Coexpression cluster:C1660

Full id: C1660_CD14_substantia_corpus_globus_thalamus_optic_spinal

Phase1 CAGE Peaks

Hg19::chr12:121570672..121570772,+	p1@P2RX7
Hg19::chr17:9939865..9939889,-	p5@GAS7
Hg19::chr17:9939908..9939926,-	p8@GAS7
Hg19::chr18:21166841..21166864,-	p3@NPC1
Hg19::chr18:21977258..21977276,+	p2@LOC100289533

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:0046686	response to cadmium ion	0.0174762390536148
GO:0004931	ATP-gated cation channel activity	0.0174762390536148
GO:0033344	cholesterol efflux	0.0174762390536148
GO:0015248	sterol transporter activity	0.0174762390536148
GO:0007041	lysosomal transport	0.0174762390536148
GO:0008206	bile acid metabolic process	0.0174762390536148
GO:0042632	cholesterol homeostasis	0.0174762390536148
GO:0055092	sterol homeostasis	0.0174762390536148
GO:0008158	hedgehog receptor activity	0.0174762390536148
GO:0055088	lipid homeostasis	0.0174762390536148
GO:0015918	sterol transport	0.0174762390536148
GO:0030301	cholesterol transport	0.0174762390536148
GO:0007034	vacuolar transport	0.0224008173644822
GO:0031902	late endosome membrane	0.0241260387178422
GO:0010038	response to metal ion	0.0271716563837915
GO:0010035	response to inorganic substance	0.0302408687262414
GO:0005887	integral to plasma membrane	0.0302408687262414
GO:0005765	lysosomal membrane	0.0302408687262414
GO:0005770	late endosome	0.0302408687262414
GO:0031226	intrinsic to plasma membrane	0.0302408687262414
GO:0005774	vacuolar membrane	0.0323758025332802
GO:0048471	perinuclear region of cytoplasm	0.0323758025332802
GO:0044437	vacuolar part	0.0323758025332802
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0348969376001375
GO:0044440	endosomal part	0.038241615401665
GO:0010008	endosome membrane	0.038241615401665
GO:0022892	substrate-specific transporter activity	0.038241615401665
GO:0005319	lipid transporter activity	0.0398540249595936
GO:0007050	cell cycle arrest	0.0404779378738486

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	6.71e-39	48
phagocyte	6.71e-39	48
myeloid leukocyte	2.40e-37	72
monopoietic cell	2.40e-36	59
monocyte	2.40e-36	59
monoblast	2.40e-36	59
promonocyte	2.40e-36	59
macrophage dendritic cell progenitor	9.86e-36	61
classical monocyte	4.75e-35	42
CD14-positive, CD16-negative classical monocyte	4.75e-35	42
granulocyte monocyte progenitor cell	3.43e-32	67
myeloid lineage restricted progenitor cell	9.09e-32	66
stuff accumulating cell	5.11e-26	87
leukocyte	2.60e-22	136
myeloid cell	8.93e-21	108
common myeloid progenitor	8.93e-21	108
nongranular leukocyte	4.96e-20	115
hematopoietic lineage restricted progenitor cell	2.06e-17	120
hematopoietic stem cell	3.19e-15	168
angioblastic mesenchymal cell	3.19e-15	168
hematopoietic oligopotent progenitor cell	1.96e-13	161
hematopoietic multipotent progenitor cell	1.96e-13	161
hematopoietic cell	2.12e-13	177
intermediate monocyte	3.83e-07	9
CD14-positive, CD16-positive monocyte	3.83e-07	9

Uber Anatomy

Ontology term	p-value	n
adult organism	1.85e-48	114
hemolymphoid system	1.47e-32	108
hematopoietic system	8.17e-32	98
blood island	8.17e-32	98
bone marrow	3.72e-29	76
immune system	3.19e-28	93
bone element	4.06e-26	82
neural tube	5.35e-26	56
neural rod	5.35e-26	56
future spinal cord	5.35e-26	56
neural keel	5.35e-26	56
regional part of nervous system	1.03e-23	53
regional part of brain	1.03e-23	53
skeletal element	1.52e-21	90
central nervous system	5.36e-19	81
skeletal system	1.37e-18	100
regional part of forebrain	1.51e-18	41
forebrain	1.51e-18	41
anterior neural tube	1.51e-18	41
future forebrain	1.51e-18	41
brain	1.91e-18	68
future brain	1.91e-18	68
brain grey matter	4.07e-16	34
gray matter	4.07e-16	34
nervous system	4.75e-16	89
telencephalon	5.48e-16	34
neural plate	8.67e-15	82
presumptive neural plate	8.67e-15	82
regional part of telencephalon	1.52e-14	32
cerebral hemisphere	2.36e-14	32
neurectoderm	3.20e-13	86
regional part of cerebral cortex	2.82e-11	22
pre-chordal neural plate	2.03e-10	61
neocortex	4.95e-10	20
lateral plate mesoderm	6.53e-10	203
cerebral cortex	7.02e-10	25
pallium	7.02e-10	25
ecto-epithelium	8.78e-10	104
organ	3.00e-09	503
posterior neural tube	1.18e-08	15
chordal neural plate	1.18e-08	15
neural nucleus	2.51e-08	9
nucleus of brain	2.51e-08	9
structure with developmental contribution from neural crest	2.91e-08	132
germ layer	7.63e-08	560
germ layer / neural crest	7.63e-08	560
embryonic tissue	7.63e-08	560
presumptive structure	7.63e-08	560
germ layer / neural crest derived structure	7.63e-08	560
epiblast (generic)	7.63e-08	560
basal ganglion	1.50e-07	9
nuclear complex of neuraxis	1.50e-07	9
aggregate regional part of brain	1.50e-07	9
collection of basal ganglia	1.50e-07	9
cerebral subcortex	1.50e-07	9
embryonic structure	2.02e-07	564
segmental subdivision of nervous system	2.81e-07	13
musculoskeletal system	8.38e-07	167

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
SREBF2#6721	1	87.3886524822695	0.0113909976229849	0.0417440752569185

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.