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Coexpression cluster:C3416: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003075!5.40e-26!86;UBERON:0007284!5.40e-26!86;UBERON:0002346!2.15e-25!90;UBERON:0005743!1.68e-23!86;UBERON:0000073!3.91e-22!94;UBERON:0001016!3.91e-22!94;UBERON:0003056!5.75e-22!61;UBERON:0001017!3.12e-21!82;UBERON:0001049!4.05e-19!57;UBERON:0005068!4.05e-19!57;UBERON:0006241!4.05e-19!57;UBERON:0007135!4.05e-19!57;UBERON:0002616!8.15e-19!59;UBERON:0000153!1.67e-16!129;UBERON:0007811!1.67e-16!129;UBERON:0000955!1.95e-16!69;UBERON:0006238!1.95e-16!69;UBERON:0000033!6.70e-16!123;UBERON:0004121!7.30e-16!169;UBERON:0000924!8.01e-16!173;UBERON:0006601!8.01e-16!173;UBERON:0007023!2.11e-15!115;UBERON:0002780!5.04e-13!41;UBERON:0001890!5.04e-13!41;UBERON:0006240!5.04e-13!41;UBERON:0003080!6.23e-13!42;UBERON:0000064!2.06e-12!219;UBERON:0003887!3.39e-11!21;UBERON:0002020!3.50e-11!34;UBERON:0003528!3.50e-11!34;UBERON:0000080!4.68e-11!18;UBERON:0002120!4.68e-11!18;UBERON:0004875!4.68e-11!18;UBERON:0005721!4.68e-11!18;UBERON:0005754!4.68e-11!18;UBERON:0007297!4.68e-11!18;UBERON:0001893!5.64e-11!34;UBERON:0002104!6.50e-11!21;UBERON:0002791!9.01e-11!33;UBERON:0006555!9.90e-11!17;UBERON:0005103!9.90e-11!17;UBERON:0000083!9.90e-11!17;UBERON:0009201!9.90e-11!17;UBERON:0004819!9.90e-11!17;UBERON:0006553!9.90e-11!17;UBERON:0003074!9.90e-11!17;UBERON:0003060!9.90e-11!17;UBERON:0004211!1.17e-10!16;UBERON:0001285!1.17e-10!16;UBERON:0007684!1.17e-10!16;UBERON:0003220!1.17e-10!16;UBERON:0004208!1.17e-10!16;UBERON:0000970!1.34e-10!20;UBERON:0000019!1.41e-10!19;UBERON:0000047!1.41e-10!19;UBERON:0004088!1.41e-10!19;UBERON:0003072!1.41e-10!19;UBERON:0003071!1.41e-10!19;UBERON:0004128!1.41e-10!19;UBERON:0001869!1.55e-10!32;UBERON:0004876!1.23e-09!20;UBERON:0001032!2.85e-09!24;UBERON:0004456!2.85e-09!24;UBERON:0001456!5.51e-09!21;UBERON:0000020!6.05e-09!23;UBERON:0000956!7.10e-09!25;UBERON:0000203!7.10e-09!25;UBERON:0001225!1.06e-08!13;UBERON:0008987!1.06e-08!13;UBERON:0009773!2.35e-08!12;UBERON:0001231!2.35e-08!12;UBERON:0004810!2.35e-08!12;UBERON:0000119!5.99e-08!312;UBERON:0007625!6.20e-08!11;UBERON:0000483!1.02e-07!309;UBERON:0003076!1.25e-07!15;UBERON:0003057!1.25e-07!15;UBERON:0001801!1.50e-07!14;UBERON:0000058!2.74e-07!26;UBERON:0002619!2.89e-07!22;UBERON:0000353!3.28e-07!17;UBERON:0000481!3.99e-07!347;UBERON:0001851!4.06e-07!16;UBERON:0000025!4.95e-07!194;UBERON:0004732!6.16e-07!13;UBERON:0000922!7.62e-07!612;UBERON:0001950!8.27e-07!20
