Coexpression cluster:C370

Full id: C370_acute_chronic_leukemia_CD34_testicular_Mast_H9

Phase1 CAGE Peaks

Hg19::chr11:75063275..75063314,-	p6@ARRB1
Hg19::chr12:42836335..42836348,+	p6@PPHLN1
Hg19::chr12:62654594..62654600,-	p@chr12:62654594..62654600 -
Hg19::chr13:109248512..109248524,+	p5@MYO16
Hg19::chr13:75900665..75900679,-	p17@TBC1D4
Hg19::chr13:76056524..76056549,-	p7@TBC1D4
Hg19::chr13:95713920..95713924,-	p@chr13:95713920..95713924 -
Hg19::chr14:93460574..93460583,-	p@chr14:93460574..93460583 -
Hg19::chr16:20837868..20837883,+	p@chr16:20837868..20837883 +
Hg19::chr16:81685852..81685866,+	p@chr16:81685852..81685866 +
Hg19::chr16:89043267..89043276,-	p13@CBFA2T3
Hg19::chr17:80159702..80159743,-	p1@CU691842
Hg19::chr18:9191997..9192008,+	p@chr18:9191997..9192008 +
Hg19::chr1:110922677..110922681,-	p@chr1:110922677..110922681 -
Hg19::chr1:35309235..35309266,-	p@chr1:35309235..35309266 -
Hg19::chr2:190448678..190448702,-	p5@SLC40A1
Hg19::chr3:77248792..77248797,+	p@chr3:77248792..77248797 +
Hg19::chr4:83763487..83763502,-	p16@SEC31A
Hg19::chr6:136687008..136687031,-	p@chr6:136687008..136687031 -
Hg19::chr8:129057463..129057484,+	p@chr8:129057463..129057484 +
Hg19::chr8:129057486..129057490,+	p@chr8:129057486..129057490 +
Hg19::chr8:129057497..129057520,+	p@chr8:129057497..129057520 +
Hg19::chr8:129057554..129057590,+	p@chr8:129057554..129057590 +
Hg19::chr8:129057598..129057610,+	p@chr8:129057598..129057610 +
Hg19::chr8:129057633..129057641,+	p@chr8:129057633..129057641 +
Hg19::chr8:130393776..130393785,-	p@chr8:130393776..130393785 -
Hg19::chr9:14214432..14214451,-	p@chr9:14214432..14214451 -
Hg19::chr9:21975236..21975249,-	p15@CDKN2A
Hg19::chrX:109564494..109564506,-	p@chrX:109564494..109564506 -
Hg19::chrX:49005043..49005049,-	p@chrX:49005043..49005049 -

