Coexpression cluster:C4448

Full id: C4448_Neutrophils_pons_brain_frontal_Eosinophils_Mast_spinal

Phase1 CAGE Peaks

Hg19::chr5:108745603..108745631,-	p1@PJA2
Hg19::chr6:122792919..122792970,-	p1@SERINC1
Hg19::chr6:122792978..122792992,-	p2@SERINC1

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:0032329	serine transport	0.00238428140252734
GO:0015825	L-serine transport	0.00238428140252734
GO:0022889	serine transmembrane transporter activity	0.00238428140252734
GO:0015194	L-serine transmembrane transporter activity	0.00238428140252734
GO:0005789	endoplasmic reticulum membrane	0.0025456993930067
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.0025456993930067
GO:0044432	endoplasmic reticulum part	0.00270600274992411
GO:0006658	phosphatidylserine metabolic process	0.00476814168412872
GO:0015807	L-amino acid transport	0.00529777923387416
GO:0005783	endoplasmic reticulum	0.00575482801364196
GO:0015804	neutral amino acid transport	0.00617501311531734
GO:0012505	endomembrane system	0.00617501311531734
GO:0015175	neutral amino acid transmembrane transporter activity	0.00623443615742896
GO:0015179	L-amino acid transmembrane transporter activity	0.0106759301763204
GO:0031090	organelle membrane	0.0106759301763204
GO:0015171	amino acid transmembrane transporter activity	0.0185258503936613
GO:0006665	sphingolipid metabolic process	0.0185258503936613
GO:0006865	amino acid transport	0.0185258503936613
GO:0015837	amine transport	0.0200384602203091
GO:0046943	carboxylic acid transmembrane transporter activity	0.0200384602203091
GO:0046942	carboxylic acid transport	0.0200384602203091
GO:0015849	organic acid transport	0.0200384602203091
GO:0005342	organic acid transmembrane transporter activity	0.0200384602203091
GO:0006650	glycerophospholipid metabolic process	0.0200384602203091
GO:0051347	positive regulation of transferase activity	0.027268406000498
GO:0045211	postsynaptic membrane	0.027268406000498
GO:0044456	synapse part	0.0283682184882672
GO:0005886	plasma membrane	0.0352423033661863
GO:0006644	phospholipid metabolic process	0.0352423033661863
GO:0051338	regulation of transferase activity	0.0368541894013872
GO:0044446	intracellular organelle part	0.0368541894013872
GO:0044422	organelle part	0.0368541894013872
GO:0043085	positive regulation of catalytic activity	0.0368541894013872
GO:0006643	membrane lipid metabolic process	0.0379968989070936
GO:0044444	cytoplasmic part	0.0422762736071943
GO:0000139	Golgi membrane	0.0480896116943764

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	2.35e-10	72
myeloid lineage restricted progenitor cell	7.37e-09	66
granulocyte monocyte progenitor cell	2.37e-07	67
monopoietic cell	4.94e-07	59
monocyte	4.94e-07	59
monoblast	4.94e-07	59
promonocyte	4.94e-07	59
macrophage dendritic cell progenitor	9.36e-07	61

Uber Anatomy

Ontology term	p-value	n
adult organism	1.43e-34	114
neural tube	6.52e-23	56
neural rod	6.52e-23	56
future spinal cord	6.52e-23	56
neural keel	6.52e-23	56
regional part of nervous system	8.70e-22	53
regional part of brain	8.70e-22	53
central nervous system	1.03e-20	81
regional part of forebrain	1.30e-20	41
forebrain	1.30e-20	41
anterior neural tube	1.30e-20	41
future forebrain	1.30e-20	41
brain	1.19e-19	68
future brain	1.19e-19	68
nervous system	1.29e-18	89
telencephalon	6.54e-17	34
brain grey matter	8.61e-17	34
gray matter	8.61e-17	34
cerebral hemisphere	9.10e-16	32
regional part of telencephalon	1.11e-15	32
neural plate	5.78e-14	82
presumptive neural plate	5.78e-14	82
regional part of cerebral cortex	1.67e-13	22
neurectoderm	5.74e-13	86
neocortex	2.25e-12	20
cerebral cortex	7.40e-12	25
pallium	7.40e-12	25
pre-chordal neural plate	3.16e-11	61
structure with developmental contribution from neural crest	1.15e-10	132
ectoderm-derived structure	1.98e-09	171
ectoderm	1.98e-09	171
presumptive ectoderm	1.98e-09	171
ecto-epithelium	2.00e-09	104
organ	5.80e-08	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)
{{{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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327001757273558
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464277641911201
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154630913938925
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128576463464584
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00486003141989741
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277872029481876
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247558759805297
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329381733826194
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330726321207605

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.