|ontology_enrichment_uberon=UBERON:0003075!5.40e-26!86;UBERON:0007284!5.40e-26!86;UBERON:0002346!2.15e-25!90;UBERON:0005743!1.68e-23!86;UBERON:0000073!3.91e-22!94;UBERON:0001016!3.91e-22!94;UBERON:0003056!5.75e-22!61;UBERON:0001017!3.12e-21!82;UBERON:0001049!4.05e-19!57;UBERON:0005068!4.05e-19!57;UBERON:0006241!4.05e-19!57;UBERON:0007135!4.05e-19!57;UBERON:0002616!8.15e-19!59;UBERON:0000153!1.67e-16!129;UBERON:0007811!1.67e-16!129;UBERON:0000955!1.95e-16!69;UBERON:0006238!1.95e-16!69;UBERON:0000033!6.70e-16!123;UBERON:0004121!7.30e-16!169;UBERON:0000924!8.01e-16!173;UBERON:0006601!8.01e-16!173;UBERON:0007023!2.11e-15!115;UBERON:0002780!5.04e-13!41;UBERON:0001890!5.04e-13!41;UBERON:0006240!5.04e-13!41;UBERON:0003080!6.23e-13!42;UBERON:0000064!2.06e-12!219;UBERON:0003887!3.39e-11!21;UBERON:0002020!3.50e-11!34;UBERON:0003528!3.50e-11!34;UBERON:0000080!4.68e-11!18;UBERON:0002120!4.68e-11!18;UBERON:0004875!4.68e-11!18;UBERON:0005721!4.68e-11!18;UBERON:0005754!4.68e-11!18;UBERON:0007297!4.68e-11!18;UBERON:0001893!5.64e-11!34;UBERON:0002104!6.50e-11!21;UBERON:0002791!9.01e-11!33;UBERON:0006555!9.90e-11!17;UBERON:0005103!9.90e-11!17;UBERON:0000083!9.90e-11!17;UBERON:0009201!9.90e-11!17;UBERON:0004819!9.90e-11!17;UBERON:0006553!9.90e-11!17;UBERON:0003074!9.90e-11!17;UBERON:0003060!9.90e-11!17;UBERON:0004211!1.17e-10!16;UBERON:0001285!1.17e-10!16;UBERON:0007684!1.17e-10!16;UBERON:0003220!1.17e-10!16;UBERON:0004208!1.17e-10!16;UBERON:0000970!1.34e-10!20;UBERON:0000019!1.41e-10!19;UBERON:0000047!1.41e-10!19;UBERON:0004088!1.41e-10!19;UBERON:0003072!1.41e-10!19;UBERON:0003071!1.41e-10!19;UBERON:0004128!1.41e-10!19;UBERON:0001869!1.55e-10!32;UBERON:0004876!1.23e-09!20;UBERON:0001032!2.85e-09!24;UBERON:0004456!2.85e-09!24;UBERON:0001456!5.51e-09!21;UBERON:0000020!6.05e-09!23;UBERON:0000956!7.10e-09!25;UBERON:0000203!7.10e-09!25;UBERON:0001225!1.06e-08!13;UBERON:0008987!1.06e-08!13;UBERON:0009773!2.35e-08!12;UBERON:0001231!2.35e-08!12;UBERON:0004810!2.35e-08!12;UBERON:0000119!5.99e-08!312;UBERON:0007625!6.20e-08!11;UBERON:0000483!1.02e-07!309;UBERON:0003076!1.25e-07!15;UBERON:0003057!1.25e-07!15;UBERON:0001801!1.50e-07!14;UBERON:0000058!2.74e-07!26;UBERON:0002619!2.89e-07!22;UBERON:0000353!3.28e-07!17;UBERON:0000481!3.99e-07!347;UBERON:0001851!4.06e-07!16;UBERON:0000025!4.95e-07!194;UBERON:0004732!6.16e-07!13;UBERON:0000922!7.62e-07!612;UBERON:0001950!8.27e-07!20
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}}
}}

