Coexpression cluster:C2530

Full id: C2530_Retinal_Mallassezderived_Bronchial_Keratinocyte_small_Hep2_Tracheal

Phase1 CAGE Peaks

Hg19::chr1:155278605..155278621,+	p2@FDPS
Hg19::chr1:155278625..155278745,+	p1@FDPS
Hg19::chr8:11660227..11660306,+	p1@FDFT1
Hg19::chrX:151999599..151999615,+	p1@NSDHL

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
1.25863435561633e-06	0.000265571849035045	2	19	Steroid biosynthesis (KEGG):00100
6.31961929821581e-05	0.0100007975394265	3	1138	Metabolic pathways (KEGG):01100
1.17374162251993e-10	7.42978447055117e-08	3	15	Cholesterol Biosynthesis (Wikipathways):WP1795
1.02702753121762e-06	0.000265571849035045	3	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

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GO ID	GO name	FDR corrected p-value
GO:0006695	cholesterol biosynthetic process	2.35846206673679e-08
GO:0016126	sterol biosynthetic process	2.7973410948078e-08
GO:0008203	cholesterol metabolic process	2.60032406071113e-07
GO:0006694	steroid biosynthetic process	2.7490233849884e-07
GO:0016125	sterol metabolic process	2.7490233849884e-07
GO:0008202	steroid metabolic process	3.11636752412651e-06
GO:0008610	lipid biosynthetic process	8.93433186074538e-06
GO:0004659	prenyltransferase activity	9.14037355238191e-06
GO:0006066	alcohol metabolic process	1.66208797318529e-05
GO:0008299	isoprenoid biosynthetic process	1.95292984653651e-05
GO:0006720	isoprenoid metabolic process	3.13236575847922e-05
GO:0044255	cellular lipid metabolic process	6.42619524810821e-05
GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	9.10383300825682e-05
GO:0006629	lipid metabolic process	0.000103018853577011
GO:0004310	farnesyl-diphosphate farnesyltransferase activity	0.000369789826916284
GO:0047012	sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity	0.000369789826916284
GO:0004337	geranyltranstransferase activity	0.000657384784818225
GO:0004161	dimethylallyltranstransferase activity	0.000657384784818225
GO:0004311	farnesyltranstransferase activity	0.00124549783979476
GO:0009058	biosynthetic process	0.00126128254597198
GO:0003854	3-beta-hydroxy-delta5-steroid dehydrogenase activity	0.00309827870602796
GO:0022404	molting cycle process	0.00409408397409858
GO:0001942	hair follicle development	0.00409408397409858
GO:0042633	hair cycle	0.00409408397409858
GO:0042303	molting cycle	0.00409408397409858
GO:0022405	hair cycle process	0.00409408397409858
GO:0005783	endoplasmic reticulum	0.00519523953746089
GO:0016229	steroid dehydrogenase activity	0.0067557024387043
GO:0016491	oxidoreductase activity	0.0140882656807064
GO:0005737	cytoplasm	0.0238510504393937
GO:0008544	epidermis development	0.0256644984393836
GO:0007398	ectoderm development	0.0268795976235625
GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	0.0274868037710153
GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	0.0285746974756521
GO:0016740	transferase activity	0.049679821594233
GO:0009888	tissue development	0.049679821594233

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>

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Cell Type

Ontology term	p-value	n
animal cell	5.00e-23	679
eukaryotic cell	5.00e-23	679
embryonic cell	4.11e-19	250
somatic cell	1.47e-17	588
epithelial cell	1.01e-14	253
native cell	2.42e-14	722
mesodermal cell	1.32e-11	121
contractile cell	6.89e-09	59
electrically responsive cell	8.04e-08	61
electrically active cell	8.04e-08	61
muscle precursor cell	9.97e-08	58
myoblast	9.97e-08	58
multi-potent skeletal muscle stem cell	9.97e-08	58
muscle cell	1.03e-07	55
non-terminally differentiated cell	3.53e-07	106
ectodermal cell	7.43e-07	72

