Coexpression cluster:C747

Full id: C747_Mesenchymal_alveolar_Trabecular_Alveolar_carcinoid_Renal_chronic

Phase1 CAGE Peaks

Hg19::chr12:2986206..2986258,-	p2@FOXM1
Hg19::chr12:6960407..6960464,-	p1@CDCA3
Hg19::chr16:23690138..23690158,+	p3@PLK1
Hg19::chr16:23690160..23690176,+	p2@PLK1
Hg19::chr16:23690184..23690267,+	p1@PLK1
Hg19::chr17:76210318..76210366,+	p1@BIRC5
Hg19::chr17:76210367..76210385,+	p2@BIRC5
Hg19::chr17:76220151..76220166,+	p@chr17:76220151..76220166 +
Hg19::chr20:44441304..44441319,+	p2@UBE2C
Hg19::chr3:52188397..52188450,-	p1@POC1A
Hg19::chr9:91926103..91926119,+	p1@CKS2

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
2.59719623007301e-05	0.00822012606818106	3	315	Cell Cycle, Mitotic (Reactome):REACT_152
3.12165196450452e-07	0.000197600569353136	4	346	{CDC2,351} (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:0000279	M phase	6.90478736690457e-08
GO:0022403	cell cycle phase	8.83920725918899e-08
GO:0022402	cell cycle process	8.25432434157677e-07
GO:0007067	mitosis	1.31800666603262e-06
GO:0000087	M phase of mitotic cell cycle	1.31800666603262e-06
GO:0051301	cell division	1.31800666603262e-06
GO:0007049	cell cycle	1.54018451911913e-06
GO:0000278	mitotic cell cycle	3.10586241182863e-06
GO:0031536	positive regulation of exit from mitosis	3.50012641760176e-06
GO:0010458	exit from mitosis	3.72023214421962e-05
GO:0007096	regulation of exit from mitosis	3.72023214421962e-05
GO:0007051	spindle organization and biogenesis	7.47271452394409e-05
GO:0000074	regulation of progression through cell cycle	0.000329835940259241
GO:0051726	regulation of cell cycle	0.000329835940259241
GO:0007088	regulation of mitosis	0.000770058464162874
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.00167727124825463
GO:0031021	interphase microtubule organizing center	0.00209861408357055
GO:0048015	phosphoinositide-mediated signaling	0.00225905088143288
GO:0005813	centrosome	0.00225905088143288
GO:0005815	microtubule organizing center	0.00278551449326256
GO:0008054	cyclin catabolic process	0.00339750608701829
GO:0031503	protein complex localization	0.00486425299265298
GO:0045931	positive regulation of progression through mitotic cell cycle	0.00766592103107661
GO:0019932	second-messenger-mediated signaling	0.00766592103107661
GO:0050000	chromosome localization	0.00792518087701449
GO:0043027	caspase inhibitor activity	0.00792518087701449
GO:0051303	establishment of chromosome localization	0.00792518087701449
GO:0031577	spindle checkpoint	0.00844579235707201
GO:0005814	centriole	0.00844579235707201
GO:0007017	microtubule-based process	0.00844579235707201
GO:0030496	midbody	0.00891451629983814
GO:0005881	cytoplasmic microtubule	0.00891451629983814
GO:0043154	negative regulation of caspase activity	0.00972421121857813
GO:0016538	cyclin-dependent protein kinase regulator activity	0.0115338861723623
GO:0000086	G2/M transition of mitotic cell cycle	0.0173081643590862
GO:0005876	spindle microtubule	0.0178159169112155
GO:0015630	microtubule cytoskeleton	0.0181776697464586
GO:0043028	caspase regulator activity	0.0193994720605775
GO:0006512	ubiquitin cycle	0.0193994720605775
GO:0043161	proteasomal ubiquitin-dependent protein catabolic process	0.0195054927304112
GO:0044450	microtubule organizing center part	0.0195054927304112
GO:0051656	establishment of organelle localization	0.0195054927304112
GO:0045787	positive regulation of progression through cell cycle	0.0198787562119038
GO:0050790	regulation of catalytic activity	0.0207930693452798
GO:0043687	post-translational protein modification	0.0219524760693981
GO:0065009	regulation of a molecular function	0.0234910667351854
GO:0007346	regulation of progression through mitotic cell cycle	0.0234910667351854
GO:0007010	cytoskeleton organization and biogenesis	0.0234910667351854
GO:0051640	organelle localization	0.0234910667351854
GO:0007127	meiosis I	0.0234910667351854
GO:0000910	cytokinesis	0.023726604291929
GO:0008283	cell proliferation	0.026393228548436
GO:0004869	cysteine protease inhibitor activity	0.0275176371779979
GO:0006464	protein modification process	0.031106816416925
GO:0000079	regulation of cyclin-dependent protein kinase activity	0.031106816416925
GO:0008017	microtubule binding	0.031106816416925
GO:0050794	regulation of cellular process	0.0316698104268787
GO:0043412	biopolymer modification	0.0326941435235869
GO:0000075	cell cycle checkpoint	0.0337256129752269
GO:0044430	cytoskeletal part	0.0342664867856905
GO:0043281	regulation of caspase activity	0.0349395606960469
GO:0050789	regulation of biological process	0.0376828890740395
GO:0015631	tubulin binding	0.0376828890740395
GO:0051327	M phase of meiotic cell cycle	0.0376828890740395
GO:0007126	meiosis	0.0376828890740395
GO:0051321	meiotic cell cycle	0.0381820259946129
GO:0016567	protein ubiquitination	0.0386659523883696
GO:0000775	chromosome, pericentric region	0.0395291491514415
GO:0032446	protein modification by small protein conjugation	0.0395291491514415
GO:0005819	spindle	0.0395291491514415
GO:0016043	cellular component organization and biogenesis	0.0407942602760004
GO:0051329	interphase of mitotic cell cycle	0.0418585026518499
GO:0051325	interphase	0.0436975580360055
GO:0065007	biological regulation	0.0447251946760065
GO:0019887	protein kinase regulator activity	0.0489140954037165
GO:0046982	protein heterodimerization activity	0.0489140954037165

