Coexpression cluster:C3724

Full id: C3724_retinoblastoma_Reticulocytes_acute_adrenal_NK_myxofibrosarcoma_Mesenchymal

Phase1 CAGE Peaks

Hg19::chr18:47901365..47901404,+	p3@SKA1
Hg19::chr18:47901408..47901430,+	p2@SKA1
Hg19::chr18:47901433..47901491,+	p1@SKA1

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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No GOStat results

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
animal cell	2.83e-19	679
eukaryotic cell	2.83e-19	679
epithelial cell	2.46e-15	254
native cell	8.18e-11	722
embryonic cell	1.44e-10	248
non-terminally differentiated cell	2.09e-09	180

Disease

Ontology term	p-value	n
cancer	1.37e-40	235
disease of cellular proliferation	2.05e-40	239
organ system cancer	6.63e-23	137
hematologic cancer	6.79e-21	51
immune system cancer	6.79e-21	51
cell type cancer	1.62e-16	143
leukemia	1.71e-16	39
carcinoma	2.82e-12	106
myeloid leukemia	4.03e-12	31

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	22.4631745260087	8.81932387510763e-05	0.00129601993273162
BATF#10538	3	24.3578017923036	6.91705216281876e-05	0.00109905676378005
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189925331013301
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115191978248663
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436834193698639
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322007970644086
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462025791477366
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.000676038887315155
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.0024298279465973
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154035033731068
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128000800346698
IRF4#3662	3	21.9145126867441	9.49854535978121e-05	0.00136528843769638
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156690410484313
MAFK#7975	3	27.1007331378299	5.02195559325033e-05	0.000857426876252201
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.0072003934195727
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269489586864544
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000605040921381342
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470972159775129
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172840570446989
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00136547636452882
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00881867673501651
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276544615328301
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246337768148102
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00542607685029464
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00629125521348245
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000646481120697898
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329195009313735

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.