Coexpression cluster:C3476

Full id: C3476_Neutrophils_Eosinophils_optic_spinal_Endothelial_CD14_locus

Phase1 CAGE Peaks

Hg19::chr15:31283767..31283793,-	p3@MTMR10
Hg19::chr15:31283798..31283851,-	p1@MTMR10
Hg19::chr20:4804051..4804099,-	p3@RASSF2

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:0046839	phospholipid dephosphorylation	0.0424705583529366
GO:0030258	lipid modification	0.0424705583529366
GO:0004437	inositol or phosphatidylinositol phosphatase activity	0.0424705583529366

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
myeloid leukocyte	5.52e-32	72
granulocyte monocyte progenitor cell	4.37e-28	67
defensive cell	4.29e-27	48
phagocyte	4.29e-27	48
macrophage dendritic cell progenitor	5.76e-27	61
myeloid lineage restricted progenitor cell	6.85e-27	66
monopoietic cell	3.91e-26	59
monocyte	3.91e-26	59
monoblast	3.91e-26	59
promonocyte	3.91e-26	59
classical monocyte	4.12e-25	42
CD14-positive, CD16-negative classical monocyte	4.12e-25	42
leukocyte	8.10e-22	136
myeloid cell	4.01e-18	108
common myeloid progenitor	4.01e-18	108
stuff accumulating cell	1.85e-17	87
hematopoietic lineage restricted progenitor cell	1.22e-16	120
nongranular leukocyte	1.84e-15	115
hematopoietic stem cell	2.24e-13	168
angioblastic mesenchymal cell	2.24e-13	168
hematopoietic cell	1.40e-12	177
hematopoietic oligopotent progenitor cell	1.56e-12	161
hematopoietic multipotent progenitor cell	1.56e-12	161

Uber Anatomy

Ontology term	p-value	n
adult organism	4.06e-29	114
hemolymphoid system	1.69e-27	108
hematopoietic system	8.25e-26	98
blood island	8.25e-26	98
immune system	4.26e-22	93
bone marrow	1.27e-21	76
lateral plate mesoderm	3.24e-19	203
bone element	1.04e-18	82
skeletal element	9.77e-14	90
neural tube	1.60e-13	56
neural rod	1.60e-13	56
future spinal cord	1.60e-13	56
neural keel	1.60e-13	56
regional part of nervous system	4.54e-12	53
regional part of brain	4.54e-12	53
skeletal system	5.82e-12	100
brain	2.94e-10	68
future brain	2.94e-10	68
regional part of forebrain	1.54e-09	41
forebrain	1.54e-09	41
anterior neural tube	1.54e-09	41
future forebrain	1.54e-09	41
central nervous system	2.23e-09	81
brain grey matter	6.53e-09	34
gray matter	6.53e-09	34
telencephalon	8.27e-09	34
mesoderm	5.33e-08	315
mesoderm-derived structure	5.33e-08	315
presumptive mesoderm	5.33e-08	315
regional part of telencephalon	6.24e-08	32
cerebral hemisphere	8.25e-08	32
neural plate	8.74e-08	82
presumptive neural plate	8.74e-08	82

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)
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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
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460311594661223
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.039002537713295
ZBTB33#10009	2	21.1098166866541	0.00292859706060324	0.0156306085656348

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.