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Coexpression cluster:C4853: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000119!4.48e-31!309;UBERON:0000483!7.69e-31!306;UBERON:0000477!1.62e-28!373;UBERON:0000481!1.96e-25!342;UBERON:0004111!2.43e-25!240;UBERON:0000025!2.42e-23!192;UBERON:0010314!7.60e-21!132;UBERON:0003075!3.20e-20!82;UBERON:0007284!3.20e-20!82;UBERON:0010371!5.34e-20!104;UBERON:0001049!7.60e-19!56;UBERON:0005068!7.60e-19!56;UBERON:0006241!7.60e-19!56;UBERON:0007135!7.60e-19!56;UBERON:0002346!9.70e-19!86;UBERON:0000073!1.32e-18!53;UBERON:0002616!1.32e-18!53;UBERON:0001017!1.89e-17!81;UBERON:0004121!5.38e-17!171;UBERON:0000924!5.38e-17!171;UBERON:0006601!5.38e-17!171;UBERON:0000955!5.80e-17!68;UBERON:0006238!5.80e-17!68;UBERON:0003056!1.43e-16!61;UBERON:0002780!1.31e-15!41;UBERON:0001890!1.31e-15!41;UBERON:0003080!1.31e-15!41;UBERON:0006240!1.31e-15!41;UBERON:0001016!3.63e-15!89;UBERON:0000468!1.29e-14!656;UBERON:0007503!4.07e-14!78;UBERON:0000480!7.24e-14!625;UBERON:0000467!7.65e-14!624;UBERON:0002049!9.48e-14!78;UBERON:0007798!9.48e-14!78;UBERON:0000064!2.17e-13!218;UBERON:0001893!3.81e-13!34;UBERON:0007500!4.65e-13!59;UBERON:0001981!4.65e-13!59;UBERON:0004537!4.65e-13!59;UBERON:0006965!4.65e-13!59;UBERON:0003528!7.62e-13!34;UBERON:0002020!7.62e-13!34;UBERON:0004872!1.55e-12!83;UBERON:0001869!1.68e-12!32;UBERON:0005423!1.94e-12!581;UBERON:0002791!2.37e-12!32;UBERON:0001637!4.10e-12!42;UBERON:0003509!4.10e-12!42;UBERON:0004572!4.10e-12!42;UBERON:0000055!4.20e-12!68;UBERON:0007524!4.62e-12!73;UBERON:0003077!6.29e-12!72;UBERON:0007285!6.29e-12!72;UBERON:0002329!1.71e-11!71;UBERON:0003059!1.71e-11!71;UBERON:0007282!1.71e-11!71;UBERON:0004290!1.71e-11!71;UBERON:0009618!1.71e-11!71;UBERON:0000486!3.68e-11!83;UBERON:0000922!4.09e-11!592;UBERON:0002050!4.38e-11!564;UBERON:0000923!5.35e-11!560;UBERON:0010316!5.35e-11!560;UBERON:0005291!5.35e-11!560;UBERON:0006598!5.35e-11!560;UBERON:0010317!5.35e-11!560;UBERON:0002532!5.35e-11!560;UBERON:0002619!7.17e-11!22;UBERON:0001134!1.57e-10!62;UBERON:0002036!1.57e-10!62;UBERON:0003082!1.57e-10!62;UBERON:0003104!1.77e-10!160;UBERON:0009142!1.77e-10!160;UBERON:0000475!2.68e-10!264;UBERON:0002385!2.85e-10!64;UBERON:0001015!2.85e-10!64;UBERON:0000383!2.85e-10!64;UBERON:0000956!3.16e-10!25;UBERON:0000203!3.16e-10!25;UBERON:0001950!3.69e-10!20;UBERON:0003914!7.34e-10!117;UBERON:0004573!1.73e-09!33;UBERON:0004571!1.73e-09!33;UBERON:0005256!3.15e-09!122;UBERON:0002100!9.33e-09!199;UBERON:0011216!2.35e-08!223;UBERON:0000490!2.47e-08!148;UBERON:0007023!1.20e-07!114;UBERON:0004535!1.41e-07!109;UBERON:0001009!6.45e-07!112
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}}
}}

