Coexpression cluster:C1949

Full id: C1949_mature_liver_Hepatocyte_seminal_ductus_pineal_immature

Phase1 CAGE Peaks

Hg19::chr5:115152347..115152363,-	p1@CDO1
Hg19::chr9:130860731..130860742,+	p6@SLC25A25
Hg19::chr9:130860748..130860774,+	p5@SLC25A25
Hg19::chr9:130860779..130860800,+	p3@SLC25A25
Hg19::chr9:130860810..130860828,+	p2@SLC25A25

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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GO ID	GO name	FDR corrected p-value
GO:0046439	L-cysteine metabolic process	0.00103026021429412
GO:0019530	taurine metabolic process	0.00103026021429412
GO:0017172	cysteine dioxygenase activity	0.00103026021429412
GO:0042412	taurine biosynthetic process	0.00103026021429412
GO:0006534	cysteine metabolic process	0.00494488509694741
GO:0000097	sulfur amino acid biosynthetic process	0.013732961356353
GO:0000096	sulfur amino acid metabolic process	0.0170658475389813
GO:0042398	amino acid derivative biosynthetic process	0.0205918601248543
GO:0044272	sulfur compound biosynthetic process	0.0205918601248543
GO:0009069	serine family amino acid metabolic process	0.0226477100970827
GO:0051213	dioxygenase activity	0.023150489273369
GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	0.023150489273369
GO:0016701	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen	0.023150489273369
GO:0008652	amino acid biosynthetic process	0.023150489273369
GO:0006790	sulfur metabolic process	0.023150489273369
GO:0006575	amino acid derivative metabolic process	0.023150489273369
GO:0009309	amine biosynthetic process	0.0287971847411023
GO:0044271	nitrogen compound biosynthetic process	0.0335828456911871

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
anatomical cluster	1.09e-16	373
multi-tissue structure	1.65e-13	342
multi-cellular organism	1.92e-13	656
organ	8.94e-12	503
adult organism	1.09e-11	114
anatomical conduit	1.11e-11	240
anatomical system	2.06e-11	624
anatomical group	4.21e-11	625
epithelium	1.40e-10	306
cell layer	2.40e-10	309
tube	1.21e-08	192
developing anatomical structure	1.80e-08	581
organ system subdivision	1.92e-08	223
embryo	2.05e-08	592
germ layer	4.01e-08	560
germ layer / neural crest	4.01e-08	560
embryonic tissue	4.01e-08	560
presumptive structure	4.01e-08	560
germ layer / neural crest derived structure	4.01e-08	560
epiblast (generic)	4.01e-08	560
embryonic structure	4.71e-08	564
organ part	1.01e-07	218
immaterial anatomical entity	3.05e-07	117
primordium	8.40e-07	160
digestive system	8.60e-07	145
digestive tract	8.60e-07	145
primitive gut	8.60e-07	145
organism subdivision	9.60e-07	264

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
BRCA1#672	4	16.147384514579	2.89130901545765e-05	0.000605262421858852
CEBPB#1051	4	6.37691810065985	0.00111394417667732	0.0076584303777238
E2F4#1874	4	10.1344482522276	0.000181820150963297	0.00220368048583681
EP300#2033	5	6.7739417262232	7.00901578206049e-05	0.0011097856265352
FOSL2#2355	4	13.5441604836494	5.7953819349229e-05	0.000965179228036059
GTF2F1#2962	4	10.1917287014061	0.00017783388942764	0.0021596271602248
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00674818054713818
HNF4A#3172	4	18.505832290363	1.68463364181741e-05	0.000387877982622947
HNF4G#3174	4	23.0027380211574	7.10515202727268e-06	0.000204874371224829
HSF1#3297	4	131.432533333333	6.79362350565572e-09	5.3267210608647e-07
IRF3#3661	4	37.5855617691917	1.00727027008258e-06	4.25215439519621e-05
JUN#3725	4	10.0102633538691	0.000190853134780107	0.00230620277025333
JUND#3727	4	5.59573115349682	0.00184959330175546	0.0109382601835809
MAX#4149	4	5.1620444072057	0.00252630900948518	0.0140037782836167
MXI1#4601	4	7.96925730300744	0.000466854638007017	0.00429622271026653
MYC#4609	4	4.17782549728752	0.00569196903682344	0.0256909786177797
NFYA#4800	4	14.7404645598644	4.14733626928016e-05	0.000752508083091297
NFYB#4801	4	13.4078346028292	6.03169250119439e-05	0.000991881488162873
RFX5#5993	4	9.63832866175608	0.00022148012581572	0.00249823553948244
SIN3A#25942	4	4.32710778145211	0.00497705285576288	0.0232499182897088
SP1#6667	4	4.55870510251272	0.0040757356578168	0.019491975289254
STAT3#6774	4	8.41557199772339	0.000377152721159863	0.0037446005366684
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135535247610234
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00920131680279011
TFAP2C#7022	4	8.64738288788818	0.000339051887817405	0.00344927334032359
ZNF263#10127	5	8.22184163701068	2.6606316672286e-05	0.000572345439121912

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.