Coexpression cluster:C1110

Full id: C1110_cord_mycosis_colon_embryonic_argyrophil_xeroderma_CD19

Phase1 CAGE Peaks

Hg19::chr10:133058641..133058652,-	p6@TCERG1L
Hg19::chr13:28494375..28494416,+	p4@PDX1
Hg19::chr13:28498703..28498710,+	p@chr13:28498703..28498710 +
Hg19::chr6:31540557..31540570,+	p4@LTA
Hg19::chr6:31541218..31541237,+	p@chr6:31541218..31541237 +
Hg19::chr6:31541408..31541421,+	p@chr6:31541408..31541421 +
Hg19::chr7:102944849..102944859,+	p@chr7:102944849..102944859 +

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:0051952	regulation of amine transport	0.00494510345594605
GO:0002036	regulation of L-glutamate transport	0.00494510345594605
GO:0051953	negative regulation of amine transport	0.00494510345594605
GO:0051956	negative regulation of amino acid transport	0.00494510345594605
GO:0002037	negative regulation of L-glutamate transport	0.00494510345594605
GO:0051955	regulation of amino acid transport	0.00494510345594605
GO:0046325	negative regulation of glucose import	0.00847582299419329
GO:0048535	lymph node development	0.00847582299419329
GO:0050806	positive regulation of synaptic transmission	0.00847582299419329
GO:0042127	regulation of cell proliferation	0.00847582299419329
GO:0051971	positive regulation of transmission of nerve impulse	0.00847582299419329
GO:0046323	glucose import	0.00847582299419329
GO:0046324	regulation of glucose import	0.00847582299419329
GO:0031646	positive regulation of neurological process	0.00847582299419329
GO:0043525	positive regulation of neuron apoptosis	0.00889935214910135
GO:0031016	pancreas development	0.00926988558275227
GO:0051222	positive regulation of protein transport	0.00959677548276263
GO:0045840	positive regulation of mitosis	0.00963982957309548
GO:0015813	L-glutamate transport	0.00963982957309548
GO:0015800	acidic amino acid transport	0.00963982957309548
GO:0050804	regulation of synaptic transmission	0.0108424725521954
GO:0008283	cell proliferation	0.0108424725521954
GO:0009612	response to mechanical stimulus	0.0109603882890473
GO:0051969	regulation of transmission of nerve impulse	0.0111212430341185
GO:0045787	positive regulation of progression through cell cycle	0.0137271002031507
GO:0031644	regulation of neurological process	0.0137271002031507
GO:0043523	regulation of neuron apoptosis	0.0137271002031507
GO:0048522	positive regulation of cellular process	0.0137671221908496
GO:0051223	regulation of protein transport	0.0137671221908496
GO:0051402	neuron apoptosis	0.0137671221908496
GO:0015758	glucose transport	0.0137671221908496
GO:0051051	negative regulation of transport	0.0137671221908496
GO:0008645	hexose transport	0.0137671221908496
GO:0015749	monosaccharide transport	0.0137671221908496
GO:0048518	positive regulation of biological process	0.0137671221908496
GO:0019722	calcium-mediated signaling	0.0144486788814349
GO:0048513	organ development	0.0144486788814349
GO:0051050	positive regulation of transport	0.0144486788814349
GO:0005164	tumor necrosis factor receptor binding	0.0144486788814349
GO:0003704	specific RNA polymerase II transcription factor activity	0.0144486788814349
GO:0032813	tumor necrosis factor receptor superfamily binding	0.014818285051059
GO:0007088	regulation of mitosis	0.0236205980833195
GO:0006865	amino acid transport	0.0241021943152424
GO:0048731	system development	0.0246724218389829
GO:0006959	humoral immune response	0.0246724218389829
GO:0015837	amine transport	0.0270252262450758
GO:0048869	cellular developmental process	0.0287158030664027
GO:0030154	cell differentiation	0.0287158030664027
GO:0046942	carboxylic acid transport	0.0287158030664027
GO:0015849	organic acid transport	0.0287158030664027
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB cascade	0.0287158030664027
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0303970611682208
GO:0051049	regulation of transport	0.0303970611682208
GO:0008643	carbohydrate transport	0.0303970611682208
GO:0048856	anatomical structure development	0.0306502575807213
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0360316312609124
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0360316312609124
GO:0007275	multicellular organismal development	0.037986522699988
GO:0009967	positive regulation of signal transduction	0.0383004752371746
GO:0009628	response to abiotic stimulus	0.0406016596967475
GO:0048534	hemopoietic or lymphoid organ development	0.0418624765584408
GO:0002520	immune system development	0.0433184679915768
GO:0006006	glucose metabolic process	0.0449599678871934
GO:0001775	cell activation	0.0475808260858078
GO:0006917	induction of apoptosis	0.0475808260858078
GO:0012502	induction of programmed cell death	0.0475808260858078
GO:0045893	positive regulation of transcription, DNA-dependent	0.0487658922195956
GO:0008285	negative regulation of cell proliferation	0.0487658922195956

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
circulating cell	5.37e-50	6

Uber Anatomy

Ontology term	p-value	n
umbilical cord	2.06e-30	10
blastocyst	2.06e-30	10
blastula	2.06e-30	10
bilaminar disc	2.06e-30	10
inner cell mass	2.06e-30	10
cleaving embryo	2.06e-30	10
connecting stalk	2.06e-30	10
inner cell mass derived epiblast	2.06e-30	10
extraembryonic mesoderm	2.06e-30	10
blood	1.37e-20	15
haemolymphatic fluid	1.37e-20	15
organism substance	1.37e-20	15
extraembryonic structure	3.48e-13	24

Disease

Ontology term	p-value	n
non-Hodgkin lymphoma	2.58e-34	1
cutaneous T cell lymphoma	2.58e-34	1
mycosis fungoides	2.58e-34	1

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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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.