Coexpression cluster:C455

Full id: C455_kidney_Macrophage_clear_endometrial_Monocytederived_large_spinal

Phase1 CAGE Peaks

Hg19::chr4:88896857..88896874,+	p1@SPP1
Hg19::chr4:88898025..88898048,+	p3@SPP1
Hg19::chr4:88898050..88898078,+	p4@SPP1
Hg19::chr4:88898200..88898221,+	p@chr4:88898200..88898221 +
Hg19::chr4:88901191..88901205,+	p5@SPP1
Hg19::chr4:88901208..88901247,+	p2@SPP1
Hg19::chr4:88901534..88901556,+	p6@SPP1
Hg19::chr4:88902619..88902651,+	p@chr4:88902619..88902651 +
Hg19::chr4:88902673..88902729,+	p@chr4:88902673..88902729 +
Hg19::chr4:88902732..88902758,+	p@chr4:88902732..88902758 +
Hg19::chr4:88902759..88902776,+	p@chr4:88902759..88902776 +
Hg19::chr4:88902837..88902854,+	p@chr4:88902837..88902854 +
Hg19::chr4:88902867..88902910,-	p1@AB019562
Hg19::chr4:88902876..88902895,+	p@chr4:88902876..88902895 +
Hg19::chr4:88902908..88902918,+	p@chr4:88902908..88902918 +
Hg19::chr4:88903662..88903681,+	p@chr4:88903662..88903681 +
Hg19::chr4:88903690..88903729,+	p@chr4:88903690..88903729 +
Hg19::chr4:88903841..88903876,-	p1@CU675498
Hg19::chr4:88903956..88903966,+	p@chr4:88903956..88903966 +
Hg19::chr4:88904052..88904068,+	p@chr4:88904052..88904068 +
Hg19::chr4:88904247..88904279,+	p@chr4:88904247..88904279 +
Hg19::chr4:88904446..88904460,+	p@chr4:88904446..88904460 +

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:0030502	negative regulation of bone mineralization	0.00250941952195926
GO:0030279	negative regulation of ossification	0.00250941952195926
GO:0030500	regulation of bone mineralization	0.00250941952195926
GO:0046851	negative regulation of bone remodeling	0.00250941952195926
GO:0030278	regulation of ossification	0.00285161309313552
GO:0030282	bone mineralization	0.00285161309313552
GO:0046850	regulation of bone remodeling	0.00285161309313552
GO:0051241	negative regulation of multicellular organismal process	0.00285161309313552
GO:0001503	ossification	0.00796377765646575
GO:0031214	biomineral formation	0.00796377765646575
GO:0046849	bone remodeling	0.00796377765646575
GO:0048771	tissue remodeling	0.00798451666077946
GO:0001501	skeletal development	0.0146704525899157
GO:0051239	regulation of multicellular organismal process	0.0176800011774402
GO:0009888	tissue development	0.0176800011774402
GO:0005125	cytokine activity	0.0176800011774402
GO:0005615	extracellular space	0.028341679306834
GO:0044421	extracellular region part	0.0438007771105616
GO:0022610	biological adhesion	0.0438007771105616
GO:0007155	cell adhesion	0.0438007771105616
GO:0005102	receptor binding	0.0450609185155282
GO:0048513	organ development	0.0468953972325035
GO:0048519	negative regulation of biological process	0.0468953972325035

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	1.27e-15	6

Uber Anatomy

Ontology term	p-value	n
neural tube	6.36e-30	56
neural rod	6.36e-30	56
future spinal cord	6.36e-30	56
neural keel	6.36e-30	56
regional part of nervous system	2.69e-27	53
regional part of brain	2.69e-27	53
neural plate	2.69e-25	82
presumptive neural plate	2.69e-25	82
nervous system	6.13e-25	89
central nervous system	9.80e-24	81
neurectoderm	1.17e-23	86
regional part of forebrain	4.98e-22	41
forebrain	4.98e-22	41
anterior neural tube	4.98e-22	41
future forebrain	4.98e-22	41
brain	8.40e-21	68
future brain	8.40e-21	68
brain grey matter	1.23e-20	34
gray matter	1.23e-20	34
pre-chordal neural plate	2.37e-20	61
telencephalon	5.37e-20	34
adult organism	2.47e-19	114
ecto-epithelium	3.40e-19	104
regional part of telencephalon	2.30e-17	32
cerebral hemisphere	5.57e-17	32
brainstem	6.75e-14	6
structure with developmental contribution from neural crest	6.80e-14	132
neural nucleus	3.26e-12	9
nucleus of brain	3.26e-12	9
ectoderm-derived structure	3.99e-12	171
ectoderm	3.99e-12	171
presumptive ectoderm	3.99e-12	171
cerebral cortex	2.30e-11	25
pallium	2.30e-11	25
regional part of cerebral cortex	3.69e-11	22
organ system subdivision	7.92e-10	223
posterior neural tube	5.33e-09	15
chordal neural plate	5.33e-09	15
basal ganglion	8.32e-09	9
nuclear complex of neuraxis	8.32e-09	9
aggregate regional part of brain	8.32e-09	9
collection of basal ganglia	8.32e-09	9
cerebral subcortex	8.32e-09	9
gyrus	9.68e-09	6
tube	1.27e-08	192
neocortex	1.78e-08	20
telencephalic nucleus	3.19e-08	7
segmental subdivision of nervous system	4.00e-08	13
organ	6.86e-08	503
pons	7.55e-08	3
medulla oblongata	1.02e-07	3
myelencephalon	1.02e-07	3
future myelencephalon	1.02e-07	3

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.