Coexpression cluster:C368

Full id: C368_Pericytes_Fibroblast_Nucleus_Anulus_Meningeal_Mesenchymal_Smooth

Phase1 CAGE Peaks

Hg19::chr11:130318529..130318547,+	p1@ADAMTS15
Hg19::chr11:60610073..60610090,+	p6@CCDC86
Hg19::chr11:61634723..61634731,+	p@chr11:61634723..61634731 +
Hg19::chr11:61634768..61634777,+	p@chr11:61634768..61634777 +
Hg19::chr12:279773..279812,+	p@chr12:279773..279812 +
Hg19::chr12:279860..279871,+	p@chr12:279860..279871 +
Hg19::chr12:57522813..57522825,-	p10@STAT6
Hg19::chr15:57598803..57598812,+	p6@LOC283663
Hg19::chr17:48346424..48346435,+	p@chr17:48346424..48346435 +
Hg19::chr17:75446704..75446713,+	p35@SEPT9
Hg19::chr17:75446731..75446743,+	p36@SEPT9
Hg19::chr17:75446774..75446783,+	p49@SEPT9
Hg19::chr17:75446796..75446809,+	p23@SEPT9
Hg19::chr17:75446824..75446838,+	p9@SEPT9
Hg19::chr17:75447512..75447527,+	p22@SEPT9
Hg19::chr17:75471711..75471726,+	p73@SEPT9
Hg19::chr1:19778678..19778689,-	p@chr1:19778678..19778689 -
Hg19::chr1:19778700..19778738,-	p@chr1:19778700..19778738 -
Hg19::chr3:147109858..147109861,+	p@chr3:147109858..147109861 +
Hg19::chr3:147112699..147112713,-	p@chr3:147112699..147112713 -
Hg19::chr3:147127904..147127942,+	p1@AB464362
Hg19::chr3:147127961..147127972,+	p3@AB464362
Hg19::chr3:147128031..147128038,+	p7@AB464362
Hg19::chr3:147128048..147128057,+	p4@AB464362
Hg19::chr5:149515832..149515837,-	p@chr5:149515832..149515837 -
Hg19::chr5:149532703..149532711,+	p@chr5:149532703..149532711 +
Hg19::chr5:149537789..149537803,-	p@chr5:149537789..149537803 -
Hg19::chr5:149537807..149537827,-	p@chr5:149537807..149537827 -
Hg19::chr5:72744336..72744359,-	p5@FOXD1
Hg19::chr9:139876143..139876170,+	p1@LCNL1

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:0048295	positive regulation of isotype switching to IgE isotypes	0.0131869235943323
GO:0048289	isotype switching to IgE isotypes	0.0131869235943323
GO:0002829	negative regulation of T-helper 2 type immune response	0.0131869235943323
GO:0002828	regulation of T-helper 2 type immune response	0.0131869235943323
GO:0048293	regulation of isotype switching to IgE isotypes	0.0131869235943323
GO:0002820	negative regulation of adaptive immune response	0.0131869235943323
GO:0002823	negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0131869235943323
GO:0045830	positive regulation of isotype switching	0.0131869235943323
GO:0051291	protein heterooligomerization	0.0131869235943323
GO:0050777	negative regulation of immune response	0.0131869235943323
GO:0045191	regulation of isotype switching	0.0131869235943323
GO:0002683	negative regulation of immune system process	0.0131869235943323
GO:0042092	T-helper 2 type immune response	0.0131869235943323
GO:0002208	somatic diversification of immunoglobulins during immune response	0.0131869235943323
GO:0002381	immunoglobulin production during immune response	0.0131869235943323
GO:0002204	somatic recombination of immunoglobulin genes during immune response	0.0131869235943323
GO:0008301	DNA bending activity	0.0131869235943323
GO:0032432	actin filament bundle	0.0131869235943323
GO:0045190	isotype switching	0.0131869235943323
GO:0001725	stress fiber	0.0131869235943323
GO:0016447	somatic recombination of immunoglobulin gene segments	0.0135501835469304
GO:0002819	regulation of adaptive immune response	0.0135501835469304
GO:0002822	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.	0.0135501835469304
GO:0016444	somatic cell DNA recombination	0.0138291801550393
GO:0016445	somatic diversification of immunoglobulins	0.0138291801550393
GO:0002562	somatic diversification of immune receptors via germline recombination within a single locus	0.0138291801550393
GO:0002200	somatic diversification of immune receptors	0.0142039512283195
GO:0002377	immunoglobulin production	0.0148756627066806
GO:0050871	positive regulation of B cell activation	0.0148756627066806
GO:0051241	negative regulation of multicellular organismal process	0.0193197341117233
GO:0050864	regulation of B cell activation	0.0193197341117233
GO:0002440	production of molecular mediator of immune response	0.0202108918231167
GO:0043565	sequence-specific DNA binding	0.0308738063090595
GO:0051251	positive regulation of lymphocyte activation	0.0345488266684464
GO:0016064	immunoglobulin mediated immune response	0.0345488266684464
GO:0019724	B cell mediated immunity	0.0345488266684464
GO:0042113	B cell activation	0.0390018187822978
GO:0051259	protein oligomerization	0.0390018187822978
GO:0048471	perinuclear region of cytoplasm	0.0392230169527433
GO:0002449	lymphocyte mediated immunity	0.0413951774132484
GO:0002250	adaptive immune response	0.0413951774132484
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0413951774132484
GO:0051249	regulation of lymphocyte activation	0.0413951774132484
GO:0048519	negative regulation of biological process	0.0413951774132484
GO:0002443	leukocyte mediated immunity	0.0413951774132484
GO:0050865	regulation of cell activation	0.0415287325000021
GO:0050776	regulation of immune response	0.0496894167890069
GO:0002682	regulation of immune system process	0.0496894167890069

