33446939..33446959 -
Hg19::chr15:33446964..33446978,-	p@chr15:33446964..33446978 -
Hg19::chr15:33446981..33446997,-	p@chr15:33446981..33446997 -
Hg19::chr15:33446999..33447010,-	p@chr15:33446999..33447010 -
Hg19::chr15:33447022..33447035,-	p@chr15:33447022..33447035 -
Hg19::chr15:33447055..33447064,-	p@chr15:33447055..33447064 -
Hg19::chr2:12454437..12454450,+	p1@ENST00000412606

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:0035173	histone kinase activity	0.00226657247144707
GO:0007089	traversing start control point of mitotic cell cycle	0.00566643117861768
GO:0000307	cyclin-dependent protein kinase holoenzyme complex	0.0060441932571922
GO:0000086	G2/M transition of mitotic cell cycle	0.00717747949291573
GO:0000080	G1 phase of mitotic cell cycle	0.00717747949291573
GO:0051318	G1 phase	0.00717747949291573
GO:0006275	regulation of DNA replication	0.00805892434292293
GO:0004693	cyclin-dependent protein kinase activity	0.00805892434292293
GO:0007346	regulation of progression through mitotic cell cycle	0.00805892434292293
GO:0051052	regulation of DNA metabolic process	0.0111062051100907
GO:0051329	interphase of mitotic cell cycle	0.016999293535853
GO:0051325	interphase	0.016999293535853
GO:0006261	DNA-dependent DNA replication	0.0287680352145205
GO:0008284	positive regulation of cell proliferation	0.0326653091473255
GO:0007067	mitosis	0.0326653091473255
GO:0000087	M phase of mitotic cell cycle	0.0326653091473255
GO:0051301	cell division	0.0326653091473255
GO:0000279	M phase	0.0348485517484987
GO:0000278	mitotic cell cycle	0.0348485517484987
GO:0000074	regulation of progression through cell cycle	0.0348485517484987
GO:0006260	DNA replication	0.0348485517484987
GO:0051726	regulation of cell cycle	0.0348485517484987
GO:0042802	identical protein binding	0.0348485517484987
GO:0022403	cell cycle phase	0.0348485517484987
GO:0042127	regulation of cell proliferation	0.0425208995643471

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
monopoietic cell	7.44e-25	63
monocyte	7.44e-25	63
monoblast	7.44e-25	63
promonocyte	7.44e-25	63
myeloid leukocyte	2.23e-23	76
macrophage dendritic cell progenitor	2.62e-23	65
myeloid lineage restricted progenitor cell	6.20e-23	70
granulocyte monocyte progenitor cell	3.03e-22	71
CD14-positive, CD16-negative classical monocyte	3.11e-22	42
classical monocyte	1.86e-19	45
myeloid cell	8.66e-10	112
common myeloid progenitor	8.66e-10	112
leukocyte	1.34e-09	140
nongranular leukocyte	2.35e-09	119
hematopoietic lineage restricted progenitor cell	7.16e-08	124

Uber Anatomy

Ontology term	p-value	n
adult organism	2.51e-37	115
hematopoietic system	1.26e-23	102
blood island	1.26e-23	102
bone marrow	3.51e-21	80
hemolymphoid system	6.67e-21	112
bone element	1.08e-20	86
neural tube	1.75e-20	57
neural rod	1.75e-20	57
future spinal cord	1.75e-20	57
neural keel	1.75e-20	57
neural plate	2.45e-17	86
presumptive neural plate	2.45e-17	86
regional part of brain	3.53e-17	59
central nervous system	3.55e-17	82
skeletal element	4.34e-17	101
skeletal system	4.34e-17	101
brain	1.46e-16	69
future brain	1.46e-16	69
regional part of nervous system	3.05e-16	94
nervous system	3.05e-16	94
neurectoderm	1.84e-15	90
immune system	1.99e-15	115
anterior neural tube	3.48e-15	42
regional part of forebrain	1.24e-14	41
forebrain	1.24e-14	41
future forebrain	1.24e-14	41
organ	1.05e-13	511
anatomical system	1.08e-12	625
anatomical group	1.56e-12	626
gray matter	3.17e-12	34
brain grey matter	3.17e-12	34
telencephalon	7.29e-12	34
pre-chordal neural plate	9.63e-12	61
regional part of telencephalon	1.80e-11	33
cerebral hemisphere	6.32e-11	32
anterior region of body	7.73e-11	129
craniocervical region	7.73e-11	129
embryo	1.01e-10	612
embryonic structure	1.13e-10	605
developing anatomical structure	1.13e-10	605
germ layer	1.66e-10	604
embryonic tissue	1.66e-10	604
presumptive structure	1.66e-10	604
epiblast (generic)	1.66e-10	604
head	1.80e-10	123
multi-cellular organism	2.26e-10	659
ectoderm-derived structure	2.67e-10	169
musculoskeletal system	5.58e-10	167
ectoderm	2.01e-09	173
presumptive ectoderm	2.01e-09	173
regional part of cerebral cortex	1.25e-08	22
cerebral cortex	3.62e-08	25
pallium	3.62e-08	25
neocortex	1.20e-07	20
tissue	5.68e-07	787

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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No analysis results for this cluster

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.