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Coexpression cluster:C3614: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005256!2.32e-12!143;UBERON:0003104!1.03e-11!238;UBERON:0009142!1.03e-11!238;UBERON:0002100!6.95e-11!216;UBERON:0000486!1.86e-10!82;UBERON:0000490!6.97e-10!138;UBERON:0004290!4.70e-09!70;UBERON:0003914!5.43e-09!118;UBERON:0000914!6.13e-09!83;UBERON:0002329!6.13e-09!83;UBERON:0003077!6.13e-09!83;UBERON:0003059!6.13e-09!83;UBERON:0007282!6.13e-09!83;UBERON:0009618!6.13e-09!83;UBERON:0007285!6.13e-09!83;UBERON:0004211!1.51e-08!16;UBERON:0001285!1.51e-08!16;UBERON:0007684!1.51e-08!16;UBERON:0003220!1.51e-08!16;UBERON:0004208!1.51e-08!16;UBERON:0001134!6.71e-08!61;UBERON:0002036!6.71e-08!61;UBERON:0003082!6.71e-08!61;UBERON:0006555!1.24e-07!17;UBERON:0005103!1.24e-07!17;UBERON:0000083!1.24e-07!17;UBERON:0009201!1.24e-07!17;UBERON:0004819!1.24e-07!17;UBERON:0006553!1.24e-07!17;UBERON:0003074!1.24e-07!17;UBERON:0003060!1.24e-07!17;UBERON:0009569!1.84e-07!113;UBERON:0002385!4.20e-07!63;UBERON:0001015!4.20e-07!63;UBERON:0000383!4.20e-07!63;UBERON:0001225!4.26e-07!13;UBERON:0008987!4.26e-07!13;UBERON:0006554!6.09e-07!44;UBERON:0000353!9.04e-07!17;UBERON:0009773!9.19e-07!12;UBERON:0001231!9.19e-07!12;UBERON:0004810!9.19e-07!12
|ontology_enrichment_uberon=UBERON:0005256!2.32e-12!143;UBERON:0003104!1.03e-11!238;UBERON:0009142!1.03e-11!238;UBERON:0002100!6.95e-11!216;UBERON:0000486!1.86e-10!82;UBERON:0000490!6.97e-10!138;UBERON:0004290!4.70e-09!70;UBERON:0003914!5.43e-09!118;UBERON:0000914!6.13e-09!83;UBERON:0002329!6.13e-09!83;UBERON:0003077!6.13e-09!83;UBERON:0003059!6.13e-09!83;UBERON:0007282!6.13e-09!83;UBERON:0009618!6.13e-09!83;UBERON:0007285!6.13e-09!83;UBERON:0004211!1.51e-08!16;UBERON:0001285!1.51e-08!16;UBERON:0007684!1.51e-08!16;UBERON:0003220!1.51e-08!16;UBERON:0004208!1.51e-08!16;UBERON:0001134!6.71e-08!61;UBERON:0002036!6.71e-08!61;UBERON:0003082!6.71e-08!61;UBERON:0006555!1.24e-07!17;UBERON:0005103!1.24e-07!17;UBERON:0000083!1.24e-07!17;UBERON:0009201!1.24e-07!17;UBERON:0004819!1.24e-07!17;UBERON:0006553!1.24e-07!17;UBERON:0003074!1.24e-07!17;UBERON:0003060!1.24e-07!17;UBERON:0009569!1.84e-07!113;UBERON:0002385!4.20e-07!63;UBERON:0001015!4.20e-07!63;UBERON:0000383!4.20e-07!63;UBERON:0001225!4.26e-07!13;UBERON:0008987!4.26e-07!13;UBERON:0006554!6.09e-07!44;UBERON:0000353!9.04e-07!17;UBERON:0009773!9.19e-07!12;UBERON:0001231!9.19e-07!12;UBERON:0004810!9.19e-07!12
|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296202038742892!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461647353233092!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401892467370434!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269328752427845!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460359206534895!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172764219944681!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370686184077201!SP1#6667;3:5.6983813781409:0.00540396270171217:0.02461765945233!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542186634602654!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328887993151948!ZBTB33#10009;2:21.1098166866541:0.00292859706060324:0.0156322062972678!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388745109968356!ZZZ3#26009;1:79.8044041450777:0.012478437908258:0.0451602875008855
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}}
}}

