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Coexpression cluster:C4175: Difference between revisions

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|full_id=C4175_putamen_pons_heart_occipital_parietal_medial_paracentral
|full_id=C4175_putamen_pons_heart_occipital_parietal_medial_paracentral
|id=C4175
|id=C4175
|ontology_enrichment_celltype=CL:0000055!9.73e-15!180;CL:0000393!1.82e-13!60;CL:0000211!1.82e-13!60;CL:0000680!3.71e-12!57;CL:0000056!3.71e-12!57;CL:0000355!3.71e-12!57;CL:0000187!1.78e-11!54;CL:0000192!2.03e-11!42;CL:0000514!2.03e-11!42;CL:0000183!1.90e-10!59;CL:0000222!2.56e-10!119;CL:0000359!1.01e-09!32;CL:0002321!6.02e-07!248
|ontology_enrichment_celltype=CL:0000055!5.62e-16!106;CL:0000393!1.26e-13!61;CL:0000211!1.26e-13!61;CL:0000680!2.74e-12!58;CL:0000056!2.74e-12!58;CL:0000355!2.74e-12!58;CL:0000187!1.57e-11!55;CL:0000192!4.55e-11!43;CL:0000514!4.55e-11!43;CL:0000183!1.08e-10!59;CL:0000222!1.11e-10!121;CL:0000359!1.77e-09!32;CL:0002321!7.81e-07!250
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!6.88e-33!94;UBERON:0001016!6.88e-33!94;UBERON:0005743!6.56e-32!86;UBERON:0001017!3.36e-31!82;UBERON:0000119!2.76e-29!312;UBERON:0000483!4.03e-29!309;UBERON:0003075!8.94e-29!86;UBERON:0007284!8.94e-29!86;UBERON:0002346!1.07e-27!90;UBERON:0001049!1.74e-27!57;UBERON:0005068!1.74e-27!57;UBERON:0006241!1.74e-27!57;UBERON:0007135!1.74e-27!57;UBERON:0000955!5.91e-26!69;UBERON:0006238!5.91e-26!69;UBERON:0002616!1.09e-25!59;UBERON:0000025!3.33e-24!194;UBERON:0002780!4.13e-22!41;UBERON:0001890!4.13e-22!41;UBERON:0006240!4.13e-22!41;UBERON:0003056!5.08e-22!61;UBERON:0004121!5.74e-22!169;UBERON:0003080!7.20e-22!42;UBERON:0000924!1.33e-21!173;UBERON:0006601!1.33e-21!173;UBERON:0004111!2.43e-21!241;UBERON:0002020!1.70e-19!34;UBERON:0003528!1.70e-19!34;UBERON:0001893!2.06e-19!34;UBERON:0000033!4.23e-19!123;UBERON:0001869!5.41e-19!32;UBERON:0000153!8.04e-19!129;UBERON:0007811!8.04e-19!129;UBERON:0002791!1.00e-18!33;UBERON:0000477!2.08e-18!286;UBERON:0000475!2.80e-17!365;UBERON:0002049!1.40e-16!79;UBERON:0007798!1.40e-16!79;UBERON:0007023!1.73e-16!115;UBERON:0001981!4.98e-16!60;UBERON:0007500!4.98e-16!60;UBERON:0004537!4.98e-16!60;UBERON:0006965!4.98e-16!60;UBERON:0001009!2.48e-15!113;UBERON:0000055!3.15e-15!69;UBERON:0004872!5.52e-15!84;UBERON:0000956!6.61e-15!25;UBERON:0000203!6.61e-15!25;UBERON:0002619!7.27e-15!22;UBERON:0004535!5.48e-14!110;UBERON:0001950!1.07e-13!20;UBERON:0000481!2.44e-13!347;UBERON:0001637!2.89e-13!42;UBERON:0003509!2.89e-13!42;UBERON:0004572!2.89e-13!42;UBERON:0001134!2.90e-12!61;UBERON:0002036!2.90e-12!61;UBERON:0003082!2.90e-12!61;UBERON:0002385!1.19e-11!63;UBERON:0001015!1.19e-11!63;UBERON:0000383!1.19e-11!63;UBERON:0000468!1.90e-11!659;UBERON:0004290!4.88e-11!70;UBERON:0000480!3.78e-10!626;UBERON:0000922!4.11e-10!612;UBERON:0000914!4.38e-10!83;UBERON:0002329!4.38e-10!83;UBERON:0003077!4.38e-10!83;UBERON:0003059!4.38e-10!83;UBERON:0007282!4.38e-10!83;UBERON:0009618!4.38e-10!83;UBERON:0007285!4.38e-10!83;UBERON:0000467!4.79e-10!625;UBERON:0004573!5.96e-10!33;UBERON:0004571!5.96e-10!33;UBERON:0002050!1.69e-08!605;UBERON:0005423!1.69e-08!605;UBERON:0000486!2.40e-08!82;UBERON:0000923!2.90e-08!604;UBERON:0005291!2.90e-08!604;UBERON:0006598!2.90e-08!604;UBERON:0002532!2.90e-08!604;UBERON:0000064!3.61e-08!219;UBERON:0000947!1.24e-07!21;UBERON:0010191!1.24e-07!21;UBERON:0000490!1.96e-07!138;UBERON:0003076!7.35e-07!15;UBERON:0003057!7.35e-07!15
