Coexpression cluster:C3260

Full id: C3260_Alveolar_Renal_hepatoblastoma_Keratinocyte_Bronchial_Endothelial_granulocyte

Phase1 CAGE Peaks

Hg19::chr12:133287378..133287390,+	p3@PGAM5
Hg19::chr12:133287392..133287412,+	p2@PGAM5
Hg19::chr12:133287419..133287465,+	p1@PGAM5

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	9.66e-37	254
embryonic cell	4.96e-21	248
animal cell	2.16e-16	679
eukaryotic cell	2.16e-16	679
squamous epithelial cell	1.52e-10	62
endodermal cell	3.70e-10	59
epithelial cell of nephron	1.21e-07	16
native cell	1.23e-07	722
endo-epithelial cell	2.65e-07	43
kidney cell	7.28e-07	18
kidney epithelial cell	7.28e-07	18
meso-epithelial cell	8.11e-07	44
mesodermal cell	9.50e-07	119

Uber Anatomy

Ontology term	p-value	n
mesenchyme	4.48e-15	238
entire embryonic mesenchyme	4.48e-15	238
trunk region element	6.65e-11	107
endoderm-derived structure	2.60e-10	169
endoderm	2.60e-10	169
presumptive endoderm	2.60e-10	169
mixed endoderm/mesoderm-derived structure	2.87e-10	130
foregut	4.29e-10	98
segment of respiratory tract	2.13e-09	46
subdivision of digestive tract	3.86e-09	129
endodermal part of digestive tract	3.86e-09	129
digestive system	4.80e-09	155
digestive tract	4.80e-09	155
primitive gut	4.80e-09	155
trunk	5.23e-09	216
subdivision of trunk	2.19e-08	113
respiratory primordium	3.29e-08	38
endoderm of foregut	3.29e-08	38
primordium	8.46e-08	168
unilaminar epithelium	8.91e-08	138
respiratory tract	1.13e-07	53
nephron epithelium	1.21e-07	16
nephron	1.21e-07	16
uriniferous tubule	1.21e-07	16
metanephric mesenchyme	1.21e-07	16
nephrogenic mesenchyme	1.21e-07	16
urinary system structure	1.71e-07	44
cortex	1.99e-07	16
abdomen element	2.44e-07	55
abdominal segment element	2.44e-07	55
respiratory system	2.57e-07	72
immaterial anatomical entity	2.70e-07	126
renal system	2.81e-07	45
epithelial tube	5.21e-07	118
kidney	7.58e-07	27
kidney mesenchyme	7.58e-07	27
kidney rudiment	7.58e-07	27
kidney field	7.58e-07	27
excretory tube	8.11e-07	17
mesonephric epithelium	8.11e-07	17
mesonephric tubule	8.11e-07	17
nephric duct	8.11e-07	17
kidney epithelium	8.11e-07	17
renal duct	8.11e-07	17
mesonephric duct	8.11e-07	17
pronephric duct	8.11e-07	17

Disease

Ontology term	p-value	n
cancer	6.18e-30	235
disease of cellular proliferation	2.57e-29	239
carcinoma	1.45e-18	106
cell type cancer	1.25e-17	143
organ system cancer	2.35e-15	137
hematologic cancer	3.83e-12	51
immune system cancer	3.83e-12	51
leukemia	3.99e-09	39
myeloid leukemia	2.29e-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
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00138923696950432
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00163976494771935
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189382111447732
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.0065889427297282
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323980512806722
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435981364019064
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320821132342973
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319406128603496
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460484394794309
ELK4#2005	3	16.235681658468	0.000233604395574599	0.0025514964933503
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00760539557571375
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153706856824865
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00390092891791166
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108423350944387
HSF1#3297	3	164.290666666667	2.24910326529255e-07	1.18993969566306e-05
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185942577821983
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00718716640757593
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293440811992055
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268790209506589
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00308157253458206
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00469891859908355
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172451041945663
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.0088018386302526
PPARGC1A#10891	3	350.051136363636	2.31814761783079e-08	1.63474016920074e-06
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027571276321
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239147714119787
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245672946765384
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.00093836941651117
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0108863869953279
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00628078799199012
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00420688504037999
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328239009063298
ZBTB33#10009	3	31.6647250299812	3.14815888737575e-05	0.000633263802077496
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242218994478461

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.