Revision as of 12:38, 5 September 2012


Full id: C3614_Alveolar_Mesenchymal_Renal_Placental_embryonic_Corneal_Smooth



Phase1 CAGE Peaks

Hg19::chr17:21117465..21117496,-p1@TMEM11
Hg19::chr17:3572087..3572119,+p1@TMEM93
Hg19::chr17:40925460..40925496,+p1@VPS25


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
animal cell2.43e-35679
eukaryotic cell2.43e-35679
epithelial cell1.19e-24254
embryonic cell1.19e-24248
native cell2.44e-21722
somatic cell3.10e-18591
non-terminally differentiated cell5.80e-16180
mesodermal cell1.05e-12119
contractile cell2.85e-1059
electrically responsive cell3.70e-0960
electrically active cell3.70e-0960
ectodermal cell6.83e-0971
epithelial cell of nephron1.51e-0816
smooth muscle cell1.92e-0842
smooth muscle myoblast1.92e-0842
muscle cell3.99e-0854
kidney cell6.97e-0818
kidney epithelial cell6.97e-0818
muscle precursor cell7.68e-0857
myoblast7.68e-0857
multi-potent skeletal muscle stem cell7.68e-0857
kidney cortical cell4.26e-0713
renal cortical epithelial cell4.26e-0713
ecto-epithelial cell5.63e-0733
kidney tubule cell9.19e-0712
nephron tubule epithelial cell9.19e-0712
Uber Anatomy
Ontology termp-valuen
trunk mesenchyme2.32e-12143
mesenchyme1.03e-11238
entire embryonic mesenchyme1.03e-11238
trunk6.95e-11216
multilaminar epithelium1.86e-1082
unilaminar epithelium6.97e-10138
dermomyotome4.70e-0970
epithelial tube5.43e-09118
somite6.13e-0983
paraxial mesoderm6.13e-0983
presomitic mesoderm6.13e-0983
presumptive segmental plate6.13e-0983
trunk paraxial mesoderm6.13e-0983
presumptive paraxial mesoderm6.13e-0983
nephron epithelium1.51e-0816
nephron1.51e-0816
uriniferous tubule1.51e-0816
metanephric mesenchyme1.51e-0816
nephrogenic mesenchyme1.51e-0816
skeletal muscle tissue6.71e-0861
striated muscle tissue6.71e-0861
myotome6.71e-0861
excretory tube1.24e-0717
mesonephric epithelium1.24e-0717
mesonephric tubule1.24e-0717
nephric duct1.24e-0717
kidney epithelium1.24e-0717
renal duct1.24e-0717
mesonephric duct1.24e-0717
pronephric duct1.24e-0717
subdivision of trunk1.84e-07113
muscle tissue4.20e-0763
musculature4.20e-0763
musculature of body4.20e-0763
cortex of kidney4.26e-0713
renal parenchyma4.26e-0713
urinary system structure6.09e-0744
parenchyma9.04e-0717
renal tubule9.19e-0712
nephron tubule9.19e-0712
nephron tubule epithelium9.19e-0712


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#672213.45615376214920.007119807716084560.0296202038742892
ELF1#199734.258097958807540.01295179875054610.0461647353233092
ELK4#2005210.8237877723120.01091284719516480.0401892467370434
NFKB1#479035.488063424193840.006049381815655430.0269328752427845
NR3C1#290829.982015554115360.01278474365547170.0460359206534895
PAX5#507936.669565531177830.003370290999677260.0172764219944681
SIX5#147912211.3911435703060.009873820081429030.0370686184077201
SP1#666735.69838137814090.005403962701712170.02461765945233
TAF7#6879311.43306940492390.0006690181981945830.00542186634602654
YY1#752834.911170749853860.008441455341808260.0328887993151948
ZBTB33#10009221.10981668665410.002928597060603240.0156322062972678
ZNF143#7702313.50087655222790.0004062804962997170.00388745109968356
ZZZ3#26009179.80440414507770.0124784379082580.0451602875008855



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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