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Coexpression cluster:C4166: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.15e-30!94;UBERON:0001016!2.15e-30!94;UBERON:0001017!9.78e-30!82;UBERON:0005743!2.31e-28!86;UBERON:0001049!6.94e-25!57;UBERON:0005068!6.94e-25!57;UBERON:0006241!6.94e-25!57;UBERON:0007135!6.94e-25!57;UBERON:0000955!1.32e-24!69;UBERON:0006238!1.32e-24!69;UBERON:0002616!5.18e-24!59;UBERON:0000924!5.18e-24!173;UBERON:0006601!5.18e-24!173;UBERON:0004121!1.95e-22!169;UBERON:0002780!2.21e-21!41;UBERON:0001890!2.21e-21!41;UBERON:0006240!2.21e-21!41;UBERON:0002346!9.76e-21!90;UBERON:0003080!1.58e-20!42;UBERON:0000153!7.04e-20!129;UBERON:0007811!7.04e-20!129;UBERON:0000033!2.15e-19!123;UBERON:0003075!4.36e-19!86;UBERON:0007284!4.36e-19!86;UBERON:0002020!2.95e-18!34;UBERON:0003528!2.95e-18!34;UBERON:0001893!3.99e-18!34;UBERON:0002791!1.43e-17!33;UBERON:0001869!2.00e-17!32;UBERON:0003056!1.03e-15!61;UBERON:0000956!4.83e-14!25;UBERON:0000203!4.83e-14!25;UBERON:0002619!2.46e-12!22;UBERON:0001950!3.99e-11!20;UBERON:0000922!2.62e-10!612;UBERON:0000468!5.85e-10!659;UBERON:0007023!3.92e-09!115;UBERON:0002050!9.21e-09!605;UBERON:0005423!9.21e-09!605;UBERON:0000480!1.04e-08!626;UBERON:0000467!1.27e-08!625;UBERON:0000475!1.33e-08!365;UBERON:0000923!1.79e-08!604;UBERON:0005291!1.79e-08!604;UBERON:0006598!1.79e-08!604;UBERON:0002532!1.79e-08!604;UBERON:0004111!1.78e-07!241;UBERON:0000025!3.26e-07!194;UBERON:0000483!6.06e-07!309;UBERON:0000062!6.67e-07!511;UBERON:0000119!9.65e-07!312
|ontology_enrichment_uberon=UBERON:0000073!2.15e-30!94;UBERON:0001016!2.15e-30!94;UBERON:0001017!9.78e-30!82;UBERON:0005743!2.31e-28!86;UBERON:0001049!6.94e-25!57;UBERON:0005068!6.94e-25!57;UBERON:0006241!6.94e-25!57;UBERON:0007135!6.94e-25!57;UBERON:0000955!1.32e-24!69;UBERON:0006238!1.32e-24!69;UBERON:0002616!5.18e-24!59;UBERON:0000924!5.18e-24!173;UBERON:0006601!5.18e-24!173;UBERON:0004121!1.95e-22!169;UBERON:0002780!2.21e-21!41;UBERON:0001890!2.21e-21!41;UBERON:0006240!2.21e-21!41;UBERON:0002346!9.76e-21!90;UBERON:0003080!1.58e-20!42;UBERON:0000153!7.04e-20!129;UBERON:0007811!7.04e-20!129;UBERON:0000033!2.15e-19!123;UBERON:0003075!4.36e-19!86;UBERON:0007284!4.36e-19!86;UBERON:0002020!2.95e-18!34;UBERON:0003528!2.95e-18!34;UBERON:0001893!3.99e-18!34;UBERON:0002791!1.43e-17!33;UBERON:0001869!2.00e-17!32;UBERON:0003056!1.03e-15!61;UBERON:0000956!4.83e-14!25;UBERON:0000203!4.83e-14!25;UBERON:0002619!2.46e-12!22;UBERON:0001950!3.99e-11!20;UBERON:0000922!2.62e-10!612;UBERON:0000468!5.85e-10!659;UBERON:0007023!3.92e-09!115;UBERON:0002050!9.21e-09!605;UBERON:0005423!9.21e-09!605;UBERON:0000480!1.04e-08!626;UBERON:0000467!1.27e-08!625;UBERON:0000475!1.33e-08!365;UBERON:0000923!1.79e-08!604;UBERON:0005291!1.79e-08!604;UBERON:0006598!1.79e-08!604;UBERON:0002532!1.79e-08!604;UBERON:0004111!1.78e-07!241;UBERON:0000025!3.26e-07!194;UBERON:0000483!6.06e-07!309;UBERON:0000062!6.67e-07!511;UBERON:0000119!9.65e-07!312
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}}
}}

Revision as of 19:47, 8 August 2012


Full id: C4166_neuroectodermal_Neural_small_Neurons_occipital_parietal_duodenum



Phase1 CAGE Peaks

Hg19::chr2:197791393..197791421,-p3@PGAP1
Hg19::chr2:197791423..197791438,-p2@PGAP1
Hg19::chr2:197791602..197791620,-p5@PGAP1


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.15e-3094
nervous system2.15e-3094
central nervous system9.78e-3082
neural tube6.94e-2557
neural rod6.94e-2557
future spinal cord6.94e-2557
neural keel6.94e-2557
brain1.32e-2469
future brain1.32e-2469
regional part of brain5.18e-2459
ectoderm5.18e-24173
presumptive ectoderm5.18e-24173
ectoderm-derived structure1.95e-22169
regional part of forebrain2.21e-2141
forebrain2.21e-2141
future forebrain2.21e-2141
neurectoderm9.76e-2190
anterior neural tube1.58e-2042
anterior region of body7.04e-20129
craniocervical region7.04e-20129
head2.15e-19123
neural plate4.36e-1986
presumptive neural plate4.36e-1986
gray matter2.95e-1834
brain grey matter2.95e-1834
telencephalon3.99e-1834
regional part of telencephalon1.43e-1733
cerebral hemisphere2.00e-1732
pre-chordal neural plate1.03e-1561
cerebral cortex4.83e-1425
pallium4.83e-1425
regional part of cerebral cortex2.46e-1222
neocortex3.99e-1120
embryo2.62e-10612
multi-cellular organism5.85e-10659
adult organism3.92e-09115
embryonic structure9.21e-09605
developing anatomical structure9.21e-09605
anatomical group1.04e-08626
anatomical system1.27e-08625
organism subdivision1.33e-08365
germ layer1.79e-08604
embryonic tissue1.79e-08604
presumptive structure1.79e-08604
epiblast (generic)1.79e-08604
anatomical conduit1.78e-07241
tube3.26e-07194
epithelium6.06e-07309
organ6.67e-07511
cell layer9.65e-07312


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)

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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.