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:0005737	cytoplasm	0.0188488682984112
GO:0051329	interphase of mitotic cell cycle	0.0188488682984112
GO:0051325	interphase	0.0188488682984112
GO:0032502	developmental process	0.0227530865416551
GO:0010149	senescence	0.0227530865416551
GO:0030135	coated vesicle	0.0227530865416551
GO:0008283	cell proliferation	0.0227530865416551
GO:0048856	anatomical structure development	0.0256749525653224
GO:0032088	inhibition of NF-kappaB transcription factor	0.0265025818339062
GO:0008285	negative regulation of cell proliferation	0.0265025818339062
GO:0045786	negative regulation of progression through cell cycle	0.0265025818339062
GO:0005622	intracellular	0.0265025818339062
GO:0005381	iron ion transmembrane transporter activity	0.0265025818339062
GO:0009653	anatomical structure morphogenesis	0.0265025818339062
GO:0001953	negative regulation of cell-matrix adhesion	0.0265025818339062
GO:0045749	negative regulation of S phase of mitotic cell cycle	0.0265025818339062
GO:0022037	metencephalon development	0.0265025818339062
GO:0021549	cerebellum development	0.0265025818339062
GO:0045736	negative regulation of cyclin-dependent protein kinase activity	0.0265025818339062
GO:0022408	negative regulation of cell-cell adhesion	0.0265025818339062
GO:0000278	mitotic cell cycle	0.0265025818339062
GO:0007090	regulation of S phase of mitotic cell cycle	0.0265025818339062
GO:0016023	cytoplasmic membrane-bound vesicle	0.0265025818339062
GO:0042326	negative regulation of phosphorylation	0.0265025818339062
GO:0031988	membrane-bound vesicle	0.0265025818339062
GO:0000074	regulation of progression through cell cycle	0.0265025818339062
GO:0051726	regulation of cell cycle	0.0265025818339062
GO:0012507	ER to Golgi transport vesicle membrane	0.0265025818339062
GO:0030127	COPII vesicle coat	0.0265025818339062
GO:0045930	negative regulation of progression through mitotic cell cycle	0.0265025818339062
GO:0022407	regulation of cell-cell adhesion	0.0265025818339062
GO:0001952	regulation of cell-matrix adhesion	0.0265025818339062
GO:0045936	negative regulation of phosphate metabolic process	0.0265025818339062
GO:0000139	Golgi membrane	0.0265025818339062
GO:0022403	cell cycle phase	0.0265025818339062
GO:0030134	ER to Golgi transport vesicle	0.0272896184018127
GO:0033261	regulation of progression through S phase	0.0272896184018127
GO:0004861	cyclin-dependent protein kinase inhibitor activity	0.0272896184018127
GO:0004857	enzyme inhibitor activity	0.0276506314564587
GO:0043433	negative regulation of transcription factor activity	0.0276506314564587
GO:0000084	S phase of mitotic cell cycle	0.0280542987215237
GO:0044431	Golgi apparatus part	0.0280542987215237
GO:0031410	cytoplasmic vesicle	0.0280542987215237
GO:0051059	NF-kappaB binding	0.0280542987215237
GO:0031982	vesicle	0.0280542987215237
GO:0051320	S phase	0.03125657187156
GO:0042127	regulation of cell proliferation	0.03125657187156
GO:0043231	intracellular membrane-bound organelle	0.03125657187156
GO:0043227	membrane-bound organelle	0.03125657187156
GO:0030902	hindbrain development	0.0317753063555054
GO:0007162	negative regulation of cell adhesion	0.0345277058246334
GO:0007568	aging	0.0345277058246334
GO:0044424	intracellular part	0.0347018085760933
GO:0048869	cellular developmental process	0.0369192915608153
GO:0030154	cell differentiation	0.0369192915608153
GO:0046915	transition metal ion transmembrane transporter activity	0.0369787330250068
GO:0030658	transport vesicle membrane	0.0374306449734218
GO:0030660	Golgi-associated vesicle membrane	0.0374306449734218
GO:0007346	regulation of progression through mitotic cell cycle	0.0374306449734218
GO:0000082	G1/S transition of mitotic cell cycle	0.039099171745683
GO:0050790	regulation of catalytic activity	0.0397954447486252
GO:0005834	heterotrimeric G-protein complex	0.0409510098350862
GO:0022402	cell cycle process	0.0409510098350862
GO:0031424	keratinization	0.0409510098350862
GO:0051015	actin filament binding	0.0411677125813885
GO:0006888	ER to Golgi vesicle-mediated transport	0.0411677125813885
GO:0004860	protein kinase inhibitor activity	0.0411677125813885
GO:0019210	kinase inhibitor activity	0.0423330587829715
GO:0065007	biological regulation	0.0423330587829715
GO:0065009	regulation of a molecular function	0.0423330587829715
GO:0005794	Golgi apparatus	0.0446511865436426
GO:0009913	epidermal cell differentiation	0.045099006639002
GO:0000079	regulation of cyclin-dependent protein kinase activity	0.045099006639002
GO:0019897	extrinsic to plasma membrane	0.045099006639002
GO:0030120	vesicle coat	0.045099006639002
GO:0030662	coated vesicle membrane	0.045099006639002
GO:0051090	regulation of transcription factor activity	0.045099006639002
GO:0030308	negative regulation of cell growth	0.045099006639002
GO:0015082	di-, tri-valent inorganic cation transmembrane transporter activity	0.045099006639002
GO:0045792	negative regulation of cell size	0.045099006639002
GO:0048730	epidermis morphogenesis	0.045099006639002
GO:0006879	cellular iron ion homeostasis	0.045099006639002
GO:0000075	cell cycle checkpoint	0.045099006639002
GO:0055072	iron ion homeostasis	0.045099006639002
GO:0006826	iron ion transport	0.045099006639002
GO:0006469	negative regulation of protein kinase activity	0.045099006639002
GO:0033673	negative regulation of kinase activity	0.045099006639002
GO:0051348	negative regulation of transferase activity	0.0461414558060958
GO:0045926	negative regulation of growth	0.0467159056500954
GO:0030133	transport vesicle	0.0467159056500954
GO:0044444	cytoplasmic part	0.0467159056500954
GO:0042325	regulation of phosphorylation	0.0467159056500954
GO:0048471	perinuclear region of cytoplasm	0.0467159056500954
GO:0043229	intracellular organelle	0.0467159056500954
GO:0043226	organelle	0.0467159056500954
GO:0030155	regulation of cell adhesion	0.0468357472001047
GO:0007049	cell cycle	0.0468357472001047
GO:0051174	regulation of phosphorus metabolic process	0.0474377394209792
GO:0019220	regulation of phosphate metabolic process	0.0474377394209792
GO:0005798	Golgi-associated vesicle	0.0474377394209792
GO:0048729	tissue morphogenesis	0.048995016963446
GO:0008021	synaptic vesicle	0.0498520403523731

