Coexpression cluster:C1279

Full id: C1279_CD14_Neutrophils_substantia_Eosinophils_optic_globus_thalamus

Phase1 CAGE Peaks

Hg19::chr6:163841233..163841239,+	p@chr6:163841233..163841239 +
Hg19::chr6:163848296..163848300,+	p@chr6:163848296..163848300 +
Hg19::chr6:163849791..163849795,+	p20@QKI
Hg19::chr6:163910016..163910030,+	p@chr6:163910016..163910030 +
Hg19::chr6:163910203..163910206,+	p@chr6:163910203..163910206 +
Hg19::chr6:163924190..163924195,+	p@chr6:163924190..163924195 +
Hg19::chr6:163928513..163928551,+	p1@BC044915

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:0051028	mRNA transport	0.0280623258369638
GO:0050658	RNA transport	0.0280623258369638
GO:0051236	establishment of RNA localization	0.0280623258369638
GO:0050657	nucleic acid transport	0.0280623258369638
GO:0006403	RNA localization	0.0280623258369638
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0280623258369638
GO:0006417	regulation of translation	0.036427057576828
GO:0031326	regulation of cellular biosynthetic process	0.036427057576828
GO:0009889	regulation of biosynthetic process	0.036427057576828
GO:0008380	RNA splicing	0.036427057576828
GO:0006397	mRNA processing	0.0401801483574708
GO:0016071	mRNA metabolic process	0.0461409395973154

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	2.55e-32	72
macrophage dendritic cell progenitor	2.33e-27	61
granulocyte monocyte progenitor cell	2.75e-27	67
monopoietic cell	3.37e-26	59
monocyte	3.37e-26	59
monoblast	3.37e-26	59
promonocyte	3.37e-26	59
classical monocyte	6.07e-26	42
CD14-positive, CD16-negative classical monocyte	6.07e-26	42
myeloid lineage restricted progenitor cell	2.04e-25	66
leukocyte	8.52e-25	136
defensive cell	1.25e-24	48
phagocyte	1.25e-24	48
myeloid cell	1.60e-22	108
common myeloid progenitor	1.60e-22	108
hematopoietic stem cell	2.73e-20	168
angioblastic mesenchymal cell	2.73e-20	168
nongranular leukocyte	3.69e-20	115
hematopoietic lineage restricted progenitor cell	5.35e-20	120
hematopoietic oligopotent progenitor cell	2.86e-19	161
hematopoietic multipotent progenitor cell	2.86e-19	161
hematopoietic cell	7.43e-19	177
stuff accumulating cell	2.16e-09	87
intermediate monocyte	4.17e-07	9
CD14-positive, CD16-positive monocyte	4.17e-07	9
granulocyte	6.94e-07	8

Uber Anatomy

Ontology term	p-value	n
neural tube	3.15e-26	56
neural rod	3.15e-26	56
future spinal cord	3.15e-26	56
neural keel	3.15e-26	56
regional part of nervous system	1.28e-23	53
regional part of brain	1.28e-23	53
brain grey matter	3.06e-23	34
gray matter	3.06e-23	34
telencephalon	8.65e-23	34
bone marrow	1.57e-22	76
bone element	4.51e-22	82
adult organism	8.48e-22	114
neural plate	1.06e-21	82
presumptive neural plate	1.06e-21	82
regional part of forebrain	1.37e-21	41
forebrain	1.37e-21	41
anterior neural tube	1.37e-21	41
future forebrain	1.37e-21	41
neurectoderm	1.39e-21	86
regional part of telencephalon	2.06e-21	32
cerebral hemisphere	4.98e-21	32
brain	9.27e-21	68
future brain	9.27e-21	68
central nervous system	1.61e-20	81
hematopoietic system	3.85e-19	98
blood island	3.85e-19	98
nervous system	7.98e-19	89
skeletal element	3.59e-18	90
immune system	3.75e-17	93
skeletal system	1.28e-16	100
hemolymphoid system	2.09e-16	108
cerebral cortex	1.05e-15	25
pallium	1.05e-15	25
pre-chordal neural plate	1.26e-15	61
regional part of cerebral cortex	1.12e-13	22
ecto-epithelium	2.54e-13	104
structure with developmental contribution from neural crest	1.47e-12	132
neocortex	6.44e-12	20
neural nucleus	3.31e-09	9
nucleus of brain	3.31e-09	9
basal ganglion	4.73e-09	9
nuclear complex of neuraxis	4.73e-09	9
aggregate regional part of brain	4.73e-09	9
collection of basal ganglia	4.73e-09	9
cerebral subcortex	4.73e-09	9
musculoskeletal system	9.90e-08	167
ectoderm-derived structure	1.39e-07	171
ectoderm	1.39e-07	171
presumptive ectoderm	1.39e-07	171
telencephalic nucleus	2.32e-07	7
organ	6.28e-07	503

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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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.