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
non-terminally differentiated cell	2.64e-21	180
contractile cell	1.68e-11	59
electrically responsive cell	8.55e-11	60
electrically active cell	8.55e-11	60
muscle cell	6.66e-10	54
muscle precursor cell	1.35e-09	57
myoblast	1.35e-09	57
multi-potent skeletal muscle stem cell	1.35e-09	57
fibroblast	3.91e-08	75
neurectodermal cell	1.90e-07	59

Uber Anatomy

Ontology term	p-value	n
cell layer	1.10e-17	312
epithelium	1.94e-16	309
central nervous system	1.41e-15	82
multi-tissue structure	2.62e-15	347
organism subdivision	3.47e-15	365
regional part of nervous system	3.69e-15	94
nervous system	3.69e-15	94
neural plate	2.11e-14	86
presumptive neural plate	2.11e-14	86
neurectoderm	6.12e-13	90
somite	1.92e-12	83
paraxial mesoderm	1.92e-12	83
presomitic mesoderm	1.92e-12	83
presumptive segmental plate	1.92e-12	83
trunk paraxial mesoderm	1.92e-12	83
presumptive paraxial mesoderm	1.92e-12	83
ectoderm-derived structure	2.56e-12	169
regional part of brain	3.44e-12	59
dermomyotome	4.12e-12	70
brain	1.12e-11	69
future brain	1.12e-11	69
anatomical cluster	1.38e-11	286
multi-cellular organism	1.72e-11	659
ectoderm	1.89e-11	173
presumptive ectoderm	1.89e-11	173
multilaminar epithelium	2.80e-11	82
trunk mesenchyme	4.64e-11	143
neural tube	5.64e-11	57
neural rod	5.64e-11	57
future spinal cord	5.64e-11	57
neural keel	5.64e-11	57
embryo	1.14e-10	612
anterior region of body	1.70e-10	129
craniocervical region	1.70e-10	129
head	2.24e-10	123
anatomical system	3.75e-10	625
tube	4.36e-10	194
anatomical group	5.12e-10	626
muscle tissue	6.27e-10	63
musculature	6.27e-10	63
musculature of body	6.27e-10	63
skeletal muscle tissue	6.46e-10	61
striated muscle tissue	6.46e-10	61
myotome	6.46e-10	61
adult organism	1.67e-09	115
embryonic structure	2.03e-09	605
developing anatomical structure	2.03e-09	605
germ layer	3.50e-09	604
embryonic tissue	3.50e-09	604
presumptive structure	3.50e-09	604
epiblast (generic)	3.50e-09	604
pre-chordal neural plate	2.59e-08	61
anatomical conduit	4.28e-08	241
vasculature of head	7.34e-08	11
vasculature of organ	7.34e-08	11
primary circulatory organ	1.61e-07	27
compound organ	4.71e-07	69
posterior neural tube	7.87e-07	15
chordal neural plate	7.87e-07	15

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
FOSL1#8061	5	6.61892995272883	0.000851082172346474	0.00640944411578406
FOSL2#2355	6	3.38604012091234	0.00736957552356816	0.0304651321289556
HNF4A#3172	6	4.62645807259074	0.00157809441712721	0.00994656625409467
HNF4G#3174	6	5.75068450528936	0.000510261340278916	0.00446698944823048
JUNB#3726	5	5.10177210997019	0.00267525284156616	0.0147487717229903
NR2C2#7182	5	5.43576848420681	0.00203186457041124	0.0118023305822681
SUZ12#23512	4	6.68210412147505	0.00286620885512734	0.0155309736754511

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.