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Coexpression cluster:C1198: Difference between revisions

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|ontology_enrichment_disease=DOID:0050687!1.39e-10!143;DOID:305!1.77e-09!106
|ontology_enrichment_disease=DOID:0050687!1.39e-10!143;DOID:305!1.77e-09!106
|ontology_enrichment_uberon=UBERON:0000073!3.42e-44!94;UBERON:0001016!3.42e-44!94;UBERON:0005743!2.38e-42!86;UBERON:0001017!5.74e-40!82;UBERON:0002346!1.02e-33!90;UBERON:0003075!1.05e-33!86;UBERON:0007284!1.05e-33!86;UBERON:0001049!1.12e-33!57;UBERON:0005068!1.12e-33!57;UBERON:0006241!1.12e-33!57;UBERON:0007135!1.12e-33!57;UBERON:0000955!1.48e-32!69;UBERON:0006238!1.48e-32!69;UBERON:0000924!1.05e-30!173;UBERON:0006601!1.05e-30!173;UBERON:0004121!2.77e-30!169;UBERON:0002616!1.45e-28!59;UBERON:0003080!2.61e-26!42;UBERON:0002780!3.47e-26!41;UBERON:0001890!3.47e-26!41;UBERON:0006240!3.47e-26!41;UBERON:0007023!1.06e-25!115;UBERON:0003056!1.10e-25!61;UBERON:0000033!9.62e-25!123;UBERON:0000153!1.59e-24!129;UBERON:0007811!1.59e-24!129;UBERON:0001893!8.49e-23!34;UBERON:0002020!1.29e-22!34;UBERON:0003528!1.29e-22!34;UBERON:0002791!3.47e-22!33;UBERON:0001869!7.80e-22!32;UBERON:0000956!1.63e-17!25;UBERON:0000203!1.63e-17!25;UBERON:0002619!1.72e-15!22;UBERON:0001950!3.00e-14!20;UBERON:0000064!2.21e-10!219;UBERON:0003076!1.78e-08!15;UBERON:0003057!1.78e-08!15;UBERON:0000062!2.14e-07!511;UBERON:0000481!2.36e-07!347;UBERON:0004732!2.60e-07!13;UBERON:0004733!5.12e-07!12;UBERON:0002028!5.12e-07!12;UBERON:0007277!5.12e-07!12;UBERON:0002420!8.00e-07!9;UBERON:0007245!8.00e-07!9;UBERON:0010009!8.00e-07!9;UBERON:0010011!8.00e-07!9;UBERON:0000454!8.00e-07!9
|ontology_enrichment_uberon=UBERON:0000073!3.42e-44!94;UBERON:0001016!3.42e-44!94;UBERON:0005743!2.38e-42!86;UBERON:0001017!5.74e-40!82;UBERON:0002346!1.02e-33!90;UBERON:0003075!1.05e-33!86;UBERON:0007284!1.05e-33!86;UBERON:0001049!1.12e-33!57;UBERON:0005068!1.12e-33!57;UBERON:0006241!1.12e-33!57;UBERON:0007135!1.12e-33!57;UBERON:0000955!1.48e-32!69;UBERON:0006238!1.48e-32!69;UBERON:0000924!1.05e-30!173;UBERON:0006601!1.05e-30!173;UBERON:0004121!2.77e-30!169;UBERON:0002616!1.45e-28!59;UBERON:0003080!2.61e-26!42;UBERON:0002780!3.47e-26!41;UBERON:0001890!3.47e-26!41;UBERON:0006240!3.47e-26!41;UBERON:0007023!1.06e-25!115;UBERON:0003056!1.10e-25!61;UBERON:0000033!9.62e-25!123;UBERON:0000153!1.59e-24!129;UBERON:0007811!1.59e-24!129;UBERON:0001893!8.49e-23!34;UBERON:0002020!1.29e-22!34;UBERON:0003528!1.29e-22!34;UBERON:0002791!3.47e-22!33;UBERON:0001869!7.80e-22!32;UBERON:0000956!1.63e-17!25;UBERON:0000203!1.63e-17!25;UBERON:0002619!1.72e-15!22;UBERON:0001950!3.00e-14!20;UBERON:0000064!2.21e-10!219;UBERON:0003076!1.78e-08!15;UBERON:0003057!1.78e-08!15;UBERON:0000062!2.14e-07!511;UBERON:0000481!2.36e-07!347;UBERON:0004732!2.60e-07!13;UBERON:0004733!5.12e-07!12;UBERON:0002028!5.12e-07!12;UBERON:0007277!5.12e-07!12;UBERON:0002420!8.00e-07!9;UBERON:0007245!8.00e-07!9;UBERON:0010009!8.00e-07!9;UBERON:0010011!8.00e-07!9;UBERON:0000454!8.00e-07!9
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}}
}}

