Coexpression cluster:C4723

Full id: C4723_osteosarcoma_acute_argyrophil_acantholytic_keratoacanthoma_chronic_NK

Phase1 CAGE Peaks

Hg19::chr8:121457339..121457350,-	p3@MRPL13
Hg19::chr8:121457352..121457377,-	p2@MRPL13
Hg19::chr8:121457380..121457397,-	p1@MRPL13

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>uberon_data<br>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	3.33e-14	253
animal cell	1.93e-12	679
eukaryotic cell	1.93e-12	679
endodermal cell	2.58e-08	58
native cell	2.19e-07	722
endo-epithelial cell	5.21e-07	42

Uber Anatomy

Ontology term	p-value	n
larynx	5.40e-07	9

Disease

Ontology term	p-value	n
disease of cellular proliferation	8.83e-38	239
cancer	1.59e-37	235
organ system cancer	6.74e-20	137
carcinoma	2.18e-19	106
cell type cancer	2.98e-17	143
hematologic cancer	1.65e-13	51
immune system cancer	1.65e-13	51
leukemia	2.00e-10	39
myeloid leukemia	4.82e-09	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
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139545743354688
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0281404039612273
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327838854596844
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438999696539196
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465091772008074
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00256463885939404
FAM48A#55578	3	1155.16875	6.36626921611971e-10	6.07757578301944e-08
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154849479255455
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.003895082147163
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00436036436219512
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00446460889668568
JUNB#3726	3	30.6106326598211	3.4847716247536e-05	0.000682825635492761
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157710772865884
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296154893576375
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270899317144858
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173719189475518
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00885878473887188
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278364294761033
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00240328487079616
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247939401925984
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00376583372813816
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00545914458951825
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00632102600475185
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00198151295495725
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191242899153122
WRNIP1#56897	3	109.819964349376	7.53682839543883e-07	3.33392130788325e-05
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331347823671633
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00390498147920542
ZZZ3#26009	3	239.413212435233	7.25894005043406e-08	4.39233163341415e-06

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.