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Coexpression cluster:C2380: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.81e-29!115;UBERON:0003075!1.71e-22!86;UBERON:0007284!1.71e-22!86;UBERON:0001049!4.24e-22!57;UBERON:0005068!4.24e-22!57;UBERON:0006241!4.24e-22!57;UBERON:0007135!4.24e-22!57;UBERON:0005743!8.24e-22!86;UBERON:0001017!6.68e-21!82;UBERON:0000477!7.89e-21!286;UBERON:0002616!2.41e-19!59;UBERON:0002346!2.64e-19!90;UBERON:0000955!2.88e-19!69;UBERON:0006238!2.88e-19!69;UBERON:0004111!3.22e-19!241;UBERON:0000025!3.28e-19!194;UBERON:0000073!7.10e-18!94;UBERON:0001016!7.10e-18!94;UBERON:0000033!6.22e-17!123;UBERON:0000153!2.40e-16!129;UBERON:0007811!2.40e-16!129;UBERON:0003080!3.83e-16!42;UBERON:0003056!5.52e-16!61;UBERON:0002780!9.98e-16!41;UBERON:0001890!9.98e-16!41;UBERON:0006240!9.98e-16!41;UBERON:0000119!1.00e-15!312;UBERON:0000483!2.48e-15!309;UBERON:0002020!1.72e-13!34;UBERON:0003528!1.72e-13!34;UBERON:0001893!2.60e-13!34;UBERON:0002791!6.99e-13!33;UBERON:0004121!9.47e-13!169;UBERON:0001869!2.48e-12!32;UBERON:0001986!2.97e-11!18;UBERON:0004638!2.97e-11!18;UBERON:0004852!2.97e-11!18;UBERON:0000924!3.23e-11!173;UBERON:0006601!3.23e-11!173;UBERON:0000956!7.19e-09!25;UBERON:0000203!7.19e-09!25;UBERON:0000481!9.80e-09!347;UBERON:0000467!9.89e-09!625;UBERON:0000487!1.56e-08!22;UBERON:0000480!1.81e-08!626;UBERON:0002619!3.12e-08!22;UBERON:0002049!8.30e-08!79;UBERON:0007798!8.30e-08!79;UBERON:0000475!2.05e-07!365;UBERON:0003076!3.35e-07!15;UBERON:0003057!3.35e-07!15;UBERON:0001950!3.47e-07!20;UBERON:0002050!9.58e-07!605;UBERON:0005423!9.58e-07!605;UBERON:0000055!9.59e-07!69
|ontology_enrichment_uberon=UBERON:0007023!1.81e-29!115;UBERON:0003075!1.71e-22!86;UBERON:0007284!1.71e-22!86;UBERON:0001049!4.24e-22!57;UBERON:0005068!4.24e-22!57;UBERON:0006241!4.24e-22!57;UBERON:0007135!4.24e-22!57;UBERON:0005743!8.24e-22!86;UBERON:0001017!6.68e-21!82;UBERON:0000477!7.89e-21!286;UBERON:0002616!2.41e-19!59;UBERON:0002346!2.64e-19!90;UBERON:0000955!2.88e-19!69;UBERON:0006238!2.88e-19!69;UBERON:0004111!3.22e-19!241;UBERON:0000025!3.28e-19!194;UBERON:0000073!7.10e-18!94;UBERON:0001016!7.10e-18!94;UBERON:0000033!6.22e-17!123;UBERON:0000153!2.40e-16!129;UBERON:0007811!2.40e-16!129;UBERON:0003080!3.83e-16!42;UBERON:0003056!5.52e-16!61;UBERON:0002780!9.98e-16!41;UBERON:0001890!9.98e-16!41;UBERON:0006240!9.98e-16!41;UBERON:0000119!1.00e-15!312;UBERON:0000483!2.48e-15!309;UBERON:0002020!1.72e-13!34;UBERON:0003528!1.72e-13!34;UBERON:0001893!2.60e-13!34;UBERON:0002791!6.99e-13!33;UBERON:0004121!9.47e-13!169;UBERON:0001869!2.48e-12!32;UBERON:0001986!2.97e-11!18;UBERON:0004638!2.97e-11!18;UBERON:0004852!2.97e-11!18;UBERON:0000924!3.23e-11!173;UBERON:0006601!3.23e-11!173;UBERON:0000956!7.19e-09!25;UBERON:0000203!7.19e-09!25;UBERON:0000481!9.80e-09!347;UBERON:0000467!9.89e-09!625;UBERON:0000487!1.56e-08!22;UBERON:0000480!1.81e-08!626;UBERON:0002619!3.12e-08!22;UBERON:0002049!8.30e-08!79;UBERON:0007798!8.30e-08!79;UBERON:0000475!2.05e-07!365;UBERON:0003076!3.35e-07!15;UBERON:0003057!3.35e-07!15;UBERON:0001950!3.47e-07!20;UBERON:0002050!9.58e-07!605;UBERON:0005423!9.58e-07!605;UBERON:0000055!9.59e-07!69
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}}
}}

