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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1775_neuroblastoma_iPS_testicular_H9_HES3GFP_skeletal_Melanocyte
|full_id=C1775_neuroblastoma_iPS_testicular_H9_HES3GFP_skeletal_Melanocyte
|gostat_on_coexpression_clusters=GO:0008115!sarcosine oxidase activity!0.00174651065699534!51268$GO:0001829!trophectodermal cell differentiation!0.00174651065699534!27022$GO:0050031!L-pipecolate oxidase activity!0.00174651065699534!51268$GO:0046653!tetrahydrofolate metabolic process!0.00174651065699534!51268$GO:0001825!blastocyst formation!0.00174651065699534!27022$GO:0016647!oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor!0.00174651065699534!51268$GO:0001892!embryonic placenta development!0.0029939301333032!27022$GO:0001824!blastocyst development!0.00873088237650159!27022$GO:0001890!placenta development!0.00873088237650159!27022$GO:0006760!folic acid and derivative metabolic process!0.0226879294561886!51268$GO:0001701!in utero embryonic development!0.0226879294561886!27022$GO:0016645!oxidoreductase activity, acting on the CH-NH group of donors!0.0226879294561886!51268$GO:0009792!embryonic development ending in birth or egg hatching!0.0326998395213866!27022$GO:0043009!chordate embryonic development!0.0326998395213866!27022$GO:0042579!microbody!0.0326998395213866!51268$GO:0005777!peroxisome!0.0326998395213866!51268$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0363413184827587!27022$GO:0046483!heterocycle metabolic process!0.0363413184827587!51268$GO:0006752!group transfer coenzyme metabolic process!0.0363413184827587!51268$GO:0045944!positive regulation of transcription from RNA polymerase II promoter!0.0363413184827587!27022$GO:0048646!anatomical structure formation!0.0380888911765254!27022$GO:0006725!aromatic compound metabolic process!0.0434672701333003!51268$GO:0045892!negative regulation of transcription, DNA-dependent!0.0461077525897228!27022$GO:0045893!positive regulation of transcription, DNA-dependent!0.0485256242130203!27022$GO:0009790!embryonic development!0.0490826948160948!27022
|gostat_on_coexpression_clusters=GO:0008115!sarcosine oxidase activity!0.00174651065699534!51268$GO:0001829!trophectodermal cell differentiation!0.00174651065699534!27022$GO:0050031!L-pipecolate oxidase activity!0.00174651065699534!51268$GO:0046653!tetrahydrofolate metabolic process!0.00174651065699534!51268$GO:0001825!blastocyst formation!0.00174651065699534!27022$GO:0016647!oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor!0.00174651065699534!51268$GO:0001892!embryonic placenta development!0.0029939301333032!27022$GO:0001824!blastocyst development!0.00873088237650159!27022$GO:0001890!placenta development!0.00873088237650159!27022$GO:0006760!folic acid and derivative metabolic process!0.0226879294561886!51268$GO:0001701!in utero embryonic development!0.0226879294561886!27022$GO:0016645!oxidoreductase activity, acting on the CH-NH group of donors!0.0226879294561886!51268$GO:0009792!embryonic development ending in birth or egg hatching!0.0326998395213866!27022$GO:0043009!chordate embryonic development!0.0326998395213866!27022$GO:0042579!microbody!0.0326998395213866!51268$GO:0005777!peroxisome!0.0326998395213866!51268$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0363413184827587!27022$GO:0046483!heterocycle metabolic process!0.0363413184827587!51268$GO:0006752!group transfer coenzyme metabolic process!0.0363413184827587!51268$GO:0045944!positive regulation of transcription from RNA polymerase II promoter!0.0363413184827587!27022$GO:0048646!anatomical structure formation!0.0380888911765254!27022$GO:0006725!aromatic compound metabolic process!0.0434672701333003!51268$GO:0045892!negative regulation of transcription, DNA-dependent!0.0461077525897228!27022$GO:0045893!positive regulation of transcription, DNA-dependent!0.0485256242130203!27022$GO:0009790!embryonic development!0.0490826948160948!27022

