Coexpression cluster:C2101

Full id: C2101_adult_B_xeroderma_lymphoma_signet_appendix_tonsil

Phase1 CAGE Peaks

Hg19::chr11:119622609..119622621,+	p@chr11:119622609..119622621 +
Hg19::chr11:119622634..119622668,+	p@chr11:119622634..119622668 +
Hg19::chr17:39928110..39928152,-	p5@JUP
Hg19::chr1:25255329..25255339,-	p21@RUNX3

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:0005916	fascia adherens	0.014008857951139
GO:0009898	internal side of plasma membrane	0.014008857951139
GO:0030057	desmosome	0.014008857951139
GO:0050680	negative regulation of epithelial cell proliferation	0.014008857951139
GO:0005913	cell-cell adherens junction	0.014008857951139
GO:0030018	Z disc	0.014008857951139
GO:0031674	I band	0.014580004135363
GO:0050678	regulation of epithelial cell proliferation	0.022007762260344
GO:0050673	epithelial cell proliferation	0.022007762260344
GO:0014704	intercalated disc	0.0249241607803606
GO:0030017	sarcomere	0.0249241607803606
GO:0030016	myofibril	0.0249241607803606
GO:0005912	adherens junction	0.0249241607803606
GO:0044449	contractile fiber part	0.0255973422701364
GO:0043292	contractile fiber	0.0255973422701364
GO:0043296	apical junction complex	0.0370325943749413
GO:0016327	apicolateral plasma membrane	0.0370325943749413

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
lymphocyte of B lineage	1.23e-36	24
pro-B cell	1.23e-36	24
lymphoid lineage restricted progenitor cell	8.91e-25	52
lymphocyte	3.22e-24	53
common lymphoid progenitor	3.22e-24	53
nucleate cell	3.64e-23	55
leukocyte	3.81e-17	136
hematopoietic cell	1.75e-16	177
hematopoietic lineage restricted progenitor cell	1.72e-15	120
hematopoietic oligopotent progenitor cell	1.14e-14	161
hematopoietic multipotent progenitor cell	1.14e-14	161
hematopoietic stem cell	8.94e-14	168
angioblastic mesenchymal cell	8.94e-14	168
nongranular leukocyte	3.42e-12	115
B cell	3.69e-10	14
mature B cell	6.77e-09	2
pre-B-II cell	6.77e-09	2
transitional stage B cell	6.77e-09	2
small pre-B-II cell	6.77e-09	2
immature B cell	6.77e-09	2
Langerhans cell	4.45e-08	5
histamine secreting cell	1.00e-07	5
biogenic amine secreting cell	1.00e-07	5
granulocytopoietic cell	1.00e-07	5
mast cell	1.00e-07	5
mast cell progenitor	1.00e-07	5
basophil mast progenitor cell	1.00e-07	5
circulating cell	5.74e-07	6

Uber Anatomy

Ontology term	p-value	n
hemopoietic organ	2.84e-14	7
immune organ	2.84e-14	7
spleen	4.91e-13	3
gastrointestinal system mesentery	4.91e-13	3
stomach region	4.91e-13	3
mesentery	4.91e-13	3
gastrointestinal system serosa	4.91e-13	3
mesentery of stomach	4.91e-13	3
gut mesentery	4.91e-13	3
dorsal mesentery	4.91e-13	3
dorsal mesogastrium	4.91e-13	3
peritoneal cavity	4.91e-13	3
spleen primordium	4.91e-13	3

Disease

Ontology term	p-value	n
lymphoma	5.70e-26	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)
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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
EBF1#1879	4	8.906466846569	0.0001588790747201	0.00199365273155023

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.