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Coexpression cluster:C4755: Difference between revisions

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|full_id=C4755_heart_oral_salivary_cervical_Mammary_Keratinocyte_skeletal
|full_id=C4755_heart_oral_salivary_cervical_Mammary_Keratinocyte_skeletal
|id=C4755
|id=C4755
|ontology_enrichment_celltype=CL:0002076!4.38e-08!43
|ontology_enrichment_celltype=CL:0002076!2.64e-09!42;CL:0000223!2.31e-07!58;CL:0002251!6.57e-07!20
|ontology_enrichment_disease=DOID:1749!4.73e-07!14
|ontology_enrichment_disease=DOID:1749!1.87e-08!14
|ontology_enrichment_uberon=UBERON:0007023!1.04e-32!115;UBERON:0000475!7.25e-23!365;UBERON:0001049!5.92e-22!57;UBERON:0005068!5.92e-22!57;UBERON:0006241!5.92e-22!57;UBERON:0007135!5.92e-22!57;UBERON:0004121!5.66e-21!169;UBERON:0002616!1.42e-20!59;UBERON:0000924!1.70e-19!173;UBERON:0006601!1.70e-19!173;UBERON:0000153!4.24e-19!129;UBERON:0007811!4.24e-19!129;UBERON:0001017!1.54e-18!82;UBERON:0000033!2.45e-18!123;UBERON:0005743!4.58e-18!86;UBERON:0000468!4.94e-18!659;UBERON:0000073!2.58e-17!94;UBERON:0001016!2.58e-17!94;UBERON:0004111!5.03e-17!241;UBERON:0000955!1.52e-16!69;UBERON:0006238!1.52e-16!69;UBERON:0000119!2.18e-16!312;UBERON:0000480!2.85e-16!626;UBERON:0000467!4.27e-16!625;UBERON:0000483!7.82e-16!309;UBERON:0003075!1.28e-15!86;UBERON:0007284!1.28e-15!86;UBERON:0003080!1.89e-15!42;UBERON:0002780!4.61e-15!41;UBERON:0001890!4.61e-15!41;UBERON:0006240!4.61e-15!41;UBERON:0000477!3.20e-14!286;UBERON:0002346!8.13e-14!90;UBERON:0000481!6.83e-13!347;UBERON:0002020!2.10e-12!34;UBERON:0003528!2.10e-12!34;UBERON:0001893!2.95e-12!34;UBERON:0002791!8.13e-12!33;UBERON:0001869!4.02e-11!32;UBERON:0000062!8.66e-11!511;UBERON:0000922!3.12e-10!612;UBERON:0000064!9.08e-10!219;UBERON:0003056!1.16e-09!61;UBERON:0000025!1.62e-09!194;UBERON:0002050!5.62e-09!605;UBERON:0005423!5.62e-09!605;UBERON:0000923!8.50e-09!604;UBERON:0005291!8.50e-09!604;UBERON:0006598!8.50e-09!604;UBERON:0002532!8.50e-09!604;UBERON:0002619!2.41e-08!22;UBERON:0000956!2.49e-08!25;UBERON:0000203!2.49e-08!25;UBERON:0003076!8.37e-08!15;UBERON:0003057!8.37e-08!15;UBERON:0001950!1.85e-07!20;UBERON:0003102!3.31e-07!95;UBERON:0000161!8.65e-07!35
|ontology_enrichment_uberon=UBERON:0007023!4.13e-37!114;UBERON:0010371!7.15e-23!104;UBERON:0001049!3.34e-22!56;UBERON:0005068!3.34e-22!56;UBERON:0006241!3.34e-22!56;UBERON:0007135!3.34e-22!56;UBERON:0000073!3.27e-20!53;UBERON:0002616!3.27e-20!53;UBERON:0004121!8.10e-19!171;UBERON:0000924!8.10e-19!171;UBERON:0006601!8.10e-19!171;UBERON:0003075!1.18e-17!82;UBERON:0007284!1.18e-17!82;UBERON:0001017!1.05e-16!81;UBERON:0001016!2.04e-16!89;UBERON:0002346!6.10e-16!86;UBERON:0000955!2.48e-15!68;UBERON:0006238!2.48e-15!68;UBERON:0011216!3.73e-14!223;UBERON:0002780!6.10e-14!41;UBERON:0001890!6.10e-14!41;UBERON:0003080!6.10e-14!41;UBERON:0006240!6.10e-14!41;UBERON:0000468!1.17e-13!656;UBERON:0000119!2.75e-13!309;UBERON:0010314!5.19e-13!132;UBERON:0000483!1.18e-12!306;UBERON:0004111!1.24e-12!240;UBERON:0000467!5.09e-12!624;UBERON:0000480!6.74e-12!625;UBERON:0000477!7.15e-12!373;UBERON:0000062!2.62e-11!503;UBERON:0000481!6.10e-11!342;UBERON:0003528!9.73e-11!34;UBERON:0002020!9.73e-11!34;UBERON:0001893!1.65e-10!34;UBERON:0003076!6.02e-10!15;UBERON:0003057!6.02e-10!15;UBERON:0003056!1.30e-09!61;UBERON:0000064!1.39e-09!218;UBERON:0002791!1.98e-09!32;UBERON:0001869!3.18e-09!32;UBERON:0004732!1.58e-08!13;UBERON:0000922!1.76e-08!592;UBERON:0005423!6.13e-08!581;UBERON:0004733!6.60e-08!12;UBERON:0002028!6.60e-08!12;UBERON:0007277!6.60e-08!12;UBERON:0000161!1.46e-07!36;UBERON:0002050!3.00e-07!564;UBERON:0002619!5.52e-07!22;UBERON:0000025!5.57e-07!192;UBERON:0001950!6.66e-07!20;UBERON:0000923!8.00e-07!560;UBERON:0010316!8.00e-07!560;UBERON:0005291!8.00e-07!560;UBERON:0006598!8.00e-07!560;UBERON:0010317!8.00e-07!560;UBERON:0002532!8.00e-07!560
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281509184975187!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310433065509693!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00646053902176482
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281509184975187!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310433065509693!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00646053902176482
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}}
}}