Revision as of 12:48, 5 September 2012


Full id: C2380_Melanocyte_mesothelioma_Renal_Neural_renal_Endothelial_Hepatic



Phase1 CAGE Peaks

Hg19::chr16:57662515..57662526,+p8@GPR56
Hg19::chr16:57662527..57662556,+p1@GPR56
Hg19::chr16:57662566..57662582,+p6@GPR56
Hg19::chr16:57662596..57662613,+p2@GPR56


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 organism1.81e-29115
neural plate1.71e-2286
presumptive neural plate1.71e-2286
neural tube4.24e-2257
neural rod4.24e-2257
future spinal cord4.24e-2257
neural keel4.24e-2257
central nervous system6.68e-2182
anatomical cluster7.89e-21286
regional part of brain2.41e-1959
neurectoderm2.64e-1990
brain2.88e-1969
future brain2.88e-1969
anatomical conduit3.22e-19241
tube3.28e-19194
regional part of nervous system7.10e-1894
nervous system7.10e-1894
head6.22e-17123
anterior region of body2.40e-16129
craniocervical region2.40e-16129
anterior neural tube3.83e-1642
pre-chordal neural plate5.52e-1661
regional part of forebrain9.98e-1641
forebrain9.98e-1641
future forebrain9.98e-1641
cell layer1.00e-15312
epithelium2.48e-15309
gray matter1.72e-1334
brain grey matter1.72e-1334
telencephalon2.60e-1334
regional part of telencephalon6.99e-1333
ectoderm-derived structure9.47e-13169
cerebral hemisphere2.48e-1232
endothelium2.97e-1118
blood vessel endothelium2.97e-1118
cardiovascular system endothelium2.97e-1118
ectoderm3.23e-11173
presumptive ectoderm3.23e-11173
cerebral cortex7.19e-0925
pallium7.19e-0925
multi-tissue structure9.80e-09347
anatomical system9.89e-09625
simple squamous epithelium1.56e-0822
anatomical group1.81e-08626
regional part of cerebral cortex3.12e-0822
vasculature8.30e-0879
vascular system8.30e-0879
organism subdivision2.05e-07365
posterior neural tube3.35e-0715
chordal neural plate3.35e-0715
neocortex3.47e-0720
embryonic structure9.58e-07605
developing anatomical structure9.58e-07605
vessel9.59e-0769


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
CEBPB#105147.971147625824820.0002476385788090830.00267928369752841
CTCF#1066445.360256373075030.001211145381643620.00816807519782244
EGR1#195844.988179094810140.001615011500076050.0101388666780742
ESR1#2099430.76860329615451.11467714392546e-064.60323314489643e-05
FOS#235348.99795530889440.0001525147711168630.00194748626735225
FOSL1#8061439.7135797163734.01511434669553e-071.93867095355772e-05
FOSL2#2355416.93020060456171.2165416097647e-050.000303377242555434
HDAC8#558691194.1460084033610.005140863901003430.0239028886544786
IRF1#365947.63716375356390.0002938853996185490.00307238210718335
JUN#3725412.51282919233634.07770316866756e-050.000742712314671209
JUNB#3726430.61063265982111.13787152942193e-064.65666789425146e-05
JUND#372746.994663941871030.000417684217818580.00391444023912013
NR3C1#2908414.9730233311731.98868032687801e-050.000442659387593377
RAD21#5885410.35503389545638.6948481184721e-050.00129282637050841
SMARCB1#6598418.25271578115749.00423392720929e-060.000241188301391077
SMARCC1#6599443.66335931963152.74744977017458e-071.40588391252946e-05
SMC3#9126415.04493284493281.95092670935632e-050.000437519507404906
ZNF263#1012748.221841637010680.0002187871180958320.00248611770501693



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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