Coexpression cluster:C4299

Full id: C4299_Dendritic_parietal_temporal_occipital_pituitary_gastrointestinal_cerebellum

Phase1 CAGE Peaks

Hg19::chr3:160473343..160473400,+	p1@PPM1L
Hg19::chr3:160473403..160473426,+	p2@PPM1L
Hg19::chr3:160473436..160473450,+	p3@PPM1L

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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No GOStat results

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
macrophage dendritic cell progenitor	1.33e-15	65
monopoietic cell	2.19e-15	63
monocyte	2.19e-15	63
monoblast	2.19e-15	63
promonocyte	2.19e-15	63
nongranular leukocyte	3.08e-15	119
leukocyte	8.53e-15	140
granulocyte monocyte progenitor cell	9.81e-15	71
myeloid lineage restricted progenitor cell	2.85e-14	70
myeloid leukocyte	4.90e-14	76
hematopoietic lineage restricted progenitor cell	6.96e-14	124
classical monocyte	5.42e-13	45
hematopoietic stem cell	1.61e-12	172
angioblastic mesenchymal cell	1.61e-12	172
CD14-positive, CD16-negative classical monocyte	2.15e-12	42
hematopoietic cell	2.47e-12	182
hematopoietic oligopotent progenitor cell	1.25e-11	165
hematopoietic multipotent progenitor cell	1.25e-11	165
myeloid cell	2.13e-10	112
common myeloid progenitor	2.13e-10	112

Uber Anatomy

Ontology term	p-value	n
adult organism	6.38e-43	115
neural tube	3.82e-23	57
neural rod	3.82e-23	57
future spinal cord	3.82e-23	57
neural keel	3.82e-23	57
central nervous system	1.59e-21	82
regional part of nervous system	1.16e-20	94
nervous system	1.16e-20	94
anterior neural tube	2.09e-19	42
regional part of brain	5.62e-19	59
regional part of forebrain	6.00e-19	41
forebrain	6.00e-19	41
future forebrain	6.00e-19	41
neurectoderm	1.94e-18	90
neural plate	3.92e-18	86
presumptive neural plate	3.92e-18	86
brain	7.84e-18	69
future brain	7.84e-18	69
telencephalon	5.56e-16	34
gray matter	6.76e-16	34
brain grey matter	6.76e-16	34
hematopoietic system	1.54e-15	102
blood island	1.54e-15	102
regional part of telencephalon	2.08e-15	33
cerebral hemisphere	2.26e-15	32
pre-chordal neural plate	1.81e-14	61
regional part of cerebral cortex	1.86e-13	22
neocortex	1.34e-12	20
hemolymphoid system	1.74e-12	112
cerebral cortex	2.36e-12	25
pallium	2.36e-12	25
bone marrow	5.66e-12	80
bone element	9.41e-12	86
anterior region of body	1.48e-11	129
craniocervical region	1.48e-11	129
head	2.37e-10	123
ectoderm	4.37e-10	173
presumptive ectoderm	4.37e-10	173
ectoderm-derived structure	1.03e-09	169
skeletal element	1.45e-08	101
skeletal system	1.45e-08	101
immune system	1.87e-07	115

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190595479356168
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.032659084476488
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323393221984362
EP300#2033	3	6.7739417262232	0.00321688050010379	0.016794190579872
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128449655270931
SMARCC2#6601	3	94.1553744268976	1.19621075407887e-06	4.86302276937497e-05
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00155141852968962
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190847007007146

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.