Revision as of 16:59, 8 August 2012


Full id: C1198_Neural_parietal_occipital_Astrocyte_brain_duodenum_temporal



Phase1 CAGE Peaks

Hg19::chr14:29234581..29234601,+p2@FOXG1
Hg19::chr3:13083919..13083940,-p@chr3:13083919..13083940
-
Hg19::chr3:26664291..26664329,+p1@LRRC3B
Hg19::chr6:118228389..118228435,+p1@SLC35F1
Hg19::chr8:28351707..28351781,+p1@FZD3
Hg19::chr9:126774018..126774055,+p1@LHX2
Hg19::chr9:126774058..126774081,+p3@LHX2


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:0007399nervous system development0.00857355975151682
GO:0007420brain development0.00857355975151682
GO:0048513organ development0.012219673955238
GO:0007417central nervous system development0.012219673955238
GO:0001736establishment of planar polarity0.0133886523705115
GO:0001738morphogenesis of a polarized epithelium0.0133886523705115
GO:0048731system development0.0133886523705115
GO:0007164establishment of tissue polarity0.0133886523705115
GO:0042813Wnt receptor activity0.013600369910269
GO:0001843neural tube closure0.0152905103453416
GO:0014020primary neural tube formation0.0152905103453416
GO:0048856anatomical structure development0.0152905103453416
GO:0004926non-G-protein coupled 7TM receptor activity0.0152905103453416
GO:0001839neural plate morphogenesis0.0152905103453416
GO:0001841neural tube formation0.0152905103453416
GO:0001840neural plate development0.0152905103453416
GO:0001838embryonic epithelial tube formation0.0152905103453416
GO:0007275multicellular organismal development0.0152905103453416
GO:0021915neural tube development0.0152905103453416
GO:0016331morphogenesis of embryonic epithelium0.0168165908635914
GO:0042472inner ear morphogenesis0.0194503404689869
GO:0009953dorsal/ventral pattern formation0.0194503404689869
GO:0042471ear morphogenesis0.0205943935320225
GO:0048839inner ear development0.0241829077621319
GO:0043583ear development0.0248812194198963
GO:0043565sequence-specific DNA binding0.0248812194198963
GO:0007498mesoderm development0.0248812194198963
GO:0032502developmental process0.0304572556182887
GO:0002009morphogenesis of an epithelium0.0331313768523156
GO:0032501multicellular organismal process0.038969389921935
GO:0035239tube morphogenesis0.038969389921935
GO:0045177apical part of cell0.038969389921935
GO:0007423sensory organ development0.038969389921935
GO:0003002regionalization0.038969389921935
GO:0048598embryonic morphogenesis0.0390841434722103
GO:0009792embryonic development ending in birth or egg hatching0.0390841434722103
GO:0043009chordate embryonic development0.0390841434722103
GO:0035295tube development0.0468078249567275
GO:0003700transcription factor activity0.0471084598502684
GO:0007389pattern specification process0.0471084598502684



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
neural cell3.82e-1125
neurectodermal cell1.37e-0859
ectodermal cell1.89e-0771
neuron associated cell6.12e-0717
neuron associated cell (sensu Vertebrata)6.12e-0717
Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.42e-4494
nervous system3.42e-4494
central nervous system5.74e-4082
neurectoderm1.02e-3390
neural plate1.05e-3386
presumptive neural plate1.05e-3386
neural tube1.12e-3357
neural rod1.12e-3357
future spinal cord1.12e-3357
neural keel1.12e-3357
brain1.48e-3269
future brain1.48e-3269
ectoderm1.05e-30173
presumptive ectoderm1.05e-30173
ectoderm-derived structure2.77e-30169
regional part of brain1.45e-2859
anterior neural tube2.61e-2642
regional part of forebrain3.47e-2641
forebrain3.47e-2641
future forebrain3.47e-2641
adult organism1.06e-25115
pre-chordal neural plate1.10e-2561
head9.62e-25123
anterior region of body1.59e-24129
craniocervical region1.59e-24129
telencephalon8.49e-2334
gray matter1.29e-2234
brain grey matter1.29e-2234
regional part of telencephalon3.47e-2233
cerebral hemisphere7.80e-2232
cerebral cortex1.63e-1725
pallium1.63e-1725
regional part of cerebral cortex1.72e-1522
neocortex3.00e-1420
organ part2.21e-10219
posterior neural tube1.78e-0815
chordal neural plate1.78e-0815
organ2.14e-07511
multi-tissue structure2.36e-07347
segmental subdivision of nervous system2.60e-0713
segmental subdivision of hindbrain5.12e-0712
hindbrain5.12e-0712
presumptive hindbrain5.12e-0712
basal ganglion8.00e-079
nuclear complex of neuraxis8.00e-079
aggregate regional part of brain8.00e-079
collection of basal ganglia8.00e-079
cerebral subcortex8.00e-079
Disease
Ontology termp-valuen
cell type cancer1.39e-10143
carcinoma1.77e-09106


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.