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
animal cell	3.90e-26	679
eukaryotic cell	3.90e-26	679
epithelial cell	4.56e-23	253
embryonic cell	4.27e-16	250
native cell	2.15e-14	722
migratory neural crest cell	4.78e-09	41
neurectodermal cell	2.76e-08	59
mesodermal cell	2.51e-07	121
squamous epithelial cell	2.64e-07	63
epithelial cell of nephron	3.93e-07	15
kidney cell	4.13e-07	17
kidney epithelial cell	4.13e-07	17
ectodermal cell	5.19e-07	72
lining cell	6.78e-07	58
barrier cell	6.78e-07	58
non-terminally differentiated cell	8.04e-07	106
neural cell	9.53e-07	25

Uber Anatomy

Ontology term	p-value	n
nephron epithelium	3.93e-07	15
renal tubule	3.93e-07	15
nephron tubule	3.93e-07	15
nephron	3.93e-07	15
uriniferous tubule	3.93e-07	15
nephrogenic mesenchyme	3.93e-07	15

Disease

Ontology term	p-value	n
cancer	8.91e-38	235
disease of cellular proliferation	7.43e-37	239
cell type cancer	1.44e-18	143
organ system cancer	4.43e-17	137
hematologic cancer	7.70e-15	51
immune system cancer	7.70e-15	51
carcinoma	1.26e-14	106
leukemia	6.23e-11	39
myeloid leukemia	1.21e-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
ATF3#467	3	6.12632032527511	0.0111162339916476	0.0408820466882767
BCLAF1#9774	3	5.90526753003323	0.0122864557732326	0.0445303010306995
CHD2#1106	7	6.58255998534709	1.82852745688608e-05	0.000416055727820751
E2F1#1869	10	4.46126292261757	1.10540139252827e-06	4.58123079501033e-05
E2F4#1874	10	11.5164184684404	9.56616236582045e-11	1.03854514690636e-08
E2F6#1876	9	4.1049455986615	1.83835844928222e-05	0.000418201520550175
EBF1#1879	7	5.66775162963482	4.91015352587259e-05	0.000852129485025934
ELF1#1997	8	3.09679851549639	0.000758011352761729	0.00595770226302545
ETS1#2113	7	6.19102967776512	2.74425924207753e-05	0.000583722384894777
FOSL2#2355	4	6.15643658347698	0.00286737656398896	0.015536494991774
HDAC2#3066	6	7.31761103815978	5.69712326977083e-05	0.000950482199954626
HEY1#23462	10	3.67282822100519	7.3527784911531e-06	0.000211140179498911
HNF4A#3172	6	12.6176129252475	2.49318000901648e-06	8.78492668561648e-05
HNF4G#3174	3	7.84184250721276	0.00562367765123593	0.0254211941749234
IRF1#3659	5	3.47143806980177	0.00894716207586585	0.0339324809369364
IRF3#3661	3	12.8132596940426	0.00139865858349401	0.00909951434632351
MAX#4149	9	5.27936359827855	2.09889244785612e-06	7.65652212230686e-05
MXI1#4601	8	7.2447793663704	1.28440155682788e-06	5.13166083372406e-05
MYC#4609	9	4.27277607677133	1.30375226575527e-05	0.000318732637835241
NFYA#4800	6	10.0503167453621	9.29686132166058e-06	0.000247566267101711
NFYB#4801	7	10.6653229795232	7.15961572771292e-07	3.20369797337879e-05
NRF1#4899	4	4.44010161734942	0.00927703375725097	0.0350460872666402
PBX3#5090	5	9.96114213033824	7.24136591048148e-05	0.00113863446902255
POLR2A#5430	10	1.95223016050734	0.0030407318184143	0.0161342778226577
POU2F2#5452	8	6.6226356783582	2.56270583551105e-06	9.01166446986324e-05
SIN3A#25942	10	4.9171679334683	4.26535327044908e-07	2.04907649591735e-05
SP1#6667	10	5.18034670740082	2.55812246304286e-07	1.32919279561061e-05
TAF1#6872	10	3.03913298704117	4.59104772732301e-05	0.00080707697962277
TAF7#6879	6	6.23621967541304	0.000140196002821237	0.00182886964010082
TBP#6908	10	3.36979153372399	1.6942293653553e-05	0.000390001368058942
THAP1#55145	3	8.55522125532309	0.004407746242643	0.0208828075592176
USF1#7391	9	5.20486304498833	2.37429471822852e-06	8.41143032825877e-05
USF2#7392	6	7.08665311912887	6.8302134157013e-05	0.00109040149636568
ZNF143#7702	6	7.3641144830334	5.49636173278436e-05	0.000930514707424649

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.