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Coexpression cluster:C3933: Difference between revisions

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|full_id=C3933_Hepatocyte_liver_mesenchymal_Dendritic_Adipocyte_Cardiac_chorionic
|full_id=C3933_Hepatocyte_liver_mesenchymal_Dendritic_Adipocyte_Cardiac_chorionic
|id=C3933
|id=C3933
|ontology_enrichment_celltype=CL:0000680!3.61e-14!57;CL:0000056!3.61e-14!57;CL:0000355!3.61e-14!57;CL:0000187!6.23e-14!54;CL:0000192!1.03e-12!42;CL:0000514!1.03e-12!42;CL:0000183!3.47e-11!59;CL:0000393!4.11e-11!60;CL:0000211!4.11e-11!60;CL:0000136!3.57e-10!15;CL:0000359!1.14e-08!32;CL:0000055!1.13e-07!180;CL:0002494!5.57e-07!16
|ontology_enrichment_celltype=CL:0000187!4.15e-15!55;CL:0000680!1.91e-14!58;CL:0000056!1.91e-14!58;CL:0000355!1.91e-14!58;CL:0000192!1.15e-13!43;CL:0000514!1.15e-13!43;CL:0000183!4.44e-13!59;CL:0000393!3.52e-12!61;CL:0000211!3.52e-12!61;CL:0000136!8.65e-11!15;CL:0000359!3.71e-08!32
|ontology_enrichment_disease=DOID:2394!7.22e-09!14
|ontology_enrichment_disease=DOID:2394!2.44e-10!14
|ontology_enrichment_uberon=UBERON:0007023!1.82e-27!115;UBERON:0002385!7.30e-15!63;UBERON:0001015!7.30e-15!63;UBERON:0000383!7.30e-15!63;UBERON:0001134!2.60e-14!61;UBERON:0002036!2.60e-14!61;UBERON:0003082!2.60e-14!61;UBERON:0004111!4.55e-13!241;UBERON:0004290!1.95e-12!70;UBERON:0000025!3.83e-12!194;UBERON:0000477!3.99e-11!286;UBERON:0001049!1.95e-10!57;UBERON:0005068!1.95e-10!57;UBERON:0006241!1.95e-10!57;UBERON:0007135!1.95e-10!57;UBERON:0000468!2.03e-10!659;UBERON:0000914!3.92e-10!83;UBERON:0002329!3.92e-10!83;UBERON:0003077!3.92e-10!83;UBERON:0003059!3.92e-10!83;UBERON:0007282!3.92e-10!83;UBERON:0009618!3.92e-10!83;UBERON:0007285!3.92e-10!83;UBERON:0000475!3.96e-10!365;UBERON:0007100!4.48e-10!27;UBERON:0002616!7.93e-10!59;UBERON:0000486!1.03e-09!82;UBERON:0000467!1.68e-09!625;UBERON:0000480!2.38e-09!626;UBERON:0004872!2.49e-09!84;UBERON:0000948!2.83e-09!24;UBERON:0005498!2.83e-09!24;UBERON:0004140!2.83e-09!24;UBERON:0009881!2.83e-09!24;UBERON:0004141!2.83e-09!24;UBERON:0003084!2.83e-09!24;UBERON:0007005!2.83e-09!24;UBERON:0004139!2.83e-09!24;UBERON:0004291!2.83e-09!24;UBERON:0000483!3.93e-09!309;UBERON:0004573!1.08e-08!33;UBERON:0004571!1.08e-08!33;UBERON:0000119!1.24e-08!312;UBERON:0003080!1.82e-08!42;UBERON:0000955!3.14e-08!69;UBERON:0006238!3.14e-08!69;UBERON:0002780!3.66e-08!41;UBERON:0001890!3.66e-08!41;UBERON:0006240!3.66e-08!41;UBERON:0000923!1.01e-07!604;UBERON:0005291!1.01e-07!604;UBERON:0006598!1.01e-07!604;UBERON:0002532!1.01e-07!604;UBERON:0001135!1.18e-07!15;UBERON:0005256!1.34e-07!143;UBERON:0002050!1.38e-07!605;UBERON:0005423!1.38e-07!605;UBERON:0003075!1.43e-07!86;UBERON:0007284!1.43e-07!86;UBERON:0002346!2.62e-07!90;UBERON:0000479!2.90e-07!787;UBERON:0000922!3.37e-07!612;UBERON:0000481!3.45e-07!347;UBERON:0001017!4.66e-07!82;UBERON:0001637!5.05e-07!42;UBERON:0003509!5.05e-07!42;UBERON:0004572!5.05e-07!42;UBERON:0002020!5.47e-07!34;UBERON:0003528!5.47e-07!34;UBERON:0001893!6.65e-07!34;UBERON:0005743!8.59e-07!86;UBERON:0003914!9.29e-07!118
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}}
}}

Revision as of 15:31, 19 October 2012


Full id: C3933_Hepatocyte_liver_mesenchymal_Dendritic_Adipocyte_Cardiac_chorionic



Phase1 CAGE Peaks

Hg19::chr1:209878182..209878203,+p1@HSD11B1
Hg19::chr1:209878218..209878229,+p3@HSD11B1
Hg19::chr1:209878230..209878248,+p2@HSD11B1


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism6.20e-23114
muscle tissue4.21e-1464
musculature4.21e-1464
musculature of body4.21e-1464
skeletal muscle tissue2.09e-1362
striated muscle tissue2.09e-1362
myotome2.09e-1362
tube1.57e-12192
anatomical conduit1.68e-11240
paraxial mesoderm1.79e-1172
presumptive paraxial mesoderm1.79e-1172
somite3.22e-1171
presomitic mesoderm3.22e-1171
presumptive segmental plate3.22e-1171
dermomyotome3.22e-1171
trunk paraxial mesoderm3.22e-1171
dense mesenchyme tissue4.13e-1173
trunk mesenchyme1.00e-09122
splanchnic layer of lateral plate mesoderm2.07e-0983
multilaminar epithelium4.55e-0983
mesoderm5.31e-09315
mesoderm-derived structure5.31e-09315
presumptive mesoderm5.31e-09315
epithelial vesicle6.13e-0978
primary circulatory organ7.86e-0927
systemic artery8.13e-0933
systemic arterial system8.13e-0933
tissue9.62e-09773
neural tube1.73e-0856
neural rod1.73e-0856
future spinal cord1.73e-0856
neural keel1.73e-0856
epithelium2.52e-08306
regional part of nervous system2.91e-0853
regional part of brain2.91e-0853
smooth muscle tissue4.40e-0815
cell layer5.97e-08309
heart6.51e-0824
primitive heart tube6.51e-0824
primary heart field6.51e-0824
anterior lateral plate mesoderm6.51e-0824
heart tube6.51e-0824
heart primordium6.51e-0824
cardiac mesoderm6.51e-0824
cardiogenic plate6.51e-0824
heart rudiment6.51e-0824
epithelial tube1.35e-07117
multi-cellular organism3.21e-07656
multi-tissue structure4.21e-07342
artery8.36e-0742
arterial blood vessel8.36e-0742
arterial system8.36e-0742
germ layer8.79e-07560
germ layer / neural crest8.79e-07560
embryonic tissue8.79e-07560
presumptive structure8.79e-07560
germ layer / neural crest derived structure8.79e-07560
epiblast (generic)8.79e-07560
trunk8.88e-07199
Disease
Ontology termp-valuen
ovarian cancer2.44e-1014


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

No analysis results for this cluster

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.

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