Coexpression cluster:C4009

Full id: C4009_CD4_CD133_CD8_CD19_choriocarcinoma_Retinal_CD34

Phase1 CAGE Peaks

Hg19::chr1:93297586..93297609,+	p1@RPL5
Hg19::chr5:130325570..130325577,+	p1@ENST00000498453
Hg19::chr7:156985019..156985030,+	p1@ENST00000429552

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:0008097	5S rRNA binding	0.00353232073472271
GO:0019843	rRNA binding	0.0153067231837984
GO:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	0.0153067231837984
GO:0005830	cytosolic ribosome (sensu Eukaryota)	0.0220770045920169
GO:0015934	large ribosomal subunit	0.024726245143059
GO:0044445	cytosolic part	0.0372856077554064
GO:0033279	ribosomal subunit	0.0376780878370422

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><br>disease_data<br>

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Cell Type

Ontology term	p-value	n
lymphocyte	8.87e-24	53
common lymphoid progenitor	8.87e-24	53
lymphoid lineage restricted progenitor cell	2.95e-23	52
nongranular leukocyte	4.60e-23	119
hematopoietic stem cell	2.15e-21	172
angioblastic mesenchymal cell	2.15e-21	172
hematopoietic lineage restricted progenitor cell	4.28e-21	124
hematopoietic oligopotent progenitor cell	1.21e-19	165
hematopoietic multipotent progenitor cell	1.21e-19	165
leukocyte	5.21e-19	140
hematopoietic cell	2.57e-18	182
lymphocyte of B lineage	2.92e-12	24
pro-B cell	2.92e-12	24
T cell	2.54e-11	25
pro-T cell	2.54e-11	25
mature alpha-beta T cell	5.62e-11	18
alpha-beta T cell	5.62e-11	18
immature T cell	5.62e-11	18
mature T cell	5.62e-11	18
immature alpha-beta T cell	5.62e-11	18
native cell	1.14e-09	722
B cell	4.70e-09	14
classical monocyte	2.32e-08	45
CD14-positive, CD16-negative classical monocyte	4.24e-08	42
CD8-positive, alpha-beta T cell	6.34e-08	11

Disease

Ontology term	p-value	n
disease of cellular proliferation	1.35e-09	239
cancer	2.78e-09	235
hematologic cancer	1.60e-07	51
immune system cancer	1.60e-07	51
organ system cancer	1.77e-07	137

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
KAT2A#2648	1	205.363333333333	0.00486154522073778	0.0227540970381211
ZZZ3#26009	1	79.8044041450777	0.012478437908258	0.0451649827309151

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.