Coexpression cluster:C668

Full id: C668_lymphangiectasia_lymph_submaxillary_appendix_vein_CD19_lymphoma

Phase1 CAGE Peaks

Hg19::chr2:89156701..89156711,-	p@chr2:89156701..89156711 -
Hg19::chr2:89156772..89156782,-	p@chr2:89156772..89156782 -
Hg19::chr2:89156903..89156965,+	p1@CU688247 p1@CU689025 p1@CU689831 p1@CU689833 p1@CU689835 p1@CU691143
Hg19::chr2:89156917..89156926,-	p7@AJ294735
Hg19::chr2:89156940..89156955,-	p6@AJ294735
Hg19::chr2:89156976..89157016,+	p4@CU688247 p4@CU689025 p4@CU689831 p4@CU689833 p4@CU689835 p4@CU691143
Hg19::chr2:89156995..89157014,-	p4@AJ294735
Hg19::chr2:89157015..89157033,-	p5@AJ294735
Hg19::chr2:89157041..89157057,-	p3@AJ294735
Hg19::chr2:89157058..89157093,-	p1@AJ294735
Hg19::chr2:89157095..89157160,-	p2@AJ294735
Hg19::chr2:89157161..89157206,-	p1@IGKC
Hg19::chr3:186714356..186714377,+	p6@ST6GAL1

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:0006955	immune response	0.00220245711669294
GO:0002376	immune system process	0.00220245711669294
GO:0003835	beta-galactoside alpha-2,6-sialyltransferase activity	0.00765268573207231
GO:0009311	oligosaccharide metabolic process	0.0315506045610944
GO:0032393	MHC class I receptor activity	0.0363138866499496
GO:0008373	sialyltransferase activity	0.0363138866499496
GO:0030173	integral to Golgi membrane	0.0477293874861276
GO:0031228	intrinsic to Golgi membrane	0.0477293874861276
GO:0006959	humoral immune response	0.0477293874861276

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
B cell	5.82e-32	14
lymphocyte of B lineage	8.26e-30	24
pro-B cell	8.26e-30	24
lymphoid lineage restricted progenitor cell	3.15e-14	52
lymphocyte	7.27e-14	53
common lymphoid progenitor	7.27e-14	53
nucleate cell	3.52e-13	55
nongranular leukocyte	8.90e-09	115
single nucleate cell	1.24e-07	3
mononuclear cell	1.24e-07	3
leukocyte	3.43e-07	136

Uber Anatomy

Ontology term	p-value	n
adult organism	7.27e-33	114
blood	4.63e-12	15
haemolymphatic fluid	4.63e-12	15
organism substance	4.63e-12	15
major salivary gland	8.60e-07	2

Disease

Ontology term	p-value	n
lymphoma	7.45e-09	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
POLR2A#5430	13	2.14745317655807	4.83928878402115e-05	0.000840949220157046
POU2F2#5452	12	8.40565297637771	3.58336042559485e-11	4.10804148725248e-09
TAF1#6872	13	3.34304628574529	1.53362599454097e-07	8.60668271057841e-06

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.