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
myeloid cell	5.11e-16	108
common myeloid progenitor	5.11e-16	108
hematopoietic oligopotent progenitor cell	1.96e-10	161
hematopoietic multipotent progenitor cell	1.96e-10	161
hematopoietic stem cell	5.90e-10	168
angioblastic mesenchymal cell	5.90e-10	168
hematopoietic cell	2.14e-09	177
erythroid lineage cell	7.49e-09	2
erythroblast	7.49e-09	2
megakaryocyte-erythroid progenitor cell	7.49e-09	2
erythroid progenitor cell	7.49e-09	2
reticulocyte	7.49e-09	2
proerythroblast	7.49e-09	2
basophilic erythroblast	7.49e-09	2
polychromatophilic erythroblast	7.49e-09	2
orthochromatic erythroblast	7.49e-09	2

Disease

Ontology term	p-value	n
chronic leukemia	2.97e-68	8
myeloid leukemia	2.06e-48	31
leukemia	2.40e-38	39
hematologic cancer	3.74e-29	51
immune system cancer	3.74e-29	51
chronic myeloid leukemia	5.53e-17	1
organ system cancer	3.28e-10	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	12	2.53448063078505	0.00124915426378279	0.00839837917826773
ELF1#1997	13	1.84517578214993	0.0128780585209008	0.0463256140896345
EP300#2033	11	2.48377863294851	0.00258406350004249	0.0142935759695428
GATA1#2623	18	8.13618488628026	1.49657903612219e-13	2.29854732284655e-11
GATA2#2624	15	6.372465866777	1.29303195975262e-09	1.17021633314215e-07
HDAC2#3066	11	4.91906075342963	5.6421765724406e-06	0.000170110646376768
HMGN3#9324	9	2.45356431700518	0.00782990532145298	0.0321580668475845
JUN#3725	8	3.33675445128969	0.00195883589786799	0.0115041816531201
JUNB#3726	7	7.14248095395827	4.15293116006154e-05	0.000752869254340683
REST#5978	10	3.21667623870934	0.000603459530245917	0.00503955780260301
STAT1#6772	6	4.14131749943984	0.00275947092062308	0.01512841908026
STAT2#6773	8	17.4036723163842	1.30418599998989e-08	9.62599870338831e-07
TAL1#6886	16	15.9299288946348	2.2751293851679e-16	4.47480673931357e-14

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.