|ontology_enrichment_uberon=UBERON:0001016!2.17e-31!89;UBERON:0001017!4.05e-30!81;UBERON:0000119!4.79e-29!309;UBERON:0000483!6.29e-29!306;UBERON:0003075!1.83e-28!82;UBERON:0007284!1.83e-28!82;UBERON:0002346!2.30e-27!86;UBERON:0001049!1.82e-26!56;UBERON:0005068!1.82e-26!56;UBERON:0006241!1.82e-26!56;UBERON:0007135!1.82e-26!56;UBERON:0000477!1.45e-25!373;UBERON:0000073!5.50e-25!53;UBERON:0002616!5.50e-25!53;UBERON:0000955!1.03e-24!68;UBERON:0006238!1.03e-24!68;UBERON:0000025!2.19e-23!192;UBERON:0010314!2.79e-23!132;UBERON:0010371!3.53e-22!104;UBERON:0004121!1.19e-21!171;UBERON:0000924!1.19e-21!171;UBERON:0006601!1.19e-21!171;UBERON:0002780!2.06e-21!41;UBERON:0001890!2.06e-21!41;UBERON:0003080!2.06e-21!41;UBERON:0006240!2.06e-21!41;UBERON:0004111!2.56e-21!240;UBERON:0003056!3.89e-21!61;UBERON:0003528!7.12e-19!34;UBERON:0002020!7.12e-19!34;UBERON:0001893!7.61e-19!34;UBERON:0001869!1.88e-18!32;UBERON:0002791!8.96e-18!32;UBERON:0002049!2.54e-16!78;UBERON:0007798!2.54e-16!78;UBERON:0007023!3.48e-16!114;UBERON:0007500!1.34e-15!59;UBERON:0001981!1.34e-15!59;UBERON:0004537!1.34e-15!59;UBERON:0006965!1.34e-15!59;UBERON:0000055!5.86e-15!68;UBERON:0000481!1.01e-14!342;UBERON:0001009!1.06e-14!112;UBERON:0004872!1.22e-14!83;UBERON:0002619!1.41e-14!22;UBERON:0000956!1.86e-14!25;UBERON:0000203!1.86e-14!25;UBERON:0001950!1.97e-13!20;UBERON:0004535!2.04e-13!109;UBERON:0011216!5.75e-13!223;UBERON:0001637!8.54e-13!42;UBERON:0003509!8.54e-13!42;UBERON:0004572!8.54e-13!42;UBERON:0000468!2.51e-12!656;UBERON:0001134!3.03e-12!62;UBERON:0002036!3.03e-12!62;UBERON:0003082!3.03e-12!62;UBERON:0002385!1.16e-11!64;UBERON:0001015!1.16e-11!64;UBERON:0000383!1.16e-11!64;UBERON:0007524!1.53e-11!73;UBERON:0000922!1.71e-11!592;UBERON:0003077!2.31e-11!72;UBERON:0007285!2.31e-11!72;UBERON:0002329!6.64e-11!71;UBERON:0003059!6.64e-11!71;UBERON:0007282!6.64e-11!71;UBERON:0004290!6.64e-11!71;UBERON:0009618!6.64e-11!71;UBERON:0000923!9.97e-11!560;UBERON:0010316!9.97e-11!560;UBERON:0005291!9.97e-11!560;UBERON:0006598!9.97e-11!560;UBERON:0010317!9.97e-11!560;UBERON:0002532!9.97e-11!560;UBERON:0002050!1.19e-10!564;UBERON:0000480!1.54e-10!625;UBERON:0000467!2.04e-10!624;UBERON:0007503!1.14e-09!78;UBERON:0004573!1.34e-09!33;UBERON:0004571!1.34e-09!33;UBERON:0005423!3.17e-09!581;UBERON:0000486!1.85e-08!83;UBERON:0000490!1.45e-07!148;UBERON:0000064!2.03e-07!218;UBERON:0000947!2.57e-07!21;UBERON:0010191!2.57e-07!21
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321370240844928
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321370240844928
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}}
}}

