Coexpression cluster:C1502

Full id: C1502_mature_Hepatocyte_argyrophil_hepatoblastoma_liver_hepatocellular_Adipocyte

Phase1 CAGE Peaks

Hg19::chr2:216946482..216946499,-	p2@PECR
Hg19::chr7:73038839..73038862,-	p1@MLXIPL
Hg19::chr7:73038865..73038866,-	p4@MLXIPL
Hg19::chr7:73038867..73038878,-	p2@MLXIPL
Hg19::chr7:73038889..73038905,-	p3@MLXIPL
Hg19::chr9:130659627..130659649,-	p6@ST6GALNAC6

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:0019166	trans-2-enoyl-CoA reductase (NADPH) activity	0.0174844729335235

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
fat cell	3.99e-07	15

Uber Anatomy

Ontology term	p-value	n
adult organism	7.08e-39	114
organ system subdivision	2.80e-26	223
neural tube	2.63e-21	56
neural rod	2.63e-21	56
future spinal cord	2.63e-21	56
neural keel	2.63e-21	56
regional part of nervous system	2.81e-20	53
regional part of brain	2.81e-20	53
nervous system	2.54e-17	89
central nervous system	1.65e-16	81
regional part of forebrain	2.15e-16	41
forebrain	2.15e-16	41
anterior neural tube	2.15e-16	41
future forebrain	2.15e-16	41
brain	7.96e-16	68
future brain	7.96e-16	68
neurectoderm	3.82e-15	86
neural plate	2.51e-14	82
presumptive neural plate	2.51e-14	82
brain grey matter	8.53e-13	34
gray matter	8.53e-13	34
telencephalon	1.60e-12	34
cerebral hemisphere	4.74e-12	32
regional part of telencephalon	1.18e-11	32
anatomical cluster	1.24e-11	373
regional part of cerebral cortex	1.45e-11	22
subdivision of digestive tract	6.16e-11	118
ecto-epithelium	9.55e-11	104
neocortex	1.66e-10	20
pre-chordal neural plate	2.31e-10	61
multi-tissue structure	1.50e-09	342
cerebral cortex	2.09e-09	25
pallium	2.09e-09	25
ectoderm-derived structure	1.56e-08	171
ectoderm	1.56e-08	171
presumptive ectoderm	1.56e-08	171
organ	2.80e-08	503
digestive system	5.28e-08	145
digestive tract	5.28e-08	145
primitive gut	5.28e-08	145
tube	5.97e-08	192
anatomical conduit	1.35e-07	240
foregut	2.56e-07	87
structure with developmental contribution from neural crest	3.19e-07	132
immaterial anatomical entity	6.95e-07	117

Disease

Ontology term	p-value	n
cell type cancer	3.76e-14	143
carcinoma	1.77e-13	106

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
CCNT2#905	4	4.22413438464176	0.00710980547887581	0.0296163439058835
E2F4#1874	4	8.44537354352296	0.000511119352377084	0.00443398903919846
E2F6#1876	5	4.18096310974782	0.00157359875958697	0.00997542220652524
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.00253379038623871
HMGN3#9324	4	5.45236514890039	0.00272961688233377	0.0149891402057972
IRF1#3659	4	5.09144250237593	0.00353524076589381	0.0179458058884603
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380581657372589
SIN3A#25942	5	4.50740393901261	0.00109611006120864	0.00766139999214086
SREBF1#6720	4	31.3372329603255	2.9644579358811e-06	0.000101376890100028
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.0057356360359842
TBP#6908	6	3.70677068709639	0.00038541647290796	0.00378064346896163

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.