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Coexpression cluster:C2322: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2322_Mast_Neutrophils_Eosinophils_granulocyte_cerebellum_Whole_CD4
|full_id=C2322_Mast_Neutrophils_Eosinophils_granulocyte_cerebellum_Whole_CD4
|gostat_on_coexpression_clusters=GO:0016572!histone phosphorylation!0.00488637701636642!9252$GO:0007173!epidermal growth factor receptor signaling pathway!0.0305398563522901!9252$GO:0016570!histone modification!0.0305398563522901!9252$GO:0016569!covalent chromatin modification!0.0305398563522901!9252
|gostat_on_coexpression_clusters=GO:0016572!histone phosphorylation!0.00488637701636642!9252$GO:0007173!epidermal growth factor receptor signaling pathway!0.0305398563522901!9252$GO:0016570!histone modification!0.0305398563522901!9252$GO:0016569!covalent chromatin modification!0.0305398563522901!9252

Revision as of 15:02, 12 September 2012


Full id: C2322_Mast_Neutrophils_Eosinophils_granulocyte_cerebellum_Whole_CD4



Phase1 CAGE Peaks

Hg19::chr14:91526905..91526916,-p3@RPS6KA5
Hg19::chr14:91526922..91527001,-p1@RPS6KA5
Hg19::chr14:91527015..91527034,-p2@RPS6KA5
Hg19::chr17:38278209..38278250,+p2@MSL1


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


GO IDGO nameFDR corrected p-value
GO:0016572histone phosphorylation0.00488637701636642
GO:0007173epidermal growth factor receptor signaling pathway0.0305398563522901
GO:0016570histone modification0.0305398563522901
GO:0016569covalent chromatin modification0.0305398563522901



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>


Uber Anatomy
Ontology termp-valuen
adult organism6.84e-34115
neural tube8.72e-1757
neural rod8.72e-1757
future spinal cord8.72e-1757
neural keel8.72e-1757
anterior neural tube2.50e-1342
regional part of forebrain3.19e-1341
forebrain3.19e-1341
future forebrain3.19e-1341
brain4.23e-1269
future brain4.23e-1269
central nervous system5.56e-1282
regional part of brain1.04e-1159
telencephalon2.57e-1134
gray matter2.79e-1134
brain grey matter2.79e-1134
regional part of telencephalon6.26e-1133
regional part of nervous system1.80e-1094
nervous system1.80e-1094
cerebral hemisphere2.26e-1032
regional part of cerebral cortex9.88e-0922
hematopoietic system2.63e-08102
blood island2.63e-08102
neocortex3.53e-0820
neurectoderm7.03e-0890
neural plate1.28e-0786
presumptive neural plate1.28e-0786
cerebral cortex1.59e-0725
pallium1.59e-0725
blood4.60e-0715
haemolymphatic fluid4.60e-0715
organism substance4.60e-0715
hemolymphoid system5.77e-07112


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
E2F1#186944.907389214879320.001724022357361790.0106384148289813
E2F4#187439.501045236463330.001850751034728270.0109253101580367
E2F6#187645.017155731697390.00157802193473060.0099605362529511
EGR1#195844.988179094810140.001615011500076050.0101352112760752
FOS#235336.74846648167080.005032452776317940.0234604443827107
FOXA2#3170212.31523187633260.009361916285467240.0353386285578254
HEY1#2346244.040111043105710.00375304636917980.0185773927556173
IRF1#365935.727872815172930.008097114790333330.0319996432280479
IRF3#3661335.23646415861723.79279212646878e-050.000719686440581891
NFYB#4801312.56984494015230.000811456397697350.00618596311818347
NRF1#4899412.21027944771094.49717228915276e-050.00079284297215872
PBX3#5090316.43588451505810.0003669431395554610.00365714042866999
RFX5#599339.035933120396320.002144561191324070.0123832490883339
SMARCB1#6598313.68953683586810.0006305783409379340.00518110072765454
SP2#6668319.61514787038350.0002171004269245340.00248533941549615
TAF1#687243.343046285745290.008005664898701650.0321726810972565
TBP#690843.706770687096390.005296377814784350.0243817341472325
ZNF143#7702310.12565741417090.001534861610688180.0097624489499795
ZNF263#1012748.221841637010680.0002187871180958320.00248422568241037



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.