Coexpression cluster:C1755

Full id: C1755_Reticulocytes_hepatoblastoma_acute_bone_epidermoid_Myoblast_merkel

Phase1 CAGE Peaks

Hg19::chr15:91537708..91537721,-	p3@PRC1
Hg19::chr15:91537723..91537804,-	p1@PRC1
Hg19::chr15:91537809..91537824,-	p2@PRC1
Hg19::chr20:30327143..30327154,+	p2@TPX2
Hg19::chr2:234763105..234763145,-	p2@HJURP

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:0005819	spindle	0.000260211140050149
GO:0000278	mitotic cell cycle	0.00147177864353539
GO:0051231	spindle elongation	0.00147177864353539
GO:0000022	mitotic spindle elongation	0.00147177864353539
GO:0015630	microtubule cytoskeleton	0.00231158995183011
GO:0022402	cell cycle process	0.00281613787933062
GO:0007049	cell cycle	0.00404685512039531
GO:0007052	mitotic spindle organization and biogenesis	0.00404685512039531
GO:0044430	cytoskeletal part	0.00405237908315862
GO:0005876	spindle microtubule	0.00508305403775861
GO:0007051	spindle organization and biogenesis	0.00508305403775861
GO:0005856	cytoskeleton	0.00701625588815873
GO:0000922	spindle pole	0.00701625588815873
GO:0000910	cytokinesis	0.00714527213891618
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0199867284173438
GO:0043232	intracellular non-membrane-bound organelle	0.0217224388160334
GO:0043228	non-membrane-bound organelle	0.0217224388160334
GO:0007067	mitosis	0.0335824835975614
GO:0000087	M phase of mitotic cell cycle	0.0335824835975614
GO:0051301	cell division	0.0335824835975614
GO:0044446	intracellular organelle part	0.0335824835975614
GO:0044422	organelle part	0.0335824835975614
GO:0005874	microtubule	0.0369179559006534
GO:0000279	M phase	0.0369179559006534
GO:0007017	microtubule-based process	0.0369179559006534
GO:0022403	cell cycle phase	0.0415502081008049

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
epithelial cell	2.50e-18	253
animal cell	1.04e-15	679
eukaryotic cell	1.04e-15	679
embryonic cell	3.61e-08	250
native cell	5.89e-08	722
squamous epithelial cell	8.95e-08	63

Disease

Ontology term	p-value	n
cancer	7.45e-57	235
disease of cellular proliferation	2.80e-55	239
cell type cancer	3.13e-34	143
carcinoma	3.97e-25	106
organ system cancer	1.18e-22	137
hematologic cancer	1.40e-11	51
immune system cancer	1.40e-11	51
leukemia	4.97e-10	39
disease of anatomical entity	4.42e-09	39
myeloid leukemia	1.21e-07	31
sarcoma	1.97e-07	20

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
ATF3#467	3	13.4779047156053	0.000824108855140936	0.00627325836166649
BRCA1#672	3	12.1105383859343	0.00112717647012594	0.00772752943176333
CCNT2#905	4	5.06896126157011	0.00270999809128077	0.0148947211164758
CEBPB#1051	4	6.37691810065985	0.00111394417667732	0.0076533922681404
CHD2#1106	4	8.27521826729349	0.000402837356710173	0.00387831219556174
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00352662894807503
E2F4#1874	5	12.6680603152844	3.06319883889696e-06	0.000103432726652299
E2F6#1876	5	5.01715573169739	0.000314497859929779	0.00322745818936879
EBF1#1879	3	5.3438801079414	0.0118761556386811	0.0432322697367801
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.00573055913630909
FOS#2353	5	8.9979553088944	1.69470025615156e-05	0.000389080677186663
FOSL2#2355	4	13.5441604836494	5.7953819349229e-05	0.00096456397434488
GABPB1#2553	5	7.06768383618217	5.6685482528729e-05	0.00094813823027193
GATA1#2623	4	10.8482465150404	0.000139095691709438	0.00181564991206624
GTF2F1#2962	4	10.1917287014061	0.00017783388942764	0.00215862314945761
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.0067416152568213
HMGN3#9324	5	8.17854772335059	2.73180911341838e-05	0.000581785097871741
IRF1#3659	5	7.6371637535639	3.84754333311872e-05	0.000724024465166822
IRF3#3661	2	18.7927808845958	0.00433962977712151	0.0205881073086578
JUN#3725	3	7.5076975154018	0.00451120655290603	0.02133716322535
JUND#3727	4	5.59573115349682	0.00184959330175546	0.0109333073829544
MAX#4149	5	6.45255550900712	8.93743970843928e-05	0.00130675803683283
MXI1#4601	4	7.96925730300744	0.000466854638007017	0.00429470902306129
MYC#4609	5	5.2222818716094	0.000257394484885061	0.00276478685661945
NANOG#79923	3	17.5468670886076	0.000379420009068183	0.00376031944648623
NFKB1#4790	5	5.48806342419384	0.000200816284746232	0.00239009139175062
NFYA#4800	5	18.4255806998305	4.70418681889082e-07	2.22307948949384e-05
NFYB#4801	5	16.7597932535365	7.55590255814554e-07	3.32405605421299e-05
NRF1#4899	4	9.76822355816873	0.000210129774810679	0.00244493577890514
PBX3#5090	3	13.1487076120465	0.000886046932280843	0.00660324358216633
POU2F2#5452	4	7.28489924619402	0.000663122328874386	0.0054254471527859
REST#5978	4	7.72002297290242	0.000528636377365057	0.00457265650286808
RFX5#5993	4	9.63832866175608	0.00022148012581572	0.00249607886695457
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00248007904448223
SMARCB1#6598	4	14.6021726249259	4.30486693344344e-05	0.000768277507966335
SP1#6667	5	5.6983813781409	0.00016639184371255	0.00204228437718827
SP2#6668	4	20.9228243950757	1.03516506540382e-05	0.00026940344945355
SRF#6722	3	8.27830695730069	0.00340484607377615	0.0173598281145825
STAT1#6772	4	16.5652699977594	2.61308619905866e-05	0.000563510447126754
STAT2#6773	3	39.1582627118644	3.51160213487062e-05	0.000680423405127557
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135307925602123
TAF7#6879	4	9.14645552393913	0.000272066287241299	0.00290267963767433
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00918658835134195
TCF7L2#6934	3	6.46210593788241	0.00693010875568919	0.0293215697753777
TFAP2A#7020	3	9.91118062382697	0.00202154697751128	0.0117456659128957
TFAP2C#7022	3	6.48553716591613	0.00685895151794	0.0290581712470443
THAP1#55145	3	18.8214867617108	0.000308522194815001	0.0031748693964217
USF1#7391	4	5.08919942176637	0.0026686777536004	0.0147187386939307
ZBTB33#10009	3	18.9988350179887	0.000300098236334237	0.0030985625016818
ZNF263#10127	4	6.57747330960854	0.000987510323790016	0.00709169983540573

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.