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Coexpression cluster:C2722: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.90e-55!115;UBERON:0001049!4.89e-25!57;UBERON:0005068!4.89e-25!57;UBERON:0006241!4.89e-25!57;UBERON:0007135!4.89e-25!57;UBERON:0002616!3.97e-22!59;UBERON:0003080!1.36e-21!42;UBERON:0002780!4.46e-21!41;UBERON:0001890!4.46e-21!41;UBERON:0006240!4.46e-21!41;UBERON:0000073!6.03e-20!94;UBERON:0001016!6.03e-20!94;UBERON:0005743!1.72e-18!86;UBERON:0000955!2.07e-18!69;UBERON:0006238!2.07e-18!69;UBERON:0003075!1.19e-17!86;UBERON:0007284!1.19e-17!86;UBERON:0002346!3.45e-17!90;UBERON:0001017!6.14e-17!82;UBERON:0001893!8.93e-16!34;UBERON:0002020!1.01e-15!34;UBERON:0003528!1.01e-15!34;UBERON:0002791!5.04e-15!33;UBERON:0001869!2.71e-14!32;UBERON:0003056!2.87e-14!61;UBERON:0004111!7.12e-12!241;UBERON:0002619!8.09e-12!22;UBERON:0001950!1.42e-10!20;UBERON:0004121!2.15e-10!169;UBERON:0000924!2.47e-10!173;UBERON:0006601!2.47e-10!173;UBERON:0000153!2.97e-10!129;UBERON:0007811!2.97e-10!129;UBERON:0000033!7.13e-10!123;UBERON:0000956!9.93e-10!25;UBERON:0000203!9.93e-10!25;UBERON:0000062!1.26e-09!511;UBERON:0000477!3.84e-09!286;UBERON:0000025!8.65e-09!194;UBERON:0002420!4.12e-08!9;UBERON:0007245!4.12e-08!9;UBERON:0010009!4.12e-08!9;UBERON:0010011!4.12e-08!9;UBERON:0000454!4.12e-08!9;UBERON:0000481!4.78e-08!347;UBERON:0002308!5.01e-08!9;UBERON:0000125!5.01e-08!9;UBERON:0002298!1.21e-07!8;UBERON:0000468!3.98e-07!659;UBERON:0001894!4.02e-07!7;UBERON:0006222!4.02e-07!7;UBERON:0000922!4.82e-07!612;UBERON:0001046!4.92e-07!19;UBERON:0002050!6.91e-07!605;UBERON:0005423!6.91e-07!605;UBERON:0000483!8.10e-07!309
|ontology_enrichment_uberon=UBERON:0007023!7.90e-55!115;UBERON:0001049!4.89e-25!57;UBERON:0005068!4.89e-25!57;UBERON:0006241!4.89e-25!57;UBERON:0007135!4.89e-25!57;UBERON:0002616!3.97e-22!59;UBERON:0003080!1.36e-21!42;UBERON:0002780!4.46e-21!41;UBERON:0001890!4.46e-21!41;UBERON:0006240!4.46e-21!41;UBERON:0000073!6.03e-20!94;UBERON:0001016!6.03e-20!94;UBERON:0005743!1.72e-18!86;UBERON:0000955!2.07e-18!69;UBERON:0006238!2.07e-18!69;UBERON:0003075!1.19e-17!86;UBERON:0007284!1.19e-17!86;UBERON:0002346!3.45e-17!90;UBERON:0001017!6.14e-17!82;UBERON:0001893!8.93e-16!34;UBERON:0002020!1.01e-15!34;UBERON:0003528!1.01e-15!34;UBERON:0002791!5.04e-15!33;UBERON:0001869!2.71e-14!32;UBERON:0003056!2.87e-14!61;UBERON:0004111!7.12e-12!241;UBERON:0002619!8.09e-12!22;UBERON:0001950!1.42e-10!20;UBERON:0004121!2.15e-10!169;UBERON:0000924!2.47e-10!173;UBERON:0006601!2.47e-10!173;UBERON:0000153!2.97e-10!129;UBERON:0007811!2.97e-10!129;UBERON:0000033!7.13e-10!123;UBERON:0000956!9.93e-10!25;UBERON:0000203!9.93e-10!25;UBERON:0000062!1.26e-09!511;UBERON:0000477!3.84e-09!286;UBERON:0000025!8.65e-09!194;UBERON:0002420!4.12e-08!9;UBERON:0007245!4.12e-08!9;UBERON:0010009!4.12e-08!9;UBERON:0010011!4.12e-08!9;UBERON:0000454!4.12e-08!9;UBERON:0000481!4.78e-08!347;UBERON:0002308!5.01e-08!9;UBERON:0000125!5.01e-08!9;UBERON:0002298!1.21e-07!8;UBERON:0000468!3.98e-07!659;UBERON:0001894!4.02e-07!7;UBERON:0006222!4.02e-07!7;UBERON:0000922!4.82e-07!612;UBERON:0001046!4.92e-07!19;UBERON:0002050!6.91e-07!605;UBERON:0005423!6.91e-07!605;UBERON:0000483!8.10e-07!309
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}}
}}

