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
defensive cell	4.67e-40	48
phagocyte	4.67e-40	48
monopoietic cell	2.31e-38	59
monocyte	2.31e-38	59
monoblast	2.31e-38	59
promonocyte	2.31e-38	59
macrophage dendritic cell progenitor	1.09e-36	61
classical monocyte	3.12e-36	42
CD14-positive, CD16-negative classical monocyte	3.12e-36	42
myeloid lineage restricted progenitor cell	5.97e-33	66
granulocyte monocyte progenitor cell	2.86e-32	67
myeloid leukocyte	3.73e-29	72
stuff accumulating cell	1.53e-27	87
nongranular leukocyte	1.12e-15	115
myeloid cell	2.12e-15	108
common myeloid progenitor	2.12e-15	108
hematopoietic lineage restricted progenitor cell	1.01e-12	120
leukocyte	1.92e-11	136
melanocyte	1.89e-09	10
melanoblast	1.89e-09	10
hematopoietic stem cell	3.17e-07	168
angioblastic mesenchymal cell	3.17e-07	168
adult endothelial progenitor cell	4.83e-07	3
light melanocyte	5.21e-07	3
hematopoietic oligopotent progenitor cell	7.43e-07	161
hematopoietic multipotent progenitor cell	7.43e-07	161

Uber Anatomy

Ontology term	p-value	n
bone marrow	1.49e-28	76
bone element	2.34e-28	82
hematopoietic system	1.36e-25	98
blood island	1.36e-25	98
immune system	7.31e-25	93
skeletal element	1.17e-24	90
hemolymphoid system	6.20e-22	108
skeletal system	6.88e-21	100
adult organism	6.73e-15	114
neural tube	8.93e-14	56
neural rod	8.93e-14	56
future spinal cord	8.93e-14	56
neural keel	8.93e-14	56
regional part of nervous system	3.10e-12	53
regional part of brain	3.10e-12	53
brain	1.32e-10	68
future brain	1.32e-10	68
central nervous system	1.59e-10	81
nervous system	3.05e-10	89
musculoskeletal system	4.17e-10	167
neural plate	9.05e-10	82
presumptive neural plate	9.05e-10	82
organ	5.34e-09	503
neurectoderm	5.75e-09	86
brain grey matter	1.45e-08	34
gray matter	1.45e-08	34
regional part of forebrain	2.73e-08	41
forebrain	2.73e-08	41
anterior neural tube	2.73e-08	41
future forebrain	2.73e-08	41
telencephalon	2.80e-08	34
neural nucleus	5.83e-08	9
nucleus of brain	5.83e-08	9
ecto-epithelium	1.15e-07	104
germ layer	1.16e-07	560
germ layer / neural crest	1.16e-07	560
embryonic tissue	1.16e-07	560
presumptive structure	1.16e-07	560
germ layer / neural crest derived structure	1.16e-07	560
epiblast (generic)	1.16e-07	560
embryonic structure	1.95e-07	564
posterior neural tube	2.19e-07	15
chordal neural plate	2.19e-07	15
developing anatomical structure	2.34e-07	581
lateral plate mesoderm	6.63e-07	203
regional part of telencephalon	7.02e-07	32
embryo	9.24e-07	592
brainstem	9.35e-07	6

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
EP300#2033	7	5.26862134261804	4.17034622553318e-05	0.0007557639934903
USF1#7391	7	4.94783277116175	6.35032938033638e-05	0.00103563718012641
YY1#7528	7	3.81979947210855	0.000352967281214194	0.00353675044447177

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.