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Coexpression cluster:C2345: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!4.43e-34!82;UBERON:0005743!6.42e-34!86;UBERON:0000073!2.27e-33!94;UBERON:0001016!2.27e-33!94;UBERON:0003075!3.01e-32!86;UBERON:0007284!3.01e-32!86;UBERON:0000119!2.02e-31!312;UBERON:0001049!3.15e-31!57;UBERON:0005068!3.15e-31!57;UBERON:0006241!3.15e-31!57;UBERON:0007135!3.15e-31!57;UBERON:0000475!1.81e-30!365;UBERON:0000483!2.47e-30!309;UBERON:0000955!1.12e-29!69;UBERON:0006238!1.12e-29!69;UBERON:0002616!1.27e-29!59;UBERON:0002346!2.62e-29!90;UBERON:0000025!1.45e-27!194;UBERON:0004111!3.69e-24!241;UBERON:0003056!6.29e-23!61;UBERON:0000033!9.17e-23!123;UBERON:0004121!3.00e-22!169;UBERON:0002780!3.93e-22!41;UBERON:0001890!3.93e-22!41;UBERON:0006240!3.93e-22!41;UBERON:0003080!5.23e-22!42;UBERON:0000477!1.71e-21!286;UBERON:0000481!6.90e-21!347;UBERON:0000153!8.24e-21!129;UBERON:0007811!8.24e-21!129;UBERON:0001893!8.54e-21!34;UBERON:0000924!8.69e-21!173;UBERON:0006601!8.69e-21!173;UBERON:0002020!1.11e-20!34;UBERON:0003528!1.11e-20!34;UBERON:0002791!3.70e-20!33;UBERON:0007023!1.62e-19!115;UBERON:0001869!1.71e-19!32;UBERON:0000956!2.47e-15!25;UBERON:0000203!2.47e-15!25;UBERON:0000467!7.13e-15!625;UBERON:0000480!1.45e-14!626;UBERON:0002619!7.31e-14!22;UBERON:0000468!8.67e-14!659;UBERON:0000914!1.57e-13!83;UBERON:0002329!1.57e-13!83;UBERON:0003077!1.57e-13!83;UBERON:0003059!1.57e-13!83;UBERON:0007282!1.57e-13!83;UBERON:0009618!1.57e-13!83;UBERON:0007285!1.57e-13!83;UBERON:0004290!2.60e-13!70;UBERON:0001134!7.83e-13!61;UBERON:0002036!7.83e-13!61;UBERON:0003082!7.83e-13!61;UBERON:0001950!8.44e-13!20;UBERON:0000922!1.37e-12!612;UBERON:0002385!1.44e-12!63;UBERON:0001015!1.44e-12!63;UBERON:0000383!1.44e-12!63;UBERON:0002050!3.30e-12!605;UBERON:0005423!3.30e-12!605;UBERON:0000923!4.75e-12!604;UBERON:0005291!4.75e-12!604;UBERON:0006598!4.75e-12!604;UBERON:0002532!4.75e-12!604;UBERON:0005256!5.48e-11!143;UBERON:0003076!2.39e-10!15;UBERON:0003057!2.39e-10!15;UBERON:0000486!3.12e-10!82;UBERON:0000064!7.76e-10!219;UBERON:0002049!1.15e-09!79;UBERON:0007798!1.15e-09!79;UBERON:0004732!2.82e-09!13;UBERON:0001637!3.03e-09!42;UBERON:0003509!3.03e-09!42;UBERON:0004572!3.03e-09!42;UBERON:0004872!7.26e-09!84;UBERON:0004733!1.38e-08!12;UBERON:0002028!1.38e-08!12;UBERON:0007277!1.38e-08!12;UBERON:0004573!3.24e-08!33;UBERON:0004571!3.24e-08!33;UBERON:0001981!3.85e-08!60;UBERON:0007500!3.85e-08!60;UBERON:0004537!3.85e-08!60;UBERON:0006965!3.85e-08!60;UBERON:0003914!5.12e-08!118;UBERON:0002100!6.52e-08!216;UBERON:0001009!9.43e-08!113;UBERON:0004535!1.13e-07!110;UBERON:0000055!3.54e-07!69;UBERON:0000479!5.79e-07!787;UBERON:0002308!8.17e-07!9;UBERON:0000125!8.17e-07!9;UBERON:0002680!8.23e-07!9;UBERON:0001895!8.23e-07!9;UBERON:0010092!8.23e-07!9
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}}
}}