Revision as of 14:23, 12 September 2012


Full id: C1775_neuroblastoma_iPS_testicular_H9_HES3GFP_skeletal_Melanocyte



Phase1 CAGE Peaks

Hg19::chr17:27370003..27370010,+p7@PIPOX
Hg19::chr17:27370022..27370051,+p2@PIPOX
Hg19::chr1:63788080..63788093,-p2@ENST00000418244
Hg19::chr1:63788098..63788150,-p1@ENST00000418244
p1@ENST00000449386
Hg19::chr1:63788229..63788250,+p1@FOXD3


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:0008115sarcosine oxidase activity0.00174651065699534
GO:0001829trophectodermal cell differentiation0.00174651065699534
GO:0050031L-pipecolate oxidase activity0.00174651065699534
GO:0046653tetrahydrofolate metabolic process0.00174651065699534
GO:0001825blastocyst formation0.00174651065699534
GO:0016647oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor0.00174651065699534
GO:0001892embryonic placenta development0.0029939301333032
GO:0001824blastocyst development0.00873088237650159
GO:0001890placenta development0.00873088237650159
GO:0006760folic acid and derivative metabolic process0.0226879294561886
GO:0001701in utero embryonic development0.0226879294561886
GO:0016645oxidoreductase activity, acting on the CH-NH group of donors0.0226879294561886
GO:0009792embryonic development ending in birth or egg hatching0.0326998395213866
GO:0043009chordate embryonic development0.0326998395213866
GO:0042579microbody0.0326998395213866
GO:0005777peroxisome0.0326998395213866
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0363413184827587
GO:0046483heterocycle metabolic process0.0363413184827587
GO:0006752group transfer coenzyme metabolic process0.0363413184827587
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0363413184827587
GO:0048646anatomical structure formation0.0380888911765254
GO:0006725aromatic compound metabolic process0.0434672701333003
GO:0045892negative regulation of transcription, DNA-dependent0.0461077525897228
GO:0045893positive regulation of transcription, DNA-dependent0.0485256242130203
GO:0009790embryonic development0.0490826948160948



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>


Cell Type
Ontology termp-valuen
melanocyte2.50e-0910
melanoblast2.50e-0910
neurectodermal cell3.02e-0859
migratory neural crest cell2.90e-0741
neural cell4.03e-0725
Uber Anatomy
Ontology termp-valuen
adult organism5.45e-12115
central nervous system1.45e-0982
regional part of nervous system2.12e-0994
nervous system2.12e-0994
neurectoderm8.33e-0990
neural tube6.57e-0857
neural rod6.57e-0857
future spinal cord6.57e-0857
neural keel6.57e-0857
neural plate1.93e-0786
presumptive neural plate1.93e-0786
ectoderm2.82e-07173
presumptive ectoderm2.82e-07173
Disease
Ontology termp-valuen
cell type cancer6.83e-21143
carcinoma1.34e-18106
cancer2.26e-15235
disease of cellular proliferation5.67e-15239
germ cell and embryonal cancer5.61e-0722
germ cell cancer5.61e-0722


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
ATF3#467313.47790471560530.0008241088551409360.00627371562956952
CTBP2#1488225.08680013573130.002461438599678380.0138492719487022
CTCFL#140690311.84788461538460.001201770348538230.00815010996305092
FOXA1#316936.648851849631270.006389025166568720.0278095940389793
FOXA2#3170314.77827825159910.0006289192851194480.00517398197862072
HNF4G#3174211.50136901057870.01127438304921050.0413806111852572
NANOG#79923317.54686708860760.0003794200090681830.0037606763146125
POU5F1#54602134.1756805807628.81868530743257e-050.00130160355401774
TAF1#687253.343046285745290.002394600090870310.0135329891174461
TBP#690853.706770687096390.001428755106721120.00918771963492687
USF2#739237.795318431041750.004048927661722050.0193761893357125



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.