Coexpression cluster:C1724

Full id: C1724_Mast_medulloblastoma_small_non_cerebellum_hepatoblastoma_merkel

Phase1 CAGE Peaks

Hg19::chr14:39644395..39644417,+	p2@PNN
Hg19::chr14:39644425..39644470,+	p1@PNN
Hg19::chr14:73525265..73525286,+	p2@RBM25
Hg19::chr17:48796951..48796996,+	p1@LUC7L3
Hg19::chr1:71546690..71546730,-	p1@ZRANB2

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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p.value	FDR	nGenes	nPathway	Name
4.41326987260908e-06	0.00279359982936155	2	25	{BCLAF1,25} (Static Module):NA

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:0008380	RNA splicing	2.07888694300519e-05
GO:0006397	mRNA processing	2.07888694300519e-05
GO:0016071	mRNA metabolic process	2.73085205460659e-05
GO:0006396	RNA processing	7.43177090078823e-05
GO:0016070	RNA metabolic process	0.029620301332372
GO:0003723	RNA binding	0.0328230854762404
GO:0003729	mRNA binding	0.0347091582755624
GO:0010467	gene expression	0.041196620178578
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.041196620178578
GO:0000375	RNA splicing, via transesterification reactions	0.041196620178578
GO:0000398	nuclear mRNA splicing, via spliceosome	0.041196620178578
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.041196620178578
GO:0003676	nucleic acid binding	0.041196620178578
GO:0016607	nuclear speck	0.0423044908580203

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
hematopoietic stem cell	4.40e-25	172
angioblastic mesenchymal cell	4.40e-25	172
hematopoietic oligopotent progenitor cell	1.23e-22	165
hematopoietic multipotent progenitor cell	1.23e-22	165
hematopoietic cell	6.94e-22	182
leukocyte	7.91e-15	140
hematopoietic lineage restricted progenitor cell	3.80e-13	124
lymphocyte	6.42e-13	53
common lymphoid progenitor	6.42e-13	53
lymphoid lineage restricted progenitor cell	1.57e-12	52
nongranular leukocyte	2.16e-12	119
myeloid cell	1.24e-10	112
common myeloid progenitor	1.24e-10	112
lymphocyte of B lineage	3.19e-07	24
pro-B cell	3.19e-07	24

Disease

Ontology term	p-value	n
cancer	1.60e-23	235
disease of cellular proliferation	4.28e-22	239
organ system cancer	1.34e-14	137
hematologic cancer	4.55e-14	51
immune system cancer	4.55e-14	51
leukemia	3.56e-13	39
cell type cancer	4.41e-12	143
myeloid leukemia	2.77e-11	31
carcinoma	5.24e-10	106

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	12.9915885660731	0.000917803240254255	0.00667556602889576
CHD2#1106	3	6.20641370047011	0.00777455012627559	0.0319508220453349
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00352527346467037
E2F4#1874	3	7.60083618917066	0.00435414736037571	0.0206485399886609
E2F6#1876	4	4.01372458535791	0.00663211823393388	0.0282911324688078
EGR1#1958	5	4.98817909481014	0.000323739800059071	0.00330670523015837
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.0057287987310756
ELK4#2005	4	12.9885453267744	6.83810524411663e-05	0.00109082766700824
ETS1#2113	4	7.78300873776187	0.000512103594768887	0.00443994581886666
FOS#2353	4	7.19836424711553	0.000694785845338251	0.00559595426091475
FOSL2#2355	3	10.158120362737	0.00188199070341543	0.011090290982001
FOXA1#3169	3	6.64885184963127	0.00638902516656872	0.0278061174051452
GABPB1#2553	5	7.06768383618217	5.6685482528729e-05	0.000947986406696225
GATA1#2623	3	8.13618488628026	0.00357925188368153	0.01813044366475
GATA3#2625	2	10.8946065428824	0.012515829121883	0.0452814867378094
GTF2B#2959	3	19.1662979605945	0.000292422965447241	0.00310211905417414
GTF2F1#2962	5	12.7396608767577	2.97806917252935e-06	0.000101048267157177
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00673974180531183
HSF1#3297	2	65.7162666666667	0.000365682980578607	0.00364945674234584
IRF3#3661	2	18.7927808845958	0.00433962977712151	0.0205862370227468
JUN#3725	3	7.5076975154018	0.00451120655290603	0.021335230773851
MAX#4149	5	6.45255550900712	8.93743970843928e-05	0.00130639225431727
MXI1#4601	3	5.97694297725558	0.00865300488936688	0.0329484897783501
MYC#4609	5	5.2222818716094	0.000257394484885061	0.00276364990304419
NFKB1#4790	5	5.48806342419384	0.000200816284746232	0.00238927454575207
NFYA#4800	3	11.0553484198983	0.00147089290764443	0.00941117345962606
POU2F2#5452	4	7.28489924619402	0.000663122328874386	0.00542417237666917
RFX5#5993	4	9.63832866175608	0.00022148012581572	0.00249580954467716
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00247898866020239
SIX5#147912	5	17.086715355459	6.86007756253503e-07	3.09887387782697e-05
SP1#6667	5	5.6983813781409	0.00016639184371255	0.00204180446075608
SP2#6668	4	20.9228243950757	1.03516506540382e-05	0.000269336333497034
SREBF1#6720	3	28.203509664293	9.31681575395428e-05	0.00135464140404738
SRF#6722	4	11.0377426097342	0.000129925581484675	0.00171027196933173
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135271332156212
TAF7#6879	5	11.4330694049239	5.11611886715123e-06	0.000157338733323442
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00918319617150885
TCF12#6938	3	6.38067894131185	0.00718516865325884	0.0298279604490699
TCF7L2#6934	3	6.46210593788241	0.00693010875568919	0.0293180065757452
USF1#7391	4	5.08919942176637	0.0026686777536004	0.0147164071972265
YY1#7528	5	4.91117074985386	0.0003499314082136	0.00352629161929951
ZBTB33#10009	3	18.9988350179887	0.000300098236334237	0.00309825619854799
ZNF143#7702	3	8.10052593133674	0.00362487051209098	0.018328629940076

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.