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Coexpression cluster:C3052: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.25e-27!57;UBERON:0005068!1.25e-27!57;UBERON:0006241!1.25e-27!57;UBERON:0007135!1.25e-27!57;UBERON:0000073!3.86e-27!94;UBERON:0001016!3.86e-27!94;UBERON:0001017!5.33e-27!82;UBERON:0005743!3.94e-26!86;UBERON:0002616!4.11e-23!59;UBERON:0007023!5.92e-22!115;UBERON:0000955!8.69e-22!69;UBERON:0006238!8.69e-22!69;UBERON:0002780!8.17e-21!41;UBERON:0001890!8.17e-21!41;UBERON:0006240!8.17e-21!41;UBERON:0003080!1.96e-20!42;UBERON:0002346!1.81e-19!90;UBERON:0003075!3.16e-19!86;UBERON:0007284!3.16e-19!86;UBERON:0001893!3.54e-17!34;UBERON:0002020!3.75e-17!34;UBERON:0003528!3.75e-17!34;UBERON:0000924!5.40e-17!173;UBERON:0006601!5.40e-17!173;UBERON:0004121!1.35e-16!169;UBERON:0002791!1.51e-16!33;UBERON:0001869!7.29e-16!32;UBERON:0003056!5.68e-15!61;UBERON:0000033!8.05e-14!123;UBERON:0000153!2.68e-13!129;UBERON:0007811!2.68e-13!129;UBERON:0002619!9.56e-12!22;UBERON:0000956!1.17e-11!25;UBERON:0000203!1.17e-11!25;UBERON:0001950!1.34e-10!20;UBERON:0003076!2.46e-08!15;UBERON:0003057!2.46e-08!15;UBERON:0002308!3.68e-07!9;UBERON:0000125!3.68e-07!9;UBERON:0004732!3.89e-07!13;UBERON:0002420!5.18e-07!9;UBERON:0007245!5.18e-07!9;UBERON:0010009!5.18e-07!9;UBERON:0010011!5.18e-07!9;UBERON:0000454!5.18e-07!9
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}}
}}

Revision as of 14:45, 19 October 2012


Full id: C3052_testis_corpus_spinal_thalamus_pons_optic_diencephalon



Phase1 CAGE Peaks

Hg19::chr10:86211964..86211988,+p5@FAM190B
Hg19::chr11:111749942..111749989,+p3@C11orf1
Hg19::chr8:18666347..18666356,-p26@PSD3


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
neural tube2.05e-9856
neural rod2.05e-9856
future spinal cord2.05e-9856
neural keel2.05e-9856
regional part of nervous system2.28e-8953
regional part of brain2.28e-8953
central nervous system3.12e-8181
nervous system1.43e-7589
brain4.25e-7468
future brain4.25e-7468
neural plate4.32e-7482
presumptive neural plate4.32e-7482
adult organism2.93e-70114
neurectoderm3.65e-7086
regional part of forebrain1.89e-6841
forebrain1.89e-6841
anterior neural tube1.89e-6841
future forebrain1.89e-6841
telencephalon3.91e-6734
brain grey matter4.23e-6734
gray matter4.23e-6734
regional part of telencephalon7.16e-6132
cerebral hemisphere8.79e-6132
ecto-epithelium3.39e-56104
pre-chordal neural plate6.26e-5061
structure with developmental contribution from neural crest2.13e-48132
regional part of cerebral cortex1.01e-4622
neocortex3.13e-4120
cerebral cortex9.68e-4125
pallium9.68e-4125
ectoderm-derived structure7.99e-38171
ectoderm7.99e-38171
presumptive ectoderm7.99e-38171
posterior neural tube1.21e-2915
chordal neural plate1.21e-2915
neural nucleus4.36e-299
nucleus of brain4.36e-299
basal ganglion2.90e-289
nuclear complex of neuraxis2.90e-289
aggregate regional part of brain2.90e-289
collection of basal ganglia2.90e-289
cerebral subcortex2.90e-289
organ system subdivision1.36e-27223
tube2.40e-25192
segmental subdivision of nervous system7.48e-2413
telencephalic nucleus1.07e-227
segmental subdivision of hindbrain4.67e-2112
hindbrain4.67e-2112
presumptive hindbrain4.67e-2112
brainstem9.77e-216
gyrus1.52e-196
anatomical conduit4.42e-18240
limbic system8.85e-165
epithelium3.14e-15306
anatomical cluster5.05e-15373
organ part5.27e-15218
cell layer5.72e-15309
corpus striatum4.37e-134
striatum4.37e-134
ventral part of telencephalon4.37e-134
future corpus striatum4.37e-134
regional part of metencephalon1.17e-129
metencephalon1.17e-129
future metencephalon1.17e-129
temporal lobe1.73e-116
multi-tissue structure1.93e-11342
pons2.13e-113
medulla oblongata4.49e-113
myelencephalon4.49e-113
future myelencephalon4.49e-113
parietal lobe4.64e-115
occipital lobe8.41e-115
spinal cord8.74e-113
dorsal region element8.74e-113
dorsum8.74e-113
frontal cortex1.92e-103
caudate-putamen3.90e-103
dorsal striatum3.90e-103
organ1.06e-08503
globus pallidus4.07e-082
pallidum4.07e-082
locus ceruleus4.22e-082
brainstem nucleus4.22e-082
hindbrain nucleus4.22e-082
multi cell component structure5.35e-082
neuron projection bundle5.35e-082
dorsal plus ventral thalamus6.34e-082
thalamic complex6.34e-082
middle temporal gyrus1.05e-072
germ layer1.20e-07560
germ layer / neural crest1.20e-07560
embryonic tissue1.20e-07560
presumptive structure1.20e-07560
germ layer / neural crest derived structure1.20e-07560
epiblast (generic)1.20e-07560
middle frontal gyrus1.56e-072
embryonic structure1.67e-07564
caudate nucleus2.31e-072
future caudate nucleus2.31e-072
amygdala2.89e-072


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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