Coexpression cluster:C4856

Full id: C4856_pituitary_cerebellum_pineal_Fibroblast_liposarcoma_acute_colon

Phase1 CAGE Peaks

Hg19::chrX:1510670..1510699,+	p@chrX:1510670..1510699 +
Hg19::chrX:1511254..1511272,+	p@chrX:1511254..1511272 +
Hg19::chrX:1511278..1511319,+	p@chrX:1511278..1511319 +

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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No GOStat results

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
neural tube	6.88e-14	56
neural rod	6.88e-14	56
future spinal cord	6.88e-14	56
neural keel	6.88e-14	56
regional part of nervous system	3.38e-12	53
regional part of brain	3.38e-12	53
regional part of forebrain	6.87e-11	41
forebrain	6.87e-11	41
anterior neural tube	6.87e-11	41
future forebrain	6.87e-11	41
brain grey matter	2.00e-09	34
gray matter	2.00e-09	34
central nervous system	3.60e-09	81
female organism	1.32e-08	41
brain	1.52e-08	68
future brain	1.52e-08	68
regional part of telencephalon	3.83e-08	32
nervous system	1.32e-07	89
female reproductive organ	1.93e-07	37
female reproductive system	1.93e-07	37
neural nucleus	2.06e-07	9
nucleus of brain	2.06e-07	9
ecto-epithelium	2.18e-07	104
basal ganglion	2.40e-07	9
nuclear complex of neuraxis	2.40e-07	9
aggregate regional part of brain	2.40e-07	9
collection of basal ganglia	2.40e-07	9
cerebral subcortex	2.40e-07	9
telencephalon	2.74e-07	34
cerebral hemisphere	4.31e-07	32
neurectoderm	7.48e-07	86
internal female genitalia	9.95e-07	22

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	3	6.33620157696263	0.00393075003576489	0.0191466630747283
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324854240272643
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465491899139091
ESRRA#2101	2	322.560209424084	1.27639599649441e-05	0.000313217860615318
HNF4G#3174	2	19.1689483509645	0.00354398661128422	0.0179814621888803
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128873325180021
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0271027149176457
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0325015061207227
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381664096496774
NR2C2#7182	2	21.7430739368272	0.00276220797549601	0.0151418349124936
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460867680047567
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00474007927766407
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173804968257601
PPARGC1A#10891	2	233.367424242424	2.43900419981513e-05	0.000528918520814977
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.0298403309397297
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0248212006598697
THAP1#55145	2	20.9127630685675	0.00298344741373694	0.0158795364612818
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191414360793549
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.0378295611782954

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.