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Coexpression cluster:C2803: Difference between revisions

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|full_id=C2803_granulosa_Fibroblast_Smooth_cholangiocellular_Mesenchymal_hepatic_mesenchymal
|full_id=C2803_granulosa_Fibroblast_Smooth_cholangiocellular_Mesenchymal_hepatic_mesenchymal
|id=C2803
|id=C2803
|ontology_enrichment_celltype=CL:0000055!1.45e-19!180;CL:0000057!1.00e-10!75;CL:0000222!3.03e-10!119;CL:0000680!5.65e-10!57;CL:0000056!5.65e-10!57;CL:0000355!5.65e-10!57;CL:0000187!3.14e-09!54;CL:0000393!1.27e-08!60;CL:0000211!1.27e-08!60;CL:0000359!1.46e-08!32;CL:0000183!1.85e-08!59;CL:0000192!1.17e-07!42;CL:0000514!1.17e-07!42
|ontology_enrichment_celltype=CL:0000680!1.99e-08!58;CL:0000056!1.99e-08!58;CL:0000355!1.99e-08!58;CL:0000057!2.12e-08!76;CL:0000187!1.16e-07!55;CL:0000359!2.22e-07!32;CL:0000055!5.79e-07!106;CL:0000393!7.14e-07!61;CL:0000211!7.14e-07!61;CL:0000222!8.64e-07!121
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000483!1.36e-25!309;UBERON:0000025!2.07e-25!194;UBERON:0000119!6.44e-25!312;UBERON:0000477!8.55e-25!286;UBERON:0004111!1.30e-24!241;UBERON:0000475!2.25e-23!365;UBERON:0001049!7.51e-19!57;UBERON:0005068!7.51e-19!57;UBERON:0006241!7.51e-19!57;UBERON:0007135!7.51e-19!57;UBERON:0000468!1.17e-18!659;UBERON:0003075!1.54e-17!86;UBERON:0007284!1.54e-17!86;UBERON:0004872!8.92e-17!84;UBERON:0002616!1.86e-16!59;UBERON:0002346!8.56e-16!90;UBERON:0000073!1.14e-15!94;UBERON:0001016!1.14e-15!94;UBERON:0000467!2.33e-15!625;UBERON:0001017!2.37e-15!82;UBERON:0005743!3.41e-15!86;UBERON:0000480!4.70e-15!626;UBERON:0002780!6.20e-15!41;UBERON:0001890!6.20e-15!41;UBERON:0006240!6.20e-15!41;UBERON:0003080!6.81e-15!42;UBERON:0001981!9.11e-15!60;UBERON:0007500!9.11e-15!60;UBERON:0004537!9.11e-15!60;UBERON:0006965!9.11e-15!60;UBERON:0001637!1.02e-14!42;UBERON:0003509!1.02e-14!42;UBERON:0004572!1.02e-14!42;UBERON:0000955!1.59e-14!69;UBERON:0006238!1.59e-14!69;UBERON:0000481!5.49e-14!347;UBERON:0002049!1.85e-13!79;UBERON:0007798!1.85e-13!79;UBERON:0003056!2.78e-13!61;UBERON:0000055!3.17e-13!69;UBERON:0002020!1.11e-12!34;UBERON:0003528!1.11e-12!34;UBERON:0001893!1.16e-12!34;UBERON:0002791!2.36e-12!33;UBERON:0004573!5.91e-12!33;UBERON:0004571!5.91e-12!33;UBERON:0001869!9.50e-12!32;UBERON:0000033!1.11e-11!123;UBERON:0004121!1.43e-11!169;UBERON:0000922!3.20e-11!612;UBERON:0002050!4.53e-11!605;UBERON:0005423!4.53e-11!605;UBERON:0000153!5.08e-11!129;UBERON:0007811!5.08e-11!129;UBERON:0000923!7.48e-11!604;UBERON:0005291!7.48e-11!604;UBERON:0006598!7.48e-11!604;UBERON:0002532!7.48e-11!604;UBERON:0000924!1.04e-10!173;UBERON:0006601!1.04e-10!173;UBERON:0003914!2.35e-10!118;UBERON:0004535!3.90e-10!110;UBERON:0001009!3.94e-10!113;UBERON:0000956!4.98e-10!25;UBERON:0000203!4.98e-10!25;UBERON:0001134!6.39e-10!61;UBERON:0002036!6.39e-10!61;UBERON:0003082!6.39e-10!61;UBERON:0007023!8.63e-10!115;UBERON:0002619!9.89e-10!22;UBERON:0002385!1.12e-09!63;UBERON:0001015!1.12e-09!63;UBERON:0000383!1.12e-09!63;UBERON:0000486!5.50e-09!82;UBERON:0001950!6.28e-09!20;UBERON:0000064!8.69e-09!219;UBERON:0004290!1.78e-08!70;UBERON:0000914!2.73e-08!83;UBERON:0002329!2.73e-08!83;UBERON:0003077!2.73e-08!83;UBERON:0003059!2.73e-08!83;UBERON:0007282!2.73e-08!83;UBERON:0009618!2.73e-08!83;UBERON:0007285!2.73e-08!83;UBERON:0000490!2.84e-08!138;UBERON:0000947!1.95e-07!21;UBERON:0010191!1.95e-07!21;UBERON:0000948!8.05e-07!24;UBERON:0005498!8.05e-07!24;UBERON:0004140!8.05e-07!24;UBERON:0009881!8.05e-07!24;UBERON:0004141!8.05e-07!24;UBERON:0003084!8.05e-07!24;UBERON:0007005!8.05e-07!24;UBERON:0004139!8.05e-07!24;UBERON:0004291!8.05e-07!24
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}}
}}

