Coexpression cluster:C2408

Full id: C2408_Alveolar_Renal_Mesenchymal_Mammary_chronic_Smooth_Trabecular

Phase1 CAGE Peaks

Hg19::chr17:40761660..40761748,+	p1@TUBG1
Hg19::chr17:76183121..76183140,-	p1@TK1
Hg19::chr17:79849438..79849493,-	p1@ALYREF
Hg19::chr2:242626195..242626243,-	p1@DTYMK

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

---

p.value	FDR	nGenes	nPathway	Name
3.63651983036618e-05	0.0115095852631089	2	100	Pyrimidine metabolism (KEGG):00240
2.15074464693702e-05	0.0115095852631089	2	77	Metabolism of nucleotides (Reactome):REACT_1698

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

---

GO ID	GO name	FDR corrected p-value
GO:0000212	meiotic spindle organization and biogenesis	0.00482736289747114
GO:0005827	polar microtubule	0.00482736289747114
GO:0005816	spindle pole body	0.00482736289747114
GO:0004797	thymidine kinase activity	0.0055165801495387
GO:0000242	pericentriolar material	0.0055165801495387
GO:0019136	deoxynucleoside kinase activity	0.0055165801495387
GO:0005881	cytoplasmic microtubule	0.0055165801495387
GO:0000930	gamma-tubulin complex	0.00603358190524557
GO:0019206	nucleoside kinase activity	0.00750801537250585
GO:0005876	spindle microtubule	0.00833620862192411
GO:0007051	spindle organization and biogenesis	0.00833620862192411
GO:0044450	microtubule organizing center part	0.00924972184269641
GO:0000794	condensed nuclear chromosome	0.010684755395396
GO:0000922	spindle pole	0.010684755395396
GO:0000793	condensed chromosome	0.0167227884531008
GO:0051321	meiotic cell cycle	0.0213999825167229
GO:0005819	spindle	0.0221246261206918
GO:0005200	structural constituent of cytoskeleton	0.0223487963212117
GO:0019205	nucleobase, nucleoside, nucleotide kinase activity	0.0223487963212117
GO:0051258	protein polymerization	0.0223487963212117
GO:0000228	nuclear chromosome	0.0223487963212117
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0223487963212117
GO:0005813	centrosome	0.0270249962186935
GO:0005815	microtubule organizing center	0.0295049287144001
GO:0032553	ribonucleotide binding	0.0336590258312562
GO:0032555	purine ribonucleotide binding	0.0336590258312562
GO:0017076	purine nucleotide binding	0.0348772877197093
GO:0000166	nucleotide binding	0.0454283255281328
GO:0003924	GTPase activity	0.0454283255281328
GO:0005874	microtubule	0.0477435948549856
GO:0007017	microtubule-based process	0.0488269739331223

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>

---

Cell Type

Ontology term	p-value	n
animal cell	2.27e-26	679
eukaryotic cell	2.27e-26	679
epithelial cell	3.18e-26	253
embryonic cell	1.20e-22	250
native cell	3.41e-14	722
mesodermal cell	6.91e-12	121
non-terminally differentiated cell	2.50e-09	106
somatic cell	7.09e-09	588
migratory neural crest cell	1.43e-08	41
epithelial cell of nephron	2.28e-08	15
meso-epithelial cell	4.13e-08	45
lining cell	9.28e-08	58
barrier cell	9.28e-08	58
squamous epithelial cell	9.94e-08	63
kidney cell	1.02e-07	17
kidney epithelial cell	1.02e-07	17
kidney cortical cell	1.71e-07	12
renal cortical epithelial cell	1.71e-07	12
ectodermal cell	1.88e-07	72
endothelial cell	2.14e-07	36
neurectodermal cell	3.13e-07	59

Uber Anatomy

Ontology term	p-value	n
unilaminar epithelium	1.06e-09	148
epithelial tube	8.68e-09	117
trunk	1.40e-08	199
organism subdivision	1.92e-08	264
nephron epithelium	2.28e-08	15
renal tubule	2.28e-08	15
nephron tubule	2.28e-08	15
nephron	2.28e-08	15
uriniferous tubule	2.28e-08	15
nephrogenic mesenchyme	2.28e-08	15
parenchyma	5.08e-08	15
cortex of kidney	1.71e-07	12
renal parenchyma	1.71e-07	12
simple squamous epithelium	1.90e-07	22
excretory tube	2.42e-07	16
kidney epithelium	2.42e-07	16
cortex	3.37e-07	15
epithelial vesicle	4.09e-07	78
segment of respiratory tract	4.87e-07	47

Disease

Ontology term	p-value	n
cancer	4.91e-27	235
disease of cellular proliferation	2.00e-26	239
cell type cancer	1.24e-13	143
organ system cancer	7.86e-13	137
carcinoma	7.18e-12	106
hematologic cancer	1.96e-11	51
immune system cancer	1.96e-11	51
leukemia	6.39e-09	39
myeloid leukemia	5.26e-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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00511969039219389
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106465924184312
E2F4#1874	4	12.6680603152844	3.88145892637771e-05	0.000726609945889876
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00996595711684882
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160821126247786
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00390185746241017
GATA1#2623	3	10.1702311078503	0.00151515816849827	0.00966242925809313
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185914912370521
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.00248061528419089
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0320044874385052
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466158731727191
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186332460648318
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00887193231803408
NANOG#79923	2	14.6223892405063	0.00669875771536376	0.0284858125828532
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.00618776976629042
NRF1#4899	3	9.15770958578318	0.00206195379173342	0.0119611415271521
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434856555108458
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00795791244569962
SP2#6668	2	13.0767652469223	0.00833003653661494	0.0328059386043036
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321974598103628
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140300523374332
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244000177590764
THAP1#55145	2	15.6845723014257	0.00584046967835792	0.026245549362679
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00507725183560176
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106776056716865
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00346332212167926

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

---

This analysis result is provided for C0 - C305 clusters.