Revision as of 13:16, 5 September 2012


Full id: C3416_Alveolar_Renal_Mesothelial_Retinal_mesothelioma_mesenchymal_Ciliary



Phase1 CAGE Peaks

Hg19::chr14:24641209..24641246,+p2@REC8
Hg19::chr14:24641247..24641304,+p1@REC8
Hg19::chr14:24641311..24641322,+p3@REC8


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
neural plate5.40e-2686
presumptive neural plate5.40e-2686
neurectoderm2.15e-2590
regional part of nervous system3.91e-2294
nervous system3.91e-2294
pre-chordal neural plate5.75e-2261
central nervous system3.12e-2182
neural tube4.05e-1957
neural rod4.05e-1957
future spinal cord4.05e-1957
neural keel4.05e-1957
regional part of brain8.15e-1959
anterior region of body1.67e-16129
craniocervical region1.67e-16129
brain1.95e-1669
future brain1.95e-1669
head6.70e-16123
ectoderm-derived structure7.30e-16169
ectoderm8.01e-16173
presumptive ectoderm8.01e-16173
adult organism2.11e-15115
regional part of forebrain5.04e-1341
forebrain5.04e-1341
future forebrain5.04e-1341
anterior neural tube6.23e-1342
organ part2.06e-12219
intraembryonic coelom3.39e-1121
gray matter3.50e-1134
brain grey matter3.50e-1134
mesonephros4.68e-1118
pronephros4.68e-1118
nephrogenic cord4.68e-1118
pronephric mesoderm4.68e-1118
rostral part of nephrogenic cord4.68e-1118
presumptive pronephric mesoderm4.68e-1118
telencephalon5.64e-1134
visual system6.50e-1121
regional part of telencephalon9.01e-1133
excretory tube9.90e-1117
mesonephric epithelium9.90e-1117
mesonephric tubule9.90e-1117
nephric duct9.90e-1117
kidney epithelium9.90e-1117
renal duct9.90e-1117
mesonephric duct9.90e-1117
pronephric duct9.90e-1117
nephron epithelium1.17e-1016
nephron1.17e-1016
uriniferous tubule1.17e-1016
metanephric mesenchyme1.17e-1016
nephrogenic mesenchyme1.17e-1016
eye1.34e-1020
camera-type eye1.41e-1019
simple eye1.41e-1019
ocular region1.41e-1019
optic cup1.41e-1019
eye primordium1.41e-1019
optic vesicle1.41e-1019
cerebral hemisphere1.55e-1032
urogenital ridge1.23e-0920
sensory system2.85e-0924
entire sense organ system2.85e-0924
face5.51e-0921
sense organ6.05e-0923
cerebral cortex7.10e-0925
pallium7.10e-0925
cortex of kidney1.06e-0813
renal parenchyma1.06e-0813
renal tubule2.35e-0812
nephron tubule2.35e-0812
nephron tubule epithelium2.35e-0812
cell layer5.99e-08312
pigment epithelium of eye6.20e-0811
epithelium1.02e-07309
posterior neural tube1.25e-0715
chordal neural plate1.25e-0715
anterior segment of eyeball1.50e-0714
duct2.74e-0726
regional part of cerebral cortex2.89e-0722
parenchyma3.28e-0717
multi-tissue structure3.99e-07347
cortex4.06e-0716
tube4.95e-07194
segmental subdivision of nervous system6.16e-0713
embryo7.62e-07612
neocortex8.27e-0720


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
ATF3#467214.97544968400580.005768294540793880.0259491261865081
EBF1#187938.9064668465690.00141523283560980.00913620361714998
EGR1#195834.988179094810140.008056488137383440.0319709538939201
ELF1#199734.258097958807540.01295179875054610.0461002286724928
EP300#203336.77394172622320.003216880500103790.0167164783834382
JUND#372736.994663941871030.002921845042734990.0156409315437314
PAX5#507936.669565531177830.003370290999677260.0172594793427132
POU2F2#545239.106124057742520.001324165192682130.0088080051307897
RFX5#5993312.04791082719510.0005717246050312580.00483719588665421
RXRA#6256213.38307809275550.007196434429465730.0298202037525381
SP1#666735.69838137814090.005403962701712170.0245908439982623
YY1#752834.911170749853860.008441455341808260.0328569303236103



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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