Revision as of 16:13, 19 October 2012


Full id: C4755_heart_oral_salivary_cervical_Mammary_Keratinocyte_skeletal



Phase1 CAGE Peaks

Hg19::chr8:42358653..42358670,-p10@SLC20A2
Hg19::chr8:42358682..42358693,-p8@SLC20A2
Hg19::chr8:42358694..42358706,-p7@SLC20A2


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>disease_data<br>


Cell Type
Ontology termp-valuen
endo-epithelial cell2.64e-0942
endodermal cell2.31e-0758
epithelial cell of alimentary canal6.57e-0720
Uber Anatomy
Ontology termp-valuen
adult organism4.13e-37114
ecto-epithelium7.15e-23104
neural tube3.34e-2256
neural rod3.34e-2256
future spinal cord3.34e-2256
neural keel3.34e-2256
regional part of nervous system3.27e-2053
regional part of brain3.27e-2053
ectoderm-derived structure8.10e-19171
ectoderm8.10e-19171
presumptive ectoderm8.10e-19171
neural plate1.18e-1782
presumptive neural plate1.18e-1782
central nervous system1.05e-1681
nervous system2.04e-1689
neurectoderm6.10e-1686
brain2.48e-1568
future brain2.48e-1568
organ system subdivision3.73e-14223
regional part of forebrain6.10e-1441
forebrain6.10e-1441
anterior neural tube6.10e-1441
future forebrain6.10e-1441
multi-cellular organism1.17e-13656
cell layer2.75e-13309
structure with developmental contribution from neural crest5.19e-13132
epithelium1.18e-12306
anatomical conduit1.24e-12240
anatomical system5.09e-12624
anatomical group6.74e-12625
anatomical cluster7.15e-12373
organ2.62e-11503
multi-tissue structure6.10e-11342
brain grey matter9.73e-1134
gray matter9.73e-1134
telencephalon1.65e-1034
posterior neural tube6.02e-1015
chordal neural plate6.02e-1015
pre-chordal neural plate1.30e-0961
organ part1.39e-09218
regional part of telencephalon1.98e-0932
cerebral hemisphere3.18e-0932
segmental subdivision of nervous system1.58e-0813
embryo1.76e-08592
developing anatomical structure6.13e-08581
segmental subdivision of hindbrain6.60e-0812
hindbrain6.60e-0812
presumptive hindbrain6.60e-0812
orifice1.46e-0736
embryonic structure3.00e-07564
regional part of cerebral cortex5.52e-0722
tube5.57e-07192
neocortex6.66e-0720
germ layer8.00e-07560
germ layer / neural crest8.00e-07560
embryonic tissue8.00e-07560
presumptive structure8.00e-07560
germ layer / neural crest derived structure8.00e-07560
epiblast (generic)8.00e-07560
Disease
Ontology termp-valuen
squamous cell carcinoma1.87e-0814


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
CTCF#1066435.360256373075030.0064925092527670.0281509184975187
NR3C1#2908314.9730233311730.0002978331194675480.00310433065509693
STAT3#6774310.51946499715420.0008589184530415310.00646053902176482



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.