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Coexpression cluster:C3771: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.97e-43!115;UBERON:0001049!4.40e-37!57;UBERON:0005068!4.40e-37!57;UBERON:0006241!4.40e-37!57;UBERON:0007135!4.40e-37!57;UBERON:0001017!5.57e-31!82;UBERON:0003080!3.24e-30!42;UBERON:0002616!4.19e-30!59;UBERON:0005743!7.34e-30!86;UBERON:0003075!1.03e-29!86;UBERON:0007284!1.03e-29!86;UBERON:0002780!1.83e-29!41;UBERON:0001890!1.83e-29!41;UBERON:0006240!1.83e-29!41;UBERON:0000073!4.85e-29!94;UBERON:0001016!4.85e-29!94;UBERON:0000955!2.54e-28!69;UBERON:0006238!2.54e-28!69;UBERON:0002346!1.86e-27!90;UBERON:0002020!2.54e-26!34;UBERON:0003528!2.54e-26!34;UBERON:0001893!8.60e-26!34;UBERON:0002791!5.64e-25!33;UBERON:0001869!1.01e-24!32;UBERON:0003056!1.34e-20!61;UBERON:0000956!1.60e-18!25;UBERON:0000203!1.60e-18!25;UBERON:0004121!3.86e-18!169;UBERON:0000153!2.44e-17!129;UBERON:0007811!2.44e-17!129;UBERON:0000924!3.61e-17!173;UBERON:0006601!3.61e-17!173;UBERON:0002619!3.96e-17!22;UBERON:0000033!3.62e-16!123;UBERON:0001950!2.32e-15!20;UBERON:0002308!2.56e-09!9;UBERON:0000125!2.56e-09!9;UBERON:0002420!4.09e-09!9;UBERON:0007245!4.09e-09!9;UBERON:0010009!4.09e-09!9;UBERON:0010011!4.09e-09!9;UBERON:0000454!4.09e-09!9;UBERON:0000062!3.81e-08!511;UBERON:0003076!4.07e-08!15;UBERON:0003057!4.07e-08!15;UBERON:0003135!5.96e-08!11;UBERON:0002298!6.27e-08!8;UBERON:0000473!8.74e-08!8;UBERON:0000025!1.82e-07!194;UBERON:0009663!2.08e-07!7;UBERON:0000064!2.12e-07!219
|ontology_enrichment_uberon=UBERON:0007023!1.97e-43!115;UBERON:0001049!4.40e-37!57;UBERON:0005068!4.40e-37!57;UBERON:0006241!4.40e-37!57;UBERON:0007135!4.40e-37!57;UBERON:0001017!5.57e-31!82;UBERON:0003080!3.24e-30!42;UBERON:0002616!4.19e-30!59;UBERON:0005743!7.34e-30!86;UBERON:0003075!1.03e-29!86;UBERON:0007284!1.03e-29!86;UBERON:0002780!1.83e-29!41;UBERON:0001890!1.83e-29!41;UBERON:0006240!1.83e-29!41;UBERON:0000073!4.85e-29!94;UBERON:0001016!4.85e-29!94;UBERON:0000955!2.54e-28!69;UBERON:0006238!2.54e-28!69;UBERON:0002346!1.86e-27!90;UBERON:0002020!2.54e-26!34;UBERON:0003528!2.54e-26!34;UBERON:0001893!8.60e-26!34;UBERON:0002791!5.64e-25!33;UBERON:0001869!1.01e-24!32;UBERON:0003056!1.34e-20!61;UBERON:0000956!1.60e-18!25;UBERON:0000203!1.60e-18!25;UBERON:0004121!3.86e-18!169;UBERON:0000153!2.44e-17!129;UBERON:0007811!2.44e-17!129;UBERON:0000924!3.61e-17!173;UBERON:0006601!3.61e-17!173;UBERON:0002619!3.96e-17!22;UBERON:0000033!3.62e-16!123;UBERON:0001950!2.32e-15!20;UBERON:0002308!2.56e-09!9;UBERON:0000125!2.56e-09!9;UBERON:0002420!4.09e-09!9;UBERON:0007245!4.09e-09!9;UBERON:0010009!4.09e-09!9;UBERON:0010011!4.09e-09!9;UBERON:0000454!4.09e-09!9;UBERON:0000062!3.81e-08!511;UBERON:0003076!4.07e-08!15;UBERON:0003057!4.07e-08!15;UBERON:0003135!5.96e-08!11;UBERON:0002298!6.27e-08!8;UBERON:0000473!8.74e-08!8;UBERON:0000025!1.82e-07!194;UBERON:0009663!2.08e-07!7;UBERON:0000064!2.12e-07!219
|tf_chipseq_enrich=GATA3#2625;2:18.1576775714707:0.00394454681927962:0.0189496101774951!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381283641703015
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}}
}}

Revision as of 12:08, 5 September 2012


Full id: C3771_mesothelioma_testicular_adult_neuroblastoma_testis_choriocarcinoma_teratocarcinoma



Phase1 CAGE Peaks

Hg19::chr19:22966893..22966924,-p2@ZNF99
Hg19::chr19:22966925..22966958,-p1@ZNF99
Hg19::chr19:38346040..38346055,+p@chr19:38346040..38346055
+


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
germ line cell8.56e-107
germ cell8.56e-107
Uber Anatomy
Ontology termp-valuen
adult organism1.97e-43115
neural tube4.40e-3757
neural rod4.40e-3757
future spinal cord4.40e-3757
neural keel4.40e-3757
central nervous system5.57e-3182
anterior neural tube3.24e-3042
regional part of brain4.19e-3059
neural plate1.03e-2986
presumptive neural plate1.03e-2986
regional part of forebrain1.83e-2941
forebrain1.83e-2941
future forebrain1.83e-2941
regional part of nervous system4.85e-2994
nervous system4.85e-2994
brain2.54e-2869
future brain2.54e-2869
neurectoderm1.86e-2790
gray matter2.54e-2634
brain grey matter2.54e-2634
telencephalon8.60e-2634
regional part of telencephalon5.64e-2533
cerebral hemisphere1.01e-2432
pre-chordal neural plate1.34e-2061
cerebral cortex1.60e-1825
pallium1.60e-1825
ectoderm-derived structure3.86e-18169
anterior region of body2.44e-17129
craniocervical region2.44e-17129
ectoderm3.61e-17173
presumptive ectoderm3.61e-17173
regional part of cerebral cortex3.96e-1722
head3.62e-16123
neocortex2.32e-1520
nucleus of brain2.56e-099
neural nucleus2.56e-099
basal ganglion4.09e-099
nuclear complex of neuraxis4.09e-099
aggregate regional part of brain4.09e-099
collection of basal ganglia4.09e-099
cerebral subcortex4.09e-099
organ3.81e-08511
posterior neural tube4.07e-0815
chordal neural plate4.07e-0815
male reproductive organ5.96e-0811
brainstem6.27e-088
testis8.74e-088
tube1.82e-07194
telencephalic nucleus2.08e-077
organ part2.12e-07219


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
GATA3#2625218.15767757147070.003944546819279620.0189496101774951
NFYB#4801211.17319550235760.01025467135054530.0381283641703015



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3771&oldid=2130941"