Coexpression cluster:C1677

Full id: C1677_acute_CD34_CD133_chronic_Whole_leukemia_myelodysplastic

Phase1 CAGE Peaks

Hg19::chr12:54694979..54694993,+	p2@COPZ1
Hg19::chr21:21630930..21630941,-	p3@ENST00000436373
Hg19::chr21:21630952..21630969,-	p2@ENST00000436373
Hg19::chr21:21630981..21630991,-	p4@ENST00000436373
Hg19::chr21:21630994..21631007,-	p1@ENST00000436373

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:0006890	retrograde vesicle-mediated transport, Golgi to ER	0.00610502766984575
GO:0030126	COPI vesicle coat	0.00610502766984575
GO:0030663	COPI coated vesicle membrane	0.00610502766984575
GO:0006891	intra-Golgi vesicle-mediated transport	0.00610502766984575
GO:0030137	COPI-coated vesicle	0.00610502766984575
GO:0030120	vesicle coat	0.0130822021496695
GO:0030662	coated vesicle membrane	0.0130822021496695
GO:0005798	Golgi-associated vesicle	0.0148777985231535
GO:0048193	Golgi vesicle transport	0.0148777985231535
GO:0030659	cytoplasmic vesicle membrane	0.0148777985231535
GO:0044433	cytoplasmic vesicle part	0.0148777985231535
GO:0012506	vesicle membrane	0.0148777985231535
GO:0030117	membrane coat	0.0148777985231535
GO:0048475	coated membrane	0.0148777985231535
GO:0030135	coated vesicle	0.0175968444601436
GO:0045045	secretory pathway	0.0269339456022607
GO:0032940	secretion by cell	0.0310279053338043
GO:0006461	protein complex assembly	0.0310279053338043
GO:0016023	cytoplasmic membrane-bound vesicle	0.0310279053338043
GO:0031988	membrane-bound vesicle	0.0310279053338043
GO:0000139	Golgi membrane	0.0310279053338043
GO:0046903	secretion	0.0310279053338043
GO:0044431	Golgi apparatus part	0.0310279053338043
GO:0031410	cytoplasmic vesicle	0.0310279053338043
GO:0031982	vesicle	0.0310279053338043
GO:0006886	intracellular protein transport	0.0365334800605023
GO:0016192	vesicle-mediated transport	0.0403011630493086
GO:0005794	Golgi apparatus	0.0445692671275504
GO:0065003	macromolecular complex assembly	0.0468093399432393
GO:0022607	cellular component assembly	0.0486606617214176
GO:0015031	protein transport	0.0486923487162438
GO:0005783	endoplasmic reticulum	0.0486923487162438
GO:0046907	intracellular transport	0.0486923487162438
GO:0045184	establishment of protein localization	0.0486923487162438
GO:0008104	protein localization	0.0493019461405191
GO:0033036	macromolecule localization	0.049888461403827
GO:0012505	endomembrane system	0.049888461403827

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
myeloid cell	3.20e-36	112
common myeloid progenitor	3.20e-36	112
hematopoietic stem cell	2.93e-34	172
angioblastic mesenchymal cell	2.93e-34	172
hematopoietic cell	2.34e-31	182
hematopoietic oligopotent progenitor cell	7.14e-31	165
hematopoietic multipotent progenitor cell	7.14e-31	165
CD14-positive, CD16-negative classical monocyte	4.29e-10	42
classical monocyte	4.03e-09	45
myeloid lineage restricted progenitor cell	5.83e-09	70
leukocyte	1.01e-08	140
myeloid leukocyte	1.15e-08	76
hematopoietic lineage restricted progenitor cell	5.55e-08	124
nongranular leukocyte	7.43e-08	119
granulocyte monocyte progenitor cell	8.11e-08	71
monopoietic cell	1.56e-07	63
monocyte	1.56e-07	63
monoblast	1.56e-07	63
promonocyte	1.56e-07	63
mesenchymal cell	1.57e-07	358
macrophage dendritic cell progenitor	3.72e-07	65
connective tissue cell	4.26e-07	365

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	5.53e-19	102
blood island	5.53e-19	102
hemolymphoid system	2.59e-16	112
blood	1.99e-12	15
haemolymphatic fluid	1.99e-12	15
organism substance	1.99e-12	15
hemopoietic organ	8.48e-09	7
immune system	2.51e-07	115
bone marrow	3.25e-07	80

Disease

Ontology term	p-value	n
myeloid leukemia	9.13e-44	31
leukemia	1.00e-40	39
hematologic cancer	7.87e-33	51
immune system cancer	7.87e-33	51
chronic leukemia	6.69e-13	8
organ system cancer	4.60e-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
CCNT2#905	5	6.33620157696263	9.78880505817628e-05	0.001389228171587
ELF1#1997	4	3.40647836704603	0.0123506610529955	0.0447288539327899
EP300#2033	4	5.41915338097856	0.0020938692794389	0.0121133115645776
FOSL1#8061	4	31.7708637730984	1.96715033715934e-06	7.22388235100509e-05
GATA1#2623	4	10.8482465150404	0.000139095691709438	0.00181542301255211
GATA2#2624	4	10.1959453868432	0.000177544777760982	0.00215661770697595
REST#5978	5	9.65002871612802	1.19441074361324e-05	0.000301311747952229
TAL1#6886	4	23.8948933419522	6.10828383356726e-06	0.000181491623127719
USF1#7391	4	5.08919942176637	0.0026686777536004	0.0147148532763989

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.