Revision as of 14:22, 5 September 2012


Full id: C2722_skeletal_Mast_leiomyoma_bladder_Smooth_uterus_placenta



Phase1 CAGE Peaks

Hg19::chr3:141150883..141150961,+p6@ZBTB38
Hg19::chr3:141150971..141150978,+p60@ZBTB38
Hg19::chr3:141151009..141151033,+p10@ZBTB38
Hg19::chr3:141151044..141151053,+p51@ZBTB38


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>


Uber Anatomy
Ontology termp-valuen
adult organism7.90e-55115
neural tube4.89e-2557
neural rod4.89e-2557
future spinal cord4.89e-2557
neural keel4.89e-2557
regional part of brain3.97e-2259
anterior neural tube1.36e-2142
regional part of forebrain4.46e-2141
forebrain4.46e-2141
future forebrain4.46e-2141
regional part of nervous system6.03e-2094
nervous system6.03e-2094
brain2.07e-1869
future brain2.07e-1869
neural plate1.19e-1786
presumptive neural plate1.19e-1786
neurectoderm3.45e-1790
central nervous system6.14e-1782
telencephalon8.93e-1634
gray matter1.01e-1534
brain grey matter1.01e-1534
regional part of telencephalon5.04e-1533
cerebral hemisphere2.71e-1432
pre-chordal neural plate2.87e-1461
anatomical conduit7.12e-12241
regional part of cerebral cortex8.09e-1222
neocortex1.42e-1020
ectoderm-derived structure2.15e-10169
ectoderm2.47e-10173
presumptive ectoderm2.47e-10173
anterior region of body2.97e-10129
craniocervical region2.97e-10129
head7.13e-10123
cerebral cortex9.93e-1025
pallium9.93e-1025
organ1.26e-09511
anatomical cluster3.84e-09286
tube8.65e-09194
basal ganglion4.12e-089
nuclear complex of neuraxis4.12e-089
aggregate regional part of brain4.12e-089
collection of basal ganglia4.12e-089
cerebral subcortex4.12e-089
multi-tissue structure4.78e-08347
nucleus of brain5.01e-089
neural nucleus5.01e-089
brainstem1.21e-078
multi-cellular organism3.98e-07659
diencephalon4.02e-077
future diencephalon4.02e-077
embryo4.82e-07612
hindgut4.92e-0719
embryonic structure6.91e-07605
developing anatomical structure6.91e-07605
epithelium8.10e-07309


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
BHLHE40#8553444.87181354697742.46312701995675e-071.28623261418632e-05
GATA2#2624412.7449317335543.78864877853583e-050.000723104330741053
TBP#690843.706770687096390.005296377814784350.0244734272452996
TRIM28#10155418.59052504526258.36730015875654e-060.000230694947539698
USF1#739146.361499277207960.0006105011399140830.00508575644504163
USF2#7392412.99219738506963.50833029870167e-050.00068219420604376



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.