Revision as of 18:13, 8 August 2012


Full id: C2345_optic_Neural_parietal_spinal_Myoblast_locus_globus



Phase1 CAGE Peaks

Hg19::chr15:68870949..68871019,+p3@CORO2B
Hg19::chr15:68871309..68871354,+p2@CORO2B
Hg19::chr15:68871361..68871409,+p1@CORO2B
Hg19::chr2:105470714..105470723,+p8@POU3F3


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
central nervous system4.43e-3482
regional part of nervous system2.27e-3394
nervous system2.27e-3394
neural plate3.01e-3286
presumptive neural plate3.01e-3286
cell layer2.02e-31312
neural tube3.15e-3157
neural rod3.15e-3157
future spinal cord3.15e-3157
neural keel3.15e-3157
organism subdivision1.81e-30365
epithelium2.47e-30309
brain1.12e-2969
future brain1.12e-2969
regional part of brain1.27e-2959
neurectoderm2.62e-2990
tube1.45e-27194
anatomical conduit3.69e-24241
pre-chordal neural plate6.29e-2361
head9.17e-23123
ectoderm-derived structure3.00e-22169
regional part of forebrain3.93e-2241
forebrain3.93e-2241
future forebrain3.93e-2241
anterior neural tube5.23e-2242
anatomical cluster1.71e-21286
multi-tissue structure6.90e-21347
anterior region of body8.24e-21129
craniocervical region8.24e-21129
telencephalon8.54e-2134
ectoderm8.69e-21173
presumptive ectoderm8.69e-21173
gray matter1.11e-2034
brain grey matter1.11e-2034
regional part of telencephalon3.70e-2033
adult organism1.62e-19115
cerebral hemisphere1.71e-1932
cerebral cortex2.47e-1525
pallium2.47e-1525
anatomical system7.13e-15625
anatomical group1.45e-14626
regional part of cerebral cortex7.31e-1422
multi-cellular organism8.67e-14659
somite1.57e-1383
paraxial mesoderm1.57e-1383
presomitic mesoderm1.57e-1383
presumptive segmental plate1.57e-1383
trunk paraxial mesoderm1.57e-1383
presumptive paraxial mesoderm1.57e-1383
dermomyotome2.60e-1370
skeletal muscle tissue7.83e-1361
striated muscle tissue7.83e-1361
myotome7.83e-1361
neocortex8.44e-1320
embryo1.37e-12612
muscle tissue1.44e-1263
musculature1.44e-1263
musculature of body1.44e-1263
embryonic structure3.30e-12605
developing anatomical structure3.30e-12605
germ layer4.75e-12604
embryonic tissue4.75e-12604
presumptive structure4.75e-12604
epiblast (generic)4.75e-12604
trunk mesenchyme5.48e-11143
posterior neural tube2.39e-1015
chordal neural plate2.39e-1015
multilaminar epithelium3.12e-1082
organ part7.76e-10219
vasculature1.15e-0979
vascular system1.15e-0979
segmental subdivision of nervous system2.82e-0913
artery3.03e-0942
arterial blood vessel3.03e-0942
arterial system3.03e-0942
splanchnic layer of lateral plate mesoderm7.26e-0984
segmental subdivision of hindbrain1.38e-0812
hindbrain1.38e-0812
presumptive hindbrain1.38e-0812
systemic artery3.24e-0833
systemic arterial system3.24e-0833
blood vessel3.85e-0860
epithelial tube open at both ends3.85e-0860
blood vasculature3.85e-0860
vascular cord3.85e-0860


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.