Coexpression cluster:C4638

Full id: C4638_CD4_testicular_H9_iPS_CD8_Natural_Basophils

Phase1 CAGE Peaks

Hg19::chr7:105332361..105332378,-	p10@ATXN7L1
Hg19::chr7:105332394..105332410,-	p7@ATXN7L1
Hg19::chr7:105332434..105332443,-	p11@ATXN7L1

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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No GOStat results

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><br>

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Cell Type

Ontology term	p-value	n
leukocyte	2.63e-28	140
nongranular leukocyte	1.10e-25	119
hematopoietic lineage restricted progenitor cell	1.27e-24	124
hematopoietic stem cell	1.96e-21	172
angioblastic mesenchymal cell	1.96e-21	172
mature alpha-beta T cell	5.28e-21	18
alpha-beta T cell	5.28e-21	18
immature T cell	5.28e-21	18
mature T cell	5.28e-21	18
immature alpha-beta T cell	5.28e-21	18
hematopoietic cell	7.15e-20	182
hematopoietic oligopotent progenitor cell	2.11e-19	165
hematopoietic multipotent progenitor cell	2.11e-19	165
lymphocyte	3.91e-16	53
common lymphoid progenitor	3.91e-16	53
lymphoid lineage restricted progenitor cell	1.83e-15	52
T cell	4.05e-15	25
pro-T cell	4.05e-15	25
CD14-positive, CD16-negative classical monocyte	1.60e-14	42
CD8-positive, alpha-beta T cell	3.47e-14	11
classical monocyte	4.40e-14	45
intermediate monocyte	2.64e-12	9
CD14-positive, CD16-positive monocyte	2.64e-12	9
myeloid leukocyte	5.55e-12	76
granulocyte monocyte progenitor cell	1.96e-10	71
CD4-positive, alpha-beta T cell	4.40e-10	6
myeloid lineage restricted progenitor cell	6.59e-10	70
embryonic stem cell	1.19e-08	5
macrophage dendritic cell progenitor	1.28e-08	65
monopoietic cell	2.30e-08	63
monocyte	2.30e-08	63
monoblast	2.30e-08	63
promonocyte	2.30e-08	63

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.55e-11	102
blood island	2.55e-11	102
hemolymphoid system	5.62e-10	112
bone marrow	5.30e-09	80
bone element	8.78e-08	86

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.011577411526042
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327547204640942
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168379583295915
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00584040689844686
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.00085472567980186
MYC#4609	3	5.2222818716094	0.00702084375574015	0.02959516875225
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109399214410671
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00198054695229791
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191098748477735
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00423043313078816

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.