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Coexpression cluster:C1416: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.02e-69!57;UBERON:0005068!1.02e-69!57;UBERON:0006241!1.02e-69!57;UBERON:0007135!1.02e-69!57;UBERON:0002616!5.14e-56!59;UBERON:0001017!1.46e-55!82;UBERON:0005743!4.68e-55!86;UBERON:0003075!1.35e-52!86;UBERON:0007284!1.35e-52!86;UBERON:0002346!2.88e-52!90;UBERON:0000955!1.05e-51!69;UBERON:0006238!1.05e-51!69;UBERON:0002780!1.99e-49!41;UBERON:0001890!1.99e-49!41;UBERON:0006240!1.99e-49!41;UBERON:0000073!7.73e-49!94;UBERON:0001016!7.73e-49!94;UBERON:0003080!4.36e-48!42;UBERON:0001893!4.11e-40!34;UBERON:0002020!9.06e-40!34;UBERON:0003528!9.06e-40!34;UBERON:0007023!3.09e-39!115;UBERON:0002791!1.13e-37!33;UBERON:0003056!1.45e-35!61;UBERON:0001869!3.53e-35!32;UBERON:0000033!2.24e-31!123;UBERON:0002619!4.43e-30!22;UBERON:0000153!2.02e-29!129;UBERON:0007811!2.02e-29!129;UBERON:0000025!1.08e-26!194;UBERON:0000956!4.22e-26!25;UBERON:0000203!4.22e-26!25;UBERON:0000924!1.83e-25!173;UBERON:0006601!1.83e-25!173;UBERON:0001950!3.05e-25!20;UBERON:0004121!5.32e-25!169;UBERON:0003076!5.13e-22!15;UBERON:0003057!5.13e-22!15;UBERON:0004111!4.45e-20!241;UBERON:0002298!6.32e-18!8;UBERON:0000477!6.94e-16!286;UBERON:0002308!1.94e-15!9;UBERON:0000125!1.94e-15!9;UBERON:0004733!1.33e-14!12;UBERON:0002028!1.33e-14!12;UBERON:0007277!1.33e-14!12;UBERON:0000483!2.17e-14!309;UBERON:0000119!3.96e-14!312;UBERON:0004732!2.30e-13!13;UBERON:0000475!3.51e-13!365;UBERON:0000200!1.72e-12!6;UBERON:0002420!1.35e-11!9;UBERON:0007245!1.35e-11!9;UBERON:0010009!1.35e-11!9;UBERON:0010011!1.35e-11!9;UBERON:0000454!1.35e-11!9;UBERON:0009663!1.38e-10!7;UBERON:0001894!1.41e-10!7;UBERON:0006222!1.41e-10!7;UBERON:0000349!3.40e-10!5;UBERON:0001896!4.68e-10!3;UBERON:0005290!4.68e-10!3;UBERON:0010096!4.68e-10!3;UBERON:0001872!4.82e-10!5;UBERON:0002240!4.97e-10!3;UBERON:0000988!1.24e-09!3;UBERON:0006331!1.35e-09!3;UBERON:0002771!1.61e-09!3;UBERON:0001871!2.66e-09!7;UBERON:0000064!5.19e-08!219;UBERON:0000481!7.27e-08!347;UBERON:0002680!8.46e-08!9;UBERON:0001895!8.46e-08!9;UBERON:0010092!8.46e-08!9;UBERON:0000369!1.93e-07!4;UBERON:0002435!1.93e-07!4;UBERON:0000204!1.93e-07!4;UBERON:0010082!1.93e-07!4;UBERON:0001897!3.00e-07!2;UBERON:0001954!4.43e-07!2;UBERON:0003022!4.43e-07!2;UBERON:0002421!4.43e-07!2;UBERON:0002600!4.43e-07!2;UBERON:0001873!5.96e-07!2;UBERON:0010122!5.96e-07!2;UBERON:0002148!6.90e-07!2;UBERON:0009662!6.90e-07!2
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}}
}}

