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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C4856_pituitary_cerebellum_pineal_Fibroblast_liposarcoma_acute_colon
 
|full_id=C4856_pituitary_cerebellum_pineal_Fibroblast_liposarcoma_acute_colon
 
|id=C4856
 
|id=C4856

Revision as of 09:00, 12 September 2012


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


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


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>


Uber Anatomy
Ontology termp-valuen
neural tube5.15e-1457
neural rod5.15e-1457
future spinal cord5.15e-1457
neural keel5.15e-1457
anterior neural tube3.80e-1142
regional part of forebrain1.44e-1041
forebrain1.44e-1041
future forebrain1.44e-1041
regional part of brain2.84e-1059
central nervous system3.53e-0982
gray matter4.37e-0934
brain grey matter4.37e-0934
brain1.37e-0869
future brain1.37e-0869
female organism1.89e-0841
neurectoderm7.61e-0890
neural plate9.27e-0886
presumptive neural plate9.27e-0886
female reproductive organ2.10e-0737
female reproductive system2.10e-0737
regional part of telencephalon2.16e-0733
nucleus of brain3.32e-079
neural nucleus3.32e-079
regional part of nervous system3.71e-0794
nervous system3.71e-0794
telencephalon5.51e-0734
basal ganglion6.08e-079
nuclear complex of neuraxis6.08e-079
aggregate regional part of brain6.08e-079
collection of basal ganglia6.08e-079
cerebral subcortex6.08e-079
cerebral hemisphere8.60e-0732


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#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0191466630747283
E2F6#187635.017155731697390.00791769806886330.0324854240272643
ELF1#199734.258097958807540.01295179875054610.0465491899139091
ESRRA#21012322.5602094240841.27639599649441e-050.000313217860615318
HNF4G#3174219.16894835096450.003543986611284220.0179814621888803
IRF1#365937.63716375356390.002244692747297240.0128873325180021
NFKB1#479035.488063424193840.006049381815655430.0271027149176457
NFYA#4800212.28372046655370.008516011403724430.0325015061207227
NFYB#4801211.17319550235760.01025467135054530.0381664096496774
NR2C2#7182221.74307393682720.002762207975496010.0151418349124936
NR3C1#290829.982015554115360.01278474365547170.0460867680047567
NRF1#4899312.21027944771090.0005492172401020010.00474007927766407
PAX5#507936.669565531177830.003370290999677260.0173804968257601
PPARGC1A#108912233.3674242424242.43900419981513e-050.000528918520814977
RXRA#6256213.38307809275550.007196434429465730.0298403309397297
SP1#666735.69838137814090.005403962701712170.0248212006598697
THAP1#55145220.91276306856750.002983447413736940.0158795364612818
USF1#739136.361499277207960.00388404057290560.0191414360793549
ZEB1#6935211.25895467836260.01010222676646330.0378295611782954



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


This analysis result is provided for C0 - C305 clusters.