Coexpression cluster:C4806

Full id: C4806_acute_Whole_Burkitt_Reticulocytes_chronic_CD34_Neutrophils

Phase1 CAGE Peaks

Hg19::chr9:135853243..135853257,+	p@chr9:135853243..135853257 +
Hg19::chr9:135853363..135853379,+	p@chr9:135853363..135853379 +
Hg19::chr9:135853402..135853417,+	p4@GFI1B

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	3.17e-17	172
angioblastic mesenchymal cell	3.17e-17	172
hematopoietic cell	1.18e-15	182
hematopoietic oligopotent progenitor cell	2.56e-14	165
hematopoietic multipotent progenitor cell	2.56e-14	165
myeloid cell	1.31e-11	112
common myeloid progenitor	1.31e-11	112
granulocyte	3.84e-11	8
neutrophil	7.18e-09	3
basophil	6.04e-08	3
blood cell	6.86e-08	11
mononuclear cell	1.14e-07	3
lymphocyte of B lineage	3.67e-07	24
pro-B cell	3.67e-07	24

Uber Anatomy

Ontology term	p-value	n
blood	6.52e-20	15
haemolymphatic fluid	6.52e-20	15
organism substance	6.52e-20	15

Disease

Ontology term	p-value	n
myeloid leukemia	6.51e-21	31
leukemia	1.51e-17	39
hematologic cancer	1.06e-15	51
immune system cancer	1.06e-15	51
chronic leukemia	1.51e-15	8

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
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139621521656808
CTCF#10664	3	5.36025637307503	0.006492509252767	0.028170800741576
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00172476054296309
ESRRA#2101	3	483.840314136126	8.75956906834516e-09	6.72676936712427e-07
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123561873227025
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.00076133035950625
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296442248233574
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00669417048936649
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00311125998049941
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0248124707906497
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00619570697358622
YY1#7528	3	4.91117074985386	0.00844145534180826	0.033154719809075
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0141090543214871
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00390713892753647
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0110244879740758

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.