Revision as of 11:15, 19 October 2012


Full id: C1416_corpus_diencephalon_medulla_spinal_thalamus_caudate_occipital



Phase1 CAGE Peaks

Hg19::chr15:93827399..93827403,+p@chr15:93827399..93827403
+
Hg19::chr16:70759540..70759547,+p@chr16:70759540..70759547
+
Hg19::chr17:73689469..73689476,-p@chr17:73689469..73689476
-
Hg19::chr1:234659231..234659238,-p@chr1:234659231..234659238
-
Hg19::chr5:7654271..7654280,+p14@ADCY2
Hg19::chr6:39335288..39335291,+p@chr6:39335288..39335291
+


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 tube2.54e-8456
neural rod2.54e-8456
future spinal cord2.54e-8456
neural keel2.54e-8456
regional part of nervous system2.26e-7653
regional part of brain2.26e-7653
regional part of forebrain6.28e-6441
forebrain6.28e-6441
anterior neural tube6.28e-6441
future forebrain6.28e-6441
telencephalon8.67e-6334
brain1.19e-6268
future brain1.19e-6268
brain grey matter3.09e-6234
gray matter3.09e-6234
central nervous system8.60e-6181
neural plate2.04e-5682
presumptive neural plate2.04e-5682
nervous system2.27e-5489
neurectoderm1.33e-5386
cerebral hemisphere5.66e-5332
regional part of telencephalon7.14e-5332
adult organism2.75e-46114
regional part of cerebral cortex1.14e-4422
ecto-epithelium1.39e-43104
pre-chordal neural plate5.49e-4261
neocortex1.11e-4120
cerebral cortex3.11e-3925
pallium3.11e-3925
structure with developmental contribution from neural crest3.91e-36132
brainstem6.55e-276
ectoderm-derived structure2.06e-26171
ectoderm2.06e-26171
presumptive ectoderm2.06e-26171
neural nucleus3.82e-259
nucleus of brain3.82e-259
tube1.89e-21192
organ system subdivision9.78e-21223
posterior neural tube1.82e-2015
chordal neural plate1.82e-2015
pons2.21e-193
basal ganglion5.17e-189
nuclear complex of neuraxis5.17e-189
aggregate regional part of brain5.17e-189
collection of basal ganglia5.17e-189
cerebral subcortex5.17e-189
gyrus3.88e-176
anatomical conduit3.64e-16240
telencephalic nucleus4.39e-157
temporal lobe9.77e-156
locus ceruleus1.75e-132
brainstem nucleus1.75e-132
hindbrain nucleus1.75e-132
segmental subdivision of hindbrain2.18e-1312
hindbrain2.18e-1312
presumptive hindbrain2.18e-1312
middle temporal gyrus2.92e-132
limbic system1.45e-125
segmental subdivision of nervous system2.41e-1213
occipital lobe2.41e-125
parietal lobe2.93e-125
epithelium1.40e-11306
cell layer2.04e-11309
organ part4.31e-11218
anatomical cluster2.17e-10373
medulla oblongata4.02e-103
myelencephalon4.02e-103
future myelencephalon4.02e-103
spinal cord9.30e-103
dorsal region element9.30e-103
dorsum9.30e-103
multi-tissue structure8.67e-09342
corpus callosum2.70e-081
central nervous system cell part cluster2.70e-081
axon tract2.70e-081
intercerebral commissure2.70e-081
dorsal telencephalic commissure2.70e-081
brain white matter2.70e-081
brain commissure2.70e-081
white matter2.70e-081
nervous system commissure2.70e-081
cerebral hemisphere white matter2.70e-081
nucleus accumbens5.70e-081
ventral striatum5.70e-081
olfactory region6.10e-081
primary subdivision of skull6.10e-081
cranium6.10e-081
neurocranium6.10e-081
chondrocranium6.10e-081
cartilaginous neurocranium6.10e-081
head paraxial mesoderm6.10e-081
paracentral gyrus6.52e-081
postcentral gyrus6.97e-081
occipital pole7.45e-081
pole of cerebral hemisphere7.45e-081
insula7.97e-081
substantia nigra1.04e-071
midbrain nucleus1.04e-071
regional part of midbrain1.04e-071
midbrain1.04e-071


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.

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