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Coexpression cluster:C2035: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!3.79e-27!57;UBERON:0005068!3.79e-27!57;UBERON:0006241!3.79e-27!57;UBERON:0007135!3.79e-27!57;UBERON:0002616!1.08e-26!59;UBERON:0001017!2.45e-25!82;UBERON:0000955!4.17e-25!69;UBERON:0006238!4.17e-25!69;UBERON:0005743!8.61e-24!86;UBERON:0000073!2.64e-23!94;UBERON:0001016!2.64e-23!94;UBERON:0007023!4.68e-23!115;UBERON:0002780!1.98e-22!41;UBERON:0001890!1.98e-22!41;UBERON:0006240!1.98e-22!41;UBERON:0003080!4.03e-22!42;UBERON:0000475!7.25e-22!365;UBERON:0003075!1.04e-21!86;UBERON:0007284!1.04e-21!86;UBERON:0002346!8.90e-21!90;UBERON:0000033!2.51e-19!123;UBERON:0000153!8.12e-19!129;UBERON:0007811!8.12e-19!129;UBERON:0001893!8.98e-19!34;UBERON:0002020!9.43e-19!34;UBERON:0003528!9.43e-19!34;UBERON:0002791!3.79e-18!33;UBERON:0001869!1.43e-17!32;UBERON:0004121!6.87e-17!169;UBERON:0003056!9.13e-17!61;UBERON:0000481!1.47e-16!347;UBERON:0000924!1.59e-16!173;UBERON:0006601!1.59e-16!173;UBERON:0000119!2.49e-16!312;UBERON:0000025!1.15e-15!194;UBERON:0000483!1.20e-15!309;UBERON:0002619!2.85e-15!22;UBERON:0000477!3.18e-14!286;UBERON:0001950!7.47e-14!20;UBERON:0004111!1.35e-13!241;UBERON:0000468!2.02e-13!659;UBERON:0000956!3.29e-13!25;UBERON:0000203!3.29e-13!25;UBERON:0002385!3.48e-11!63;UBERON:0001015!3.48e-11!63;UBERON:0000383!3.48e-11!63;UBERON:0000914!5.11e-11!83;UBERON:0002329!5.11e-11!83;UBERON:0003077!5.11e-11!83;UBERON:0003059!5.11e-11!83;UBERON:0007282!5.11e-11!83;UBERON:0009618!5.11e-11!83;UBERON:0007285!5.11e-11!83;UBERON:0001134!9.68e-11!61;UBERON:0002036!9.68e-11!61;UBERON:0003082!9.68e-11!61;UBERON:0000467!1.19e-10!625;UBERON:0000480!1.92e-10!626;UBERON:0004290!4.55e-10!70;UBERON:0000062!1.05e-08!511;UBERON:0000922!2.42e-08!612;UBERON:0002050!6.71e-08!605;UBERON:0005423!6.71e-08!605;UBERON:0000486!7.98e-08!82;UBERON:0000923!1.20e-07!604;UBERON:0005291!1.20e-07!604;UBERON:0006598!1.20e-07!604;UBERON:0002532!1.20e-07!604;UBERON:0002420!2.92e-07!9;UBERON:0007245!2.92e-07!9;UBERON:0010009!2.92e-07!9;UBERON:0010011!2.92e-07!9;UBERON:0000454!2.92e-07!9;UBERON:0000064!3.46e-07!219;UBERON:0002308!4.19e-07!9;UBERON:0000125!4.19e-07!9;UBERON:0000948!6.64e-07!24;UBERON:0005498!6.64e-07!24;UBERON:0004140!6.64e-07!24;UBERON:0009881!6.64e-07!24;UBERON:0004141!6.64e-07!24;UBERON:0003084!6.64e-07!24;UBERON:0007005!6.64e-07!24;UBERON:0004139!6.64e-07!24;UBERON:0004291!6.64e-07!24
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}}
}}

Revision as of 17:56, 8 August 2012


Full id: C2035_hippocampus_parietal_spinal_amygdala_middle_Fibroblast_medial



Phase1 CAGE Peaks

Hg19::chr10:111765766..111765786,+p10@ADD3
Hg19::chr10:111765775..111765802,-p1@uc001kyr.1
Hg19::chr10:111765798..111765847,+p4@ADD3
Hg19::chr10:111765852..111765862,+p16@ADD3


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

GO IDGO nameFDR corrected p-value
GO:0005200structural constituent of cytoskeleton0.0311285764747439
GO:0005516calmodulin binding0.0311285764747439



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
neural tube3.79e-2757
neural rod3.79e-2757
future spinal cord3.79e-2757
neural keel3.79e-2757
regional part of brain1.08e-2659
central nervous system2.45e-2582
brain4.17e-2569
future brain4.17e-2569
regional part of nervous system2.64e-2394
nervous system2.64e-2394
adult organism4.68e-23115
regional part of forebrain1.98e-2241
forebrain1.98e-2241
future forebrain1.98e-2241
anterior neural tube4.03e-2242
organism subdivision7.25e-22365
neural plate1.04e-2186
presumptive neural plate1.04e-2186
neurectoderm8.90e-2190
head2.51e-19123
anterior region of body8.12e-19129
craniocervical region8.12e-19129
telencephalon8.98e-1934
gray matter9.43e-1934
brain grey matter9.43e-1934
regional part of telencephalon3.79e-1833
cerebral hemisphere1.43e-1732
ectoderm-derived structure6.87e-17169
pre-chordal neural plate9.13e-1761
multi-tissue structure1.47e-16347
ectoderm1.59e-16173
presumptive ectoderm1.59e-16173
cell layer2.49e-16312
tube1.15e-15194
epithelium1.20e-15309
regional part of cerebral cortex2.85e-1522
anatomical cluster3.18e-14286
neocortex7.47e-1420
anatomical conduit1.35e-13241
multi-cellular organism2.02e-13659
cerebral cortex3.29e-1325
pallium3.29e-1325
muscle tissue3.48e-1163
musculature3.48e-1163
musculature of body3.48e-1163
somite5.11e-1183
paraxial mesoderm5.11e-1183
presomitic mesoderm5.11e-1183
presumptive segmental plate5.11e-1183
trunk paraxial mesoderm5.11e-1183
presumptive paraxial mesoderm5.11e-1183
skeletal muscle tissue9.68e-1161
striated muscle tissue9.68e-1161
myotome9.68e-1161
anatomical system1.19e-10625
anatomical group1.92e-10626
dermomyotome4.55e-1070
organ1.05e-08511
embryo2.42e-08612
embryonic structure6.71e-08605
developing anatomical structure6.71e-08605
multilaminar epithelium7.98e-0882
germ layer1.20e-07604
embryonic tissue1.20e-07604
presumptive structure1.20e-07604
epiblast (generic)1.20e-07604
basal ganglion2.92e-079
nuclear complex of neuraxis2.92e-079
aggregate regional part of brain2.92e-079
collection of basal ganglia2.92e-079
cerebral subcortex2.92e-079
organ part3.46e-07219
nucleus of brain4.19e-079
neural nucleus4.19e-079
heart6.64e-0724
primitive heart tube6.64e-0724
primary heart field6.64e-0724
anterior lateral plate mesoderm6.64e-0724
heart tube6.64e-0724
heart primordium6.64e-0724
cardiac mesoderm6.64e-0724
cardiogenic plate6.64e-0724
heart rudiment6.64e-0724


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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