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Coexpression cluster:C2449: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.97e-21!115;UBERON:0001017!4.89e-16!82;UBERON:0005743!7.23e-15!86;UBERON:0000924!1.99e-14!173;UBERON:0006601!1.99e-14!173;UBERON:0004121!2.37e-14!169;UBERON:0000073!3.18e-14!94;UBERON:0001016!3.18e-14!94;UBERON:0001049!1.34e-12!57;UBERON:0005068!1.34e-12!57;UBERON:0006241!1.34e-12!57;UBERON:0007135!1.34e-12!57;UBERON:0000955!2.06e-11!69;UBERON:0006238!2.06e-11!69;UBERON:0002616!1.16e-10!59;UBERON:0000033!3.29e-10!123;UBERON:0000153!3.90e-10!129;UBERON:0007811!3.90e-10!129;UBERON:0002346!9.68e-09!90;UBERON:0003075!9.94e-09!86;UBERON:0007284!9.94e-09!86;UBERON:0000062!7.86e-08!511;UBERON:0003076!1.81e-07!15;UBERON:0003057!1.81e-07!15;UBERON:0000468!1.96e-07!659;UBERON:0003080!2.94e-07!42;UBERON:0002780!6.90e-07!41;UBERON:0001890!6.90e-07!41;UBERON:0006240!6.90e-07!41;UBERON:0000922!7.51e-07!612
|ontology_enrichment_uberon=UBERON:0007023!3.97e-21!115;UBERON:0001017!4.89e-16!82;UBERON:0005743!7.23e-15!86;UBERON:0000924!1.99e-14!173;UBERON:0006601!1.99e-14!173;UBERON:0004121!2.37e-14!169;UBERON:0000073!3.18e-14!94;UBERON:0001016!3.18e-14!94;UBERON:0001049!1.34e-12!57;UBERON:0005068!1.34e-12!57;UBERON:0006241!1.34e-12!57;UBERON:0007135!1.34e-12!57;UBERON:0000955!2.06e-11!69;UBERON:0006238!2.06e-11!69;UBERON:0002616!1.16e-10!59;UBERON:0000033!3.29e-10!123;UBERON:0000153!3.90e-10!129;UBERON:0007811!3.90e-10!129;UBERON:0002346!9.68e-09!90;UBERON:0003075!9.94e-09!86;UBERON:0007284!9.94e-09!86;UBERON:0000062!7.86e-08!511;UBERON:0003076!1.81e-07!15;UBERON:0003057!1.81e-07!15;UBERON:0000468!1.96e-07!659;UBERON:0003080!2.94e-07!42;UBERON:0002780!6.90e-07!41;UBERON:0001890!6.90e-07!41;UBERON:0006240!6.90e-07!41;UBERON:0000922!7.51e-07!612
|tf_chipseq_enrich=EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199581088341262!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101425247177657!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00767878196951586
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}}
}}

Revision as of 11:38, 5 September 2012


Full id: C2449_Synoviocyte_Fibroblast_left_aorta_pharyngeal_anaplastic_leiomyoblastoma



Phase1 CAGE Peaks

Hg19::chr17:8924820..8924832,+p1@NTN1
Hg19::chr17:8924837..8924872,+p3@NTN1
Hg19::chr17:8924897..8924916,+p2@NTN1
Hg19::chr17:8924926..8924945,+p@chr17:8924926..8924945
+


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
adult organism3.97e-21115
central nervous system4.89e-1682
ectoderm1.99e-14173
presumptive ectoderm1.99e-14173
ectoderm-derived structure2.37e-14169
regional part of nervous system3.18e-1494
nervous system3.18e-1494
neural tube1.34e-1257
neural rod1.34e-1257
future spinal cord1.34e-1257
neural keel1.34e-1257
brain2.06e-1169
future brain2.06e-1169
regional part of brain1.16e-1059
head3.29e-10123
anterior region of body3.90e-10129
craniocervical region3.90e-10129
neurectoderm9.68e-0990
neural plate9.94e-0986
presumptive neural plate9.94e-0986
organ7.86e-08511
posterior neural tube1.81e-0715
chordal neural plate1.81e-0715
multi-cellular organism1.96e-07659
anterior neural tube2.94e-0742
regional part of forebrain6.90e-0741
forebrain6.90e-0741
future forebrain6.90e-0741
embryo7.51e-07612


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
EBF1#187948.9064668465690.00015887907472010.00199581088341262
EGR1#195844.988179094810140.001615011500076050.0101425247177657
NFKB1#479045.488063424193840.001102199566301980.00767878196951586



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:C2449&oldid=2130450"