Coexpression cluster:C997

Full id: C997_testis_Neutrophils_Reticulocytes_embryonic_Basophils_CD14_tridermal

Phase1 CAGE Peaks

Hg19::chr11:64619747..64619758,+	p@chr11:64619747..64619758 +
Hg19::chr17:4269248..4269257,-	p@chr17:4269248..4269257 -
Hg19::chr17:74732889..74732898,+	p19@MFSD11
Hg19::chr19:7621690..7621698,+	p@chr19:7621690..7621698 +
Hg19::chr1:179335101..179335112,+	p6@AXDND1
Hg19::chr22:40440578..40440589,-	p5@BC038752
Hg19::chr3:38181238..38181245,+	p10@MYD88
Hg19::chr5:176433664..176433675,-	p10@UIMC1

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:0008063	Toll signaling pathway	0.00581292669125172
GO:0002755	MyD88-dependent toll-like receptor signaling pathway	0.00581292669125172
GO:0002238	response to molecule of fungal origin	0.00581292669125172
GO:0005121	Toll binding	0.00581292669125172
GO:0032760	positive regulation of tumor necrosis factor production	0.00581292669125172
GO:0002221	pattern recognition receptor signaling pathway	0.00581292669125172
GO:0002224	toll-like receptor signaling pathway	0.00581292669125172
GO:0032496	response to lipopolysaccharide	0.00581292669125172
GO:0032680	regulation of tumor necrosis factor production	0.00581292669125172
GO:0031663	lipopolysaccharide-mediated signaling pathway	0.00581292669125172
GO:0002218	activation of innate immune response	0.00581292669125172
GO:0002758	innate immune response-activating signal transduction	0.00581292669125172
GO:0045080	positive regulation of chemokine biosynthetic process	0.00606476986366401
GO:0005123	death receptor binding	0.00606476986366401
GO:0032606	interferon type I production	0.00606476986366401
GO:0048661	positive regulation of smooth muscle cell proliferation	0.00606476986366401
GO:0045351	interferon type I biosynthetic process	0.00606476986366401
GO:0045073	regulation of chemokine biosynthetic process	0.00606476986366401
GO:0032602	chemokine production	0.00606476986366401
GO:0002237	response to molecule of bacterial origin	0.00606476986366401
GO:0050755	chemokine metabolic process	0.00606476986366401
GO:0045089	positive regulation of innate immune response	0.00606476986366401
GO:0042033	chemokine biosynthetic process	0.00606476986366401
GO:0045088	regulation of innate immune response	0.00639309001654277
GO:0048660	regulation of smooth muscle cell proliferation	0.00669511170903356
GO:0046330	positive regulation of JNK cascade	0.00671557792129226
GO:0032640	tumor necrosis factor production	0.00671557792129226
GO:0048659	smooth muscle cell proliferation	0.00697366406672733
GO:0046328	regulation of JNK cascade	0.00883200757828019
GO:0009620	response to fungus	0.00883200757828019
GO:0033002	muscle cell proliferation	0.00899668680374902
GO:0051092	activation of NF-kappaB transcription factor	0.00971828956965259
GO:0001819	positive regulation of cytokine production	0.00971828956965259
GO:0051091	positive regulation of transcription factor activity	0.0123006698922749
GO:0002757	immune response-activating signal transduction	0.0127450863918242
GO:0002764	immune response-regulating signal transduction	0.0127779004540503
GO:0042108	positive regulation of cytokine biosynthetic process	0.0150364740853321
GO:0001817	regulation of cytokine production	0.0150364740853321
GO:0019221	cytokine and chemokine mediated signaling pathway	0.0153646976845699
GO:0016064	immunoglobulin mediated immune response	0.0171711618613322
GO:0051090	regulation of transcription factor activity	0.0171711618613322
GO:0019724	B cell mediated immunity	0.0171711618613322
GO:0045727	positive regulation of translation	0.0171711618613322
GO:0042035	regulation of cytokine biosynthetic process	0.018571264058464
GO:0031328	positive regulation of cellular biosynthetic process	0.018571264058464
GO:0007254	JNK cascade	0.0192787277651109
GO:0042089	cytokine biosynthetic process	0.0192787277651109
GO:0042107	cytokine metabolic process	0.0192787277651109
GO:0031098	stress-activated protein kinase signaling pathway	0.0192787277651109
GO:0009891	positive regulation of biosynthetic process	0.0192787277651109
GO:0002253	activation of immune response	0.0192787277651109
GO:0002449	lymphocyte mediated immunity	0.0192787277651109
GO:0002250	adaptive immune response	0.01959376415031
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.01959376415031
GO:0002443	leukocyte mediated immunity	0.0197426010253207
GO:0050778	positive regulation of immune response	0.0206367145530951
GO:0051247	positive regulation of protein metabolic process	0.0206367145530951
GO:0002684	positive regulation of immune system process	0.0206367145530951
GO:0050776	regulation of immune response	0.0224387813527228
GO:0009615	response to virus	0.0224387813527228
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB cascade	0.0224387813527228
GO:0002682	regulation of immune system process	0.0224387813527228
GO:0051240	positive regulation of multicellular organismal process	0.0230377501732489
GO:0009617	response to bacterium	0.0230377501732489
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0231099484407606
GO:0002252	immune effector process	0.0231799092542062
GO:0001816	cytokine production	0.0233135133751135
GO:0045087	innate immune response	0.0233135133751135
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0275936114911375
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0275936114911375
GO:0000165	MAPKKK cascade	0.02934836211627
GO:0009967	positive regulation of signal transduction	0.0295169502447868
GO:0006417	regulation of translation	0.0349792540799756
GO:0031326	regulation of cellular biosynthetic process	0.0373030904630282
GO:0051707	response to other organism	0.0380925236663848
GO:0009889	regulation of biosynthetic process	0.0395857622340122
GO:0045893	positive regulation of transcription, DNA-dependent	0.0401448774887949
GO:0008284	positive regulation of cell proliferation	0.0413951240740178
GO:0051239	regulation of multicellular organismal process	0.0479245649695406
GO:0045941	positive regulation of transcription	0.0479245649695406
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0479245649695406
GO:0009607	response to biotic stimulus	0.0479245649695406
GO:0006954	inflammatory response	0.0479245649695406
GO:0016481	negative regulation of transcription	0.0479245649695406

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
corpus callosum	3.07e-16	1
central nervous system cell part cluster	3.07e-16	1
axon tract	3.07e-16	1
intercerebral commissure	3.07e-16	1
dorsal telencephalic commissure	3.07e-16	1
brain white matter	3.07e-16	1
brain commissure	3.07e-16	1
white matter	3.07e-16	1
nervous system commissure	3.07e-16	1
cerebral hemisphere white matter	3.07e-16	1
multi cell component structure	8.74e-09	2
neuron projection bundle	8.74e-09	2
testis	9.31e-09	8

Disease

Ontology term	p-value	n
lymphoma	5.94e-07	10

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
CHD2#1106	4	5.17201141705843	0.00443788460794178	0.0210055848886849

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.