Coexpression cluster:C431

Full id: C431_acute_leukemia_Mast_leiomyoblastoma_chronic_immature_CD34

Phase1 CAGE Peaks

Hg19::chr11:58611957..58611975,-	p2@GLYATL2
Hg19::chr12:116985635..116985640,-	p@chr12:116985635..116985640 -
Hg19::chr12:116985694..116985708,-	p@chr12:116985694..116985708 -
Hg19::chr18:45479920..45479950,-	p@chr18:45479920..45479950 -
Hg19::chr1:230410128..230410174,+	p@chr1:230410128..230410174 +
Hg19::chr1:230410177..230410188,+	p@chr1:230410177..230410188 +
Hg19::chr1:246345465..246345467,-	p@chr1:246345465..246345467 -
Hg19::chr1:246347752..246347761,-	p@chr1:246347752..246347761 -
Hg19::chr1:246347797..246347809,-	p@chr1:246347797..246347809 -
Hg19::chr1:246347830..246347835,-	p@chr1:246347830..246347835 -
Hg19::chr1:246347998..246348004,-	p@chr1:246347998..246348004 -
Hg19::chr1:246350179..246350186,-	p@chr1:246350179..246350186 -
Hg19::chr1:246350204..246350229,-	p@chr1:246350204..246350229 -
Hg19::chr1:246350240..246350281,-	p@chr1:246350240..246350281 -
Hg19::chr1:246350393..246350413,-	p@chr1:246350393..246350413 -
Hg19::chr1:3105351..3105356,-	p@chr1:3105351..3105356 -
Hg19::chr2:105277766..105277771,+	p@chr2:105277766..105277771 +
Hg19::chr4:54966328..54966335,+	p1@GSX2
Hg19::chr4:57522753..57522760,-	p18@HOPX
Hg19::chr4:96210568..96210572,+	p@chr4:96210568..96210572 +
Hg19::chr7:142411990..142411991,+	p@chr7:142411990..142411991 +
Hg19::chr7:1894156..1894165,-	p@chr7:1894156..1894165 -
Hg19::chr7:26591452..26591463,+	p1@ENST00000457000

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:0043416	regulation of skeletal muscle regeneration	0.00153655951960438
GO:0051153	regulation of striated muscle cell differentiation	0.00153655951960438
GO:0043415	positive regulation of skeletal muscle regeneration	0.00153655951960438
GO:0051149	positive regulation of muscle cell differentiation	0.00153655951960438
GO:0051155	positive regulation of striated muscle cell differentiation	0.00153655951960438
GO:0047961	glycine N-acyltransferase activity	0.00384105956936706
GO:0051147	regulation of muscle cell differentiation	0.00384105956936706
GO:0043403	skeletal muscle regeneration	0.00384105956936706
GO:0051146	striated muscle cell differentiation	0.012287049121659
GO:0042246	tissue regeneration	0.012287049121659
GO:0031099	regeneration	0.0125655603112768
GO:0043565	sequence-specific DNA binding	0.0140697158532347
GO:0048589	developmental growth	0.0218432594422842
GO:0042692	muscle cell differentiation	0.0240401833615157
GO:0045597	positive regulation of cell differentiation	0.0240401833615157
GO:0003700	transcription factor activity	0.0306706194259049
GO:0051094	positive regulation of developmental process	0.0306706194259049
GO:0014706	striated muscle development	0.0358946964492108
GO:0016410	N-acyltransferase activity	0.0358946964492108
GO:0007507	heart development	0.0360103844931409
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0455727226273163
GO:0042060	wound healing	0.0455727226273163
GO:0045595	regulation of cell differentiation	0.0475396809385267
GO:0007275	multicellular organismal development	0.0475396809385267

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	5.73e-20	172
angioblastic mesenchymal cell	5.73e-20	172
hematopoietic oligopotent progenitor cell	9.85e-20	165
hematopoietic multipotent progenitor cell	9.85e-20	165
hematopoietic cell	1.64e-17	182
myeloid cell	2.98e-14	112
common myeloid progenitor	2.98e-14	112
leukocyte	5.62e-10	140
hematopoietic lineage restricted progenitor cell	1.10e-08	124

Uber Anatomy

Ontology term	p-value	n
adult organism	3.35e-15	115

Disease

Ontology term	p-value	n
myeloid leukemia	4.90e-14	31
leukemia	2.95e-11	39
hematologic cancer	4.50e-07	51
immune system cancer	4.50e-07	51

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
GATA2#2624	6	3.32476480005756	0.00732224506839193	0.0302838568310544

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.