Coexpression cluster:C1072

Full id: C1072_leukemia_acute_chronic_Prostate_Keratinocyte_mesothelioma_Gingival

Phase1 CAGE Peaks

Hg19::chr21:16126066..16126068,-	p5@ENST00000454128
Hg19::chr21:16126160..16126176,-	p1@ENST00000455253
Hg19::chr21:16135169..16135180,-	p@chr21:16135169..16135180 -
Hg19::chr4:127519543..127519548,-	p@chr4:127519543..127519548 -
Hg19::chr4:127656672..127656696,-	p@chr4:127656672..127656696 -
Hg19::chr8:124194961..124194972,+	p4@FAM83A
Hg19::chr8:124195004..124195015,+	p6@FAM83A
Hg19::chr8:124195016..124195044,+	p3@FAM83A

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	6.26e-20	254
endo-epithelial cell	3.38e-13	43
respiratory epithelial cell	1.71e-10	13
squamous epithelial cell	1.39e-07	62
endodermal cell	2.00e-07	59
general ecto-epithelial cell	3.47e-07	13

Uber Anatomy

Ontology term	p-value	n
respiratory tract	5.02e-14	53
respiratory system	5.30e-14	72
respiratory primordium	4.29e-12	38
endoderm of foregut	4.29e-12	38
endoderm-derived structure	5.45e-12	169
endoderm	5.45e-12	169
presumptive endoderm	5.45e-12	169
segment of respiratory tract	3.51e-11	46
larynx	1.81e-09	9
digestive system	3.56e-08	155
digestive tract	3.56e-08	155
primitive gut	3.56e-08	155
mixed endoderm/mesoderm-derived structure	3.36e-07	130
foregut	7.34e-07	98
upper respiratory tract	8.42e-07	19
epithelial bud	8.65e-07	37

Disease

Ontology term	p-value	n
carcinoma	6.64e-13	106
cancer	3.34e-11	235
disease of cellular proliferation	1.61e-10	239
cell type cancer	1.27e-08	143
squamous cell carcinoma	2.08e-08	14
chronic leukemia	2.86e-08	8
myeloid leukemia	3.94e-07	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
CCNT2#905	7	5.5441763798423	1.68072647241023e-05	0.000387149078191558
CEBPB#1051	5	4.98196726614051	0.00125052377879302	0.00840650443700851
EP300#2033	7	5.9271990104453	1.06380393527283e-05	0.000276168578662589
GATA1#2623	6	10.1702311078503	3.94864064622967e-06	0.000127675566703276
GATA2#2624	7	11.1518152668597	1.36229982264474e-07	7.74087220768196e-06
GATA3#2625	3	10.2136936339523	0.00241087012618913	0.0135911079082946
HDAC2#3066	5	8.38476264789141	0.00010628730938187	0.00148125704624141
HEY1#23462	6	3.03008328232928	0.00400172346648327	0.0191872186721167
HMGN3#9324	7	7.15622925793177	2.91658210831366e-06	0.000100067318925812
JUN#3725	6	9.38462189425225	6.3249395698254e-06	0.000186707282004804
JUNB#3726	5	19.1316454123882	1.91526005463182e-06	7.04571485895361e-05
JUND#3727	7	6.12033094913715	8.53888173818505e-06	0.000232116676172386
MXI1#4601	5	6.22598226797456	0.000439395490353943	0.00409439914499246
SMARCA4#6597	5	97.97868956743	5.77233124266155e-10	5.55116484946897e-08
SMARCB1#6598	3	6.84476841793403	0.00747369013463395	0.0308247659731078
SMARCC1#6599	3	16.3737597448618	0.000616633658052275	0.0051119703614321
SMARCC2#6601	3	35.3082654100866	6.43686411657099e-05	0.00104713341350554
SMC3#9126	4	7.52246642246642	0.00109848332803718	0.00767285314987128
STAT1#6772	5	12.9416171857495	1.29944539079553e-05	0.000317977453536302
STAT2#6773	6	48.9478283898305	3.51075876587426e-10	3.51543753354882e-08
TAL1#6886	7	26.1350395927602	3.64973064517802e-10	3.64063246276741e-08
TBP#6908	7	3.24342435120934	0.000635422362049205	0.00521310888217258
TFAP2A#7020	3	6.19448788989186	0.00986148386238029	0.0370489410807272

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.