Revision as of 15:44, 19 October 2012


Full id: C4175_putamen_pons_heart_occipital_parietal_medial_paracentral



Phase1 CAGE Peaks

Hg19::chr2:207308220..207308267,+p1@ADAM23
Hg19::chr2:207308275..207308295,+p2@ADAM23
Hg19::chr2:207308554..207308568,+p5@ADAM23


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
nervous system2.17e-3189
central nervous system4.05e-3081
cell layer4.79e-29309
epithelium6.29e-29306
neural plate1.83e-2882
presumptive neural plate1.83e-2882
neurectoderm2.30e-2786
neural tube1.82e-2656
neural rod1.82e-2656
future spinal cord1.82e-2656
neural keel1.82e-2656
anatomical cluster1.45e-25373
regional part of nervous system5.50e-2553
regional part of brain5.50e-2553
brain1.03e-2468
future brain1.03e-2468
tube2.19e-23192
structure with developmental contribution from neural crest2.79e-23132
ecto-epithelium3.53e-22104
ectoderm-derived structure1.19e-21171
ectoderm1.19e-21171
presumptive ectoderm1.19e-21171
regional part of forebrain2.06e-2141
forebrain2.06e-2141
anterior neural tube2.06e-2141
future forebrain2.06e-2141
anatomical conduit2.56e-21240
pre-chordal neural plate3.89e-2161
brain grey matter7.12e-1934
gray matter7.12e-1934
telencephalon7.61e-1934
cerebral hemisphere1.88e-1832
regional part of telencephalon8.96e-1832
vasculature2.54e-1678
vascular system2.54e-1678
adult organism3.48e-16114
epithelial tube open at both ends1.34e-1559
blood vessel1.34e-1559
blood vasculature1.34e-1559
vascular cord1.34e-1559
vessel5.86e-1568
multi-tissue structure1.01e-14342
circulatory system1.06e-14112
splanchnic layer of lateral plate mesoderm1.22e-1483
regional part of cerebral cortex1.41e-1422
cerebral cortex1.86e-1425
pallium1.86e-1425
neocortex1.97e-1320
cardiovascular system2.04e-13109
organ system subdivision5.75e-13223
artery8.54e-1342
arterial blood vessel8.54e-1342
arterial system8.54e-1342
multi-cellular organism2.51e-12656
skeletal muscle tissue3.03e-1262
striated muscle tissue3.03e-1262
myotome3.03e-1262
muscle tissue1.16e-1164
musculature1.16e-1164
musculature of body1.16e-1164
dense mesenchyme tissue1.53e-1173
embryo1.71e-11592
paraxial mesoderm2.31e-1172
presumptive paraxial mesoderm2.31e-1172
somite6.64e-1171
presomitic mesoderm6.64e-1171
presumptive segmental plate6.64e-1171
dermomyotome6.64e-1171
trunk paraxial mesoderm6.64e-1171
germ layer9.97e-11560
germ layer / neural crest9.97e-11560
embryonic tissue9.97e-11560
presumptive structure9.97e-11560
germ layer / neural crest derived structure9.97e-11560
epiblast (generic)9.97e-11560
embryonic structure1.19e-10564
anatomical group1.54e-10625
anatomical system2.04e-10624
epithelial vesicle1.14e-0978
systemic artery1.34e-0933
systemic arterial system1.34e-0933
developing anatomical structure3.17e-09581
multilaminar epithelium1.85e-0883
unilaminar epithelium1.45e-07148
organ part2.03e-07218
aorta2.57e-0721
aortic system2.57e-0721


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
EGR1#195834.988179094810140.008056488137383440.0321370240844928



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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