Revision as of 17:00, 26 November 2012


Full id: C4853_Renal_aorta_Mesenchymal_pituitary_Smooth_Fibroblast_mesothelioma



Phase1 CAGE Peaks

Hg19::chrX:140270547..140270568,-p4@LDOC1
Hg19::chrX:140270647..140270745,-p3@LDOC1
Hg19::chrX:140271249..140271333,-p1@LDOC1


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
cell layer4.48e-31309
epithelium7.69e-31306
anatomical cluster1.62e-28373
multi-tissue structure1.96e-25342
anatomical conduit2.43e-25240
tube2.42e-23192
structure with developmental contribution from neural crest7.60e-21132
neural plate3.20e-2082
presumptive neural plate3.20e-2082
ecto-epithelium5.34e-20104
neural tube7.60e-1956
neural rod7.60e-1956
future spinal cord7.60e-1956
neural keel7.60e-1956
neurectoderm9.70e-1986
regional part of nervous system1.32e-1853
regional part of brain1.32e-1853
central nervous system1.89e-1781
ectoderm-derived structure5.38e-17171
ectoderm5.38e-17171
presumptive ectoderm5.38e-17171
brain5.80e-1768
future brain5.80e-1768
pre-chordal neural plate1.43e-1661
regional part of forebrain1.31e-1541
forebrain1.31e-1541
anterior neural tube1.31e-1541
future forebrain1.31e-1541
nervous system3.63e-1589
multi-cellular organism1.29e-14656
epithelial vesicle4.07e-1478
anatomical group7.24e-14625
anatomical system7.65e-14624
vasculature9.48e-1478
vascular system9.48e-1478
organ part2.17e-13218
telencephalon3.81e-1334
epithelial tube open at both ends4.65e-1359
blood vessel4.65e-1359
blood vasculature4.65e-1359
vascular cord4.65e-1359
brain grey matter7.62e-1334
gray matter7.62e-1334
splanchnic layer of lateral plate mesoderm1.55e-1283
cerebral hemisphere1.68e-1232
developing anatomical structure1.94e-12581
regional part of telencephalon2.37e-1232
artery4.10e-1242
arterial blood vessel4.10e-1242
arterial system4.10e-1242
vessel4.20e-1268
dense mesenchyme tissue4.62e-1273
paraxial mesoderm6.29e-1272
presumptive paraxial mesoderm6.29e-1272
somite1.71e-1171
presomitic mesoderm1.71e-1171
presumptive segmental plate1.71e-1171
dermomyotome1.71e-1171
trunk paraxial mesoderm1.71e-1171
multilaminar epithelium3.68e-1183
embryo4.09e-11592
embryonic structure4.38e-11564
germ layer5.35e-11560
germ layer / neural crest5.35e-11560
embryonic tissue5.35e-11560
presumptive structure5.35e-11560
germ layer / neural crest derived structure5.35e-11560
epiblast (generic)5.35e-11560
regional part of cerebral cortex7.17e-1122
skeletal muscle tissue1.57e-1062
striated muscle tissue1.57e-1062
myotome1.57e-1062
mesenchyme1.77e-10160
entire embryonic mesenchyme1.77e-10160
organism subdivision2.68e-10264
muscle tissue2.85e-1064
musculature2.85e-1064
musculature of body2.85e-1064
cerebral cortex3.16e-1025
pallium3.16e-1025
neocortex3.69e-1020
epithelial tube7.34e-10117
systemic artery1.73e-0933
systemic arterial system1.73e-0933
trunk mesenchyme3.15e-09122
trunk9.33e-09199
organ system subdivision2.35e-08223


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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