Coexpression cluster:C3237

Full id: C3237_Alveolar_Keratocytes_Bronchial_Hepatic_Adipocyte_Mammary_Mesenchymal

Phase1 CAGE Peaks

Hg19::chr12:110011288..110011347,-	p1@MMAB
Hg19::chr12:110011571..110011644,+	p1@MVK
Hg19::chr16:88729473..88729561,-	p1@MVD

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
7.72917887211087e-07	0.000244628511302309	2	15	Terpenoid backbone biosynthesis (KEGG):00900
6.31961929821581e-05	0.0133343967192354	3	1138	Metabolic pathways (KEGG):01100
7.72917887211087e-07	0.000244628511302309	2	15	Cholesterol Biosynthesis (Wikipathways):WP1795
0.00030437946951327	0.048168051050475	2	289	Metabolism of lipids and lipoproteins (Reactome):REACT_22258

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:0006695	cholesterol biosynthetic process	7.09273028841617e-05
GO:0016126	sterol biosynthetic process	7.09273028841617e-05
GO:0008299	isoprenoid biosynthetic process	7.09273028841617e-05
GO:0006720	isoprenoid metabolic process	9.38540934350304e-05
GO:0008203	cholesterol metabolic process	0.000227604976015694
GO:0006694	steroid biosynthetic process	0.000236560699903554
GO:0016125	sterol metabolic process	0.000236560699903554
GO:0008202	steroid metabolic process	0.00116921618164445
GO:0009235	cobalamin metabolic process	0.00173694229634674
GO:0009236	cobalamin biosynthetic process	0.00173694229634674
GO:0008817	cob(I)yrinic acid a,c-diamide adenosyltransferase activity	0.00173694229634674
GO:0008610	lipid biosynthetic process	0.00173694229634674
GO:0004163	diphosphomevalonate decarboxylase activity	0.00183231096230755
GO:0004496	mevalonate kinase activity	0.00183231096230755
GO:0009058	biosynthetic process	0.00183231096230755
GO:0006066	alcohol metabolic process	0.00230514148065186
GO:0005524	ATP binding	0.00230514148065186
GO:0032559	adenyl ribonucleotide binding	0.00230514148065186
GO:0030554	adenyl nucleotide binding	0.00247528120164151
GO:0016740	transferase activity	0.00324351844010408
GO:0032553	ribonucleotide binding	0.00365700248173288
GO:0032555	purine ribonucleotide binding	0.00365700248173288
GO:0017076	purine nucleotide binding	0.00390457841089428
GO:0044255	cellular lipid metabolic process	0.00458755989077455
GO:0000166	nucleotide binding	0.00577037226642438
GO:0006779	porphyrin biosynthetic process	0.00616669659674457
GO:0006629	lipid metabolic process	0.00616669659674457
GO:0033014	tetrapyrrole biosynthetic process	0.0066630865719394
GO:0006778	porphyrin metabolic process	0.0066630865719394
GO:0033013	tetrapyrrole metabolic process	0.00727100775665974
GO:0042364	water-soluble vitamin biosynthetic process	0.00727100775665974
GO:0009110	vitamin biosynthetic process	0.00764686651571054
GO:0016310	phosphorylation	0.0106005592510717
GO:0016831	carboxy-lyase activity	0.0106005592510717
GO:0006767	water-soluble vitamin metabolic process	0.0117660113535449
GO:0016830	carbon-carbon lyase activity	0.0133441943385484
GO:0016301	kinase activity	0.0133441943385484
GO:0006793	phosphorus metabolic process	0.0133441943385484
GO:0006796	phosphate metabolic process	0.0133441943385484
GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	0.0133441943385484
GO:0006766	vitamin metabolic process	0.0134880903701458
GO:0042579	microbody	0.0149481784519316
GO:0005777	peroxisome	0.0149481784519316
GO:0016772	transferase activity, transferring phosphorus-containing groups	0.0159393085126707
GO:0046483	heterocycle metabolic process	0.0185525498427985
GO:0051188	cofactor biosynthetic process	0.0306326844695493
GO:0016829	lyase activity	0.0378202022513722
GO:0051186	cofactor metabolic process	0.0456033012209741
GO:0042802	identical protein binding	0.0473782813292496

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><br>

---

Cell Type

Ontology term	p-value	n
embryonic cell	5.46e-10	250
epithelial cell	1.06e-08	253
epithelial cell of nephron	5.83e-07	15

Uber Anatomy

Ontology term	p-value	n
cell layer	1.00e-22	309
epithelium	6.24e-22	306
multi-tissue structure	1.06e-19	342
anatomical cluster	8.94e-15	373
organism subdivision	1.68e-13	264
organ part	9.49e-12	218
structure with developmental contribution from neural crest	4.72e-10	132
anatomical conduit	1.55e-09	240
tube	2.65e-09	192
ecto-epithelium	3.80e-09	104
mesenchyme	6.62e-09	160
entire embryonic mesenchyme	6.62e-09	160
trunk mesenchyme	1.95e-08	122
unilaminar epithelium	2.21e-08	148
trunk	3.18e-08	199
epithelial vesicle	3.45e-08	78
primordium	3.96e-08	160
ectoderm-derived structure	6.48e-08	171
ectoderm	6.48e-08	171
presumptive ectoderm	6.48e-08	171
organ segment	1.78e-07	98
ectodermal placode	3.32e-07	31
subdivision of trunk	4.52e-07	112
multilaminar epithelium	5.47e-07	83
excretory tube	5.62e-07	16
kidney epithelium	5.62e-07	16
nephron epithelium	5.83e-07	15
renal tubule	5.83e-07	15
nephron tubule	5.83e-07	15
nephron	5.83e-07	15
uriniferous tubule	5.83e-07	15
nephrogenic mesenchyme	5.83e-07	15
organ system subdivision	6.00e-07	223
abdomen element	7.31e-07	54
abdominal segment element	7.31e-07	54

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	3	6.33620157696263	0.00393075003576489	0.0189329706675852
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00658802255058852
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323933006591273
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435944359999032
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320734027078587
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00760488555723362
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00895274820510727
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00242462547522189
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108404879137196
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127714897491271
IRF3#3661	3	46.9819522114896	9.63568551583244e-06	0.000253231343630605
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293417327333232
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000734543190113033
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199102557915548
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245073894297381
PBX3#5090	2	14.6096751244961	0.00605612247321789	0.0268120125044681
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.0088001583556175
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00483328039702603
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275678211295149
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245630178267014
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000938067738511969
SREBF1#6720	3	47.0058494404883	9.62099323994382e-06	0.000254188442445356
SREBF2#6721	3	436.943262411348	1.19027063774682e-08	8.89840194242237e-07
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00612115892803683
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00613502334069215
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328190133061502
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.0377997442412818

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.