Revision as of 14:26, 19 October 2012


Full id: C2803_granulosa_Fibroblast_Smooth_cholangiocellular_Mesenchymal_hepatic_mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:136312914..136312928,-p@chr5:136312914..136312928
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Hg19::chr5:136313104..136313119,-p@chr5:136313104..136313119
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Hg19::chr5:136313255..136313279,-p@chr5:136313255..136313279
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Hg19::chr5:136834982..136835025,-p1@SPOCK1


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
tube2.99e-22192
anatomical conduit8.59e-21240
epithelium3.61e-20306
cell layer3.28e-19309
neural tube2.11e-1856
neural rod2.11e-1856
future spinal cord2.11e-1856
neural keel2.11e-1856
regional part of nervous system1.78e-1753
regional part of brain1.78e-1753
neural plate2.84e-1782
presumptive neural plate2.84e-1782
structure with developmental contribution from neural crest4.66e-17132
anatomical cluster6.28e-17373
neurectoderm2.43e-1586
regional part of forebrain8.67e-1541
forebrain8.67e-1541
anterior neural tube8.67e-1541
future forebrain8.67e-1541
splanchnic layer of lateral plate mesoderm1.10e-1483
multi-cellular organism4.51e-14656
artery1.97e-1342
arterial blood vessel1.97e-1342
arterial system1.97e-1342
nervous system3.00e-1389
ecto-epithelium6.45e-13104
brain grey matter7.42e-1334
gray matter7.42e-1334
telencephalon1.09e-1234
pre-chordal neural plate1.89e-1261
central nervous system2.31e-1281
multi-tissue structure2.87e-12342
epithelial tube open at both ends3.65e-1259
blood vessel3.65e-1259
blood vasculature3.65e-1259
vascular cord3.65e-1259
regional part of telencephalon4.06e-1232
anatomical system4.58e-12624
brain6.56e-1268
future brain6.56e-1268
anatomical group7.41e-12625
cerebral hemisphere7.82e-1232
systemic artery4.83e-1133
systemic arterial system4.83e-1133
vessel2.27e-1068
cerebral cortex3.03e-1025
pallium3.03e-1025
regional part of cerebral cortex7.30e-1022
vasculature1.32e-0978
vascular system1.32e-0978
epithelial tube2.37e-09117
neocortex5.66e-0920
adult organism1.58e-08114
circulatory system1.96e-08112
skeletal muscle tissue2.17e-0862
striated muscle tissue2.17e-0862
myotome2.17e-0862
embryonic structure2.27e-08564
cardiovascular system2.36e-08109
developing anatomical structure2.97e-08581
embryo3.03e-08592
germ layer3.17e-08560
germ layer / neural crest3.17e-08560
embryonic tissue3.17e-08560
presumptive structure3.17e-08560
germ layer / neural crest derived structure3.17e-08560
epiblast (generic)3.17e-08560
muscle tissue5.53e-0864
musculature5.53e-0864
musculature of body5.53e-0864
aorta2.03e-0721
aortic system2.03e-0721
heart9.31e-0724
primitive heart tube9.31e-0724
primary heart field9.31e-0724
anterior lateral plate mesoderm9.31e-0724
heart tube9.31e-0724
heart primordium9.31e-0724
cardiac mesoderm9.31e-0724
cardiogenic plate9.31e-0724
heart rudiment9.31e-0724
ectoderm-derived structure9.35e-07171
ectoderm9.35e-07171
presumptive ectoderm9.35e-07171
dense mesenchyme tissue9.76e-0773


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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