Uber Anatomy

Ontology term	p-value	n
cell layer	7.93e-16	309
epithelium	5.58e-15	306
organism subdivision	9.81e-13	264
unilaminar epithelium	3.25e-12	148
multi-tissue structure	7.25e-11	342
anatomical cluster	2.57e-10	373
multilaminar epithelium	4.39e-10	83
trunk mesenchyme	5.91e-10	122
epithelial vesicle	7.91e-10	78
mesenchyme	2.46e-09	160
entire embryonic mesenchyme	2.46e-09	160
trunk	5.61e-09	199
epithelial tube	6.46e-09	117
ectodermal placode	1.15e-08	31
somite	1.99e-08	71
presomitic mesoderm	1.99e-08	71
presumptive segmental plate	1.99e-08	71
dermomyotome	1.99e-08	71
trunk paraxial mesoderm	1.99e-08	71
vasculature	2.09e-08	78
vascular system	2.09e-08	78
paraxial mesoderm	2.64e-08	72
presumptive paraxial mesoderm	2.64e-08	72
dense mesenchyme tissue	5.94e-08	73
larynx	1.23e-07	9
primordium	1.97e-07	160
organ part	5.51e-07	218

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	2	11.2315872630044	0.0111955903992222	0.0411289973514498
BRCA1#672	3	15.1381729824178	0.000468218442143119	0.00430195002014474
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00512292916517646
CEBPB#1051	3	5.97836071936861	0.00715383248472697	0.0297297803856751
CHD2#1106	4	10.3440228341169	8.73193255208051e-05	0.00129098853879776
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.016094334932595
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418963649996097
ESR1#2099	2	15.3843016480772	0.00606557262969351	0.0268401974354953
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.00154595115261749
FOS#2353	4	8.9979553088944	0.000152514771116863	0.00194939299726766
FOSL2#2355	4	16.9302006045617	1.2165416097647e-05	0.000304030603451102
GATA1#2623	3	10.1702311078503	0.00151515816849827	0.00966419958225181
GATA2#2624	3	9.5586988001655	0.00181815161835744	0.0109004556182338
GATA3#2625	2	13.618258178603	0.0076966520809334	0.0316930428845406
GTF2F1#2962	3	9.55474565756824	0.00182036231930478	0.010899943829026
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186153310101999
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.0282976751768636
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00307607709468447
IRF3#3661	3	35.2364641586172	3.79279212646878e-05	0.000719817221327045
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466253633749122
MXI1#4601	4	9.9615716287593	0.000101522475495045	0.00142416464986259
NFYA#4800	4	18.4255806998305	8.67100748407158e-06	0.000234426961074023
NFYB#4801	4	16.7597932535365	1.26678572070404e-05	0.00031137169659828
NR2C2#7182	2	16.3073054526204	0.00541182534464822	0.0245570745207558
PBX3#5090	2	10.9572563433721	0.0117453018068803	0.0428455317991189
REST#5978	3	7.23752153709602	0.00410469730419261	0.0195802723007478
RFX5#5993	4	12.0479108271951	4.74457429336527e-05	0.000826966946970586
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00796674648720261
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00684513336229897
SP2#6668	2	13.0767652469223	0.00833003653661494	0.0328096502431561
SREBF1#6720	4	47.0058494404883	2.04523668136926e-07	1.10331856283845e-05
SREBF2#6721	4	436.943262411348	2.70480926640298e-11	3.17758801995344e-09
STAT1#6772	2	10.3532937485996	0.0131077747617126	0.0464922020152319
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322371852388765
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.014034576215014
TAL1#6886	2	14.9343083387201	0.00642807757788807	0.0279481284774594
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244334291531544
TCF7L2#6934	3	8.07763242235301	0.00297838168583462	0.0158647016314011
THAP1#55145	2	15.6845723014257	0.00584046967835792	0.0262489376339626
USF1#7391	3	4.77112445790597	0.0137046588718802	0.048305800469804
USF2#7392	3	9.7441480388022	0.00171834184841007	0.0107205438653584
ZBTB33#10009	3	23.7485437724859	0.000122945190881838	0.0016555276934642
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.00976839803526285

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.