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Coexpression cluster:C4053: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4053_papillotubular_Urothelial_mature_Chondrocyte_Prostate_Small_bile
|full_id=C4053_papillotubular_Urothelial_mature_Chondrocyte_Prostate_Small_bile
|id=C4053
|id=C4053

Revision as of 17:05, 12 September 2012


Full id: C4053_papillotubular_Urothelial_mature_Chondrocyte_Prostate_Small_bile



Phase1 CAGE Peaks

Hg19::chr20:56284940..56284953,-p5@PMEPA1
Hg19::chr20:56285010..56285034,-p2@PMEPA1
Hg19::chr20:56285061..56285080,-p1@PMEPA1


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
epithelial cell2.05e-09254
endo-epithelial cell4.38e-0843
respiratory epithelial cell1.53e-0713
Uber Anatomy
Ontology termp-valuen
embryo4.19e-13612
embryonic structure7.88e-13605
developing anatomical structure7.88e-13605
multi-cellular organism9.52e-13659
germ layer1.90e-12604
embryonic tissue1.90e-12604
presumptive structure1.90e-12604
epiblast (generic)1.90e-12604
organ3.55e-12511
anatomical system4.88e-12625
ectoderm-derived structure7.76e-12169
anatomical group9.13e-12626
ectoderm9.21e-12173
presumptive ectoderm9.21e-12173
organ part1.58e-10219
head1.93e-09123
anterior region of body7.11e-09129
craniocervical region7.11e-09129
central nervous system1.12e-0882
neural plate1.77e-0886
presumptive neural plate1.77e-0886
neurectoderm2.56e-0890
regional part of nervous system7.88e-0894
nervous system7.88e-0894
brain1.80e-0769
future brain1.80e-0769
neural tube1.86e-0757
neural rod1.86e-0757
future spinal cord1.86e-0757
neural keel1.86e-0757
organism subdivision2.14e-07365
pre-chordal neural plate3.06e-0761


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
BRCA1#672320.18423064322380.0001215704860271640.00164316034556632
CCNT2#90536.336201576962630.003930750035764890.0190321559103036
CTCF#1066435.360256373075030.0064925092527670.027988243441191
E2F1#186934.907389214879320.008460985347239390.032591629427962
EGR1#195834.988179094810140.008056488137383440.0321161710210386
EP300#203336.77394172622320.003216880500103790.016769043301739
IRF1#365937.63716375356390.002244692747297240.0128287986119611
JUND#372736.994663941871030.002921845042734990.0157012901681605
MYC#460935.22228187160940.007020843755740150.0294951689865545
NR3C1#2908314.9730233311730.0002978331194675480.00309260222351077
SP1#666735.69838137814090.005403962701712170.0246930548041703
ZBTB7A#5134137.35190930787590.002516255860282270.0140442093732375



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.