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Coexpression cluster:C3066: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!8.45e-88!56;UBERON:0005068!8.45e-88!56;UBERON:0006241!8.45e-88!56;UBERON:0007135!8.45e-88!56;UBERON:0001017!4.00e-87!81;UBERON:0001016!4.36e-82!89;UBERON:0000073!8.01e-82!53;UBERON:0002616!8.01e-82!53;UBERON:0000955!9.27e-72!68;UBERON:0006238!9.27e-72!68;UBERON:0003075!2.42e-67!82;UBERON:0007284!2.42e-67!82;UBERON:0002780!1.51e-66!41;UBERON:0001890!1.51e-66!41;UBERON:0003080!1.51e-66!41;UBERON:0006240!1.51e-66!41;UBERON:0002346!6.81e-66!86;UBERON:0003528!2.21e-61!34;UBERON:0002020!2.21e-61!34;UBERON:0001893!2.44e-61!34;UBERON:0001869!7.82e-58!32;UBERON:0002791!1.74e-57!32;UBERON:0010371!9.83e-56!104;UBERON:0003056!4.23e-53!61;UBERON:0004121!1.45e-47!171;UBERON:0000924!1.45e-47!171;UBERON:0006601!1.45e-47!171;UBERON:0000956!7.15e-45!25;UBERON:0000203!7.15e-45!25;UBERON:0002619!6.08e-44!22;UBERON:0007023!2.49e-42!114;UBERON:0010314!3.39e-42!132;UBERON:0001950!1.22e-39!20;UBERON:0011216!5.70e-31!223;UBERON:0003076!2.96e-21!15;UBERON:0003057!2.96e-21!15;UBERON:0002420!7.66e-18!9;UBERON:0007245!7.66e-18!9;UBERON:0010009!7.66e-18!9;UBERON:0010011!7.66e-18!9;UBERON:0000454!7.66e-18!9;UBERON:0000025!8.34e-18!192;UBERON:0000125!1.38e-17!9;UBERON:0002308!1.38e-17!9;UBERON:0000477!3.57e-16!373;UBERON:0004733!7.67e-16!12;UBERON:0002028!7.67e-16!12;UBERON:0007277!7.67e-16!12;UBERON:0000064!5.44e-15!218;UBERON:0004732!1.93e-14!13;UBERON:0000200!5.77e-14!6;UBERON:0009663!7.46e-14!7;UBERON:0004111!9.50e-13!240;UBERON:0002298!1.84e-12!6;UBERON:0000483!6.69e-12!306;UBERON:0000349!8.45e-12!5;UBERON:0001871!9.41e-12!6;UBERON:0000119!1.25e-11!309;UBERON:0002021!1.27e-11!5;UBERON:0001872!1.51e-11!5;UBERON:0002680!9.04e-11!9;UBERON:0001895!9.04e-11!9;UBERON:0010092!9.04e-11!9;UBERON:0000481!7.48e-09!342;UBERON:0000369!8.63e-09!4;UBERON:0002435!8.63e-09!4;UBERON:0000204!8.63e-09!4;UBERON:0010082!8.63e-09!4;UBERON:0000922!1.23e-08!592;UBERON:0002784!1.24e-08!4;UBERON:0001870!9.36e-08!3;UBERON:0000923!2.51e-07!560;UBERON:0010316!2.51e-07!560;UBERON:0005291!2.51e-07!560;UBERON:0006598!2.51e-07!560;UBERON:0010317!2.51e-07!560;UBERON:0002532!2.51e-07!560;UBERON:0001894!2.86e-07!7;UBERON:0006222!2.86e-07!7;UBERON:0002240!3.05e-07!3;UBERON:0005174!3.05e-07!3;UBERON:0001137!3.05e-07!3;UBERON:0005423!3.33e-07!581;UBERON:0000988!3.69e-07!3;UBERON:0002050!3.93e-07!564;UBERON:0001896!5.94e-07!3;UBERON:0005290!5.94e-07!3;UBERON:0010096!5.94e-07!3;UBERON:0005383!6.58e-07!3;UBERON:0005382!6.58e-07!3
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}}
}}

Revision as of 15:54, 26 November 2012


Full id: C3066_Neurons_occipital_amygdala_medial_hippocampus_cerebellum_Neural



Phase1 CAGE Peaks

Hg19::chr10:99609717..99609780,+p2@GOLGA7B
Hg19::chr2:210565005..210565017,+p@chr2:210565005..210565017
+
Hg19::chr4:176733558..176733609,-p7@GPM6A


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:0009986cell surface0.0435652890615801



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>

Cell Type
Ontology termp-valuen
neuronal stem cell5.72e-078
Uber Anatomy
Ontology termp-valuen
neural tube8.45e-8856
neural rod8.45e-8856
future spinal cord8.45e-8856
neural keel8.45e-8856
central nervous system4.00e-8781
nervous system4.36e-8289
regional part of nervous system8.01e-8253
regional part of brain8.01e-8253
brain9.27e-7268
future brain9.27e-7268
neural plate2.42e-6782
presumptive neural plate2.42e-6782
regional part of forebrain1.51e-6641
forebrain1.51e-6641
anterior neural tube1.51e-6641
future forebrain1.51e-6641
neurectoderm6.81e-6686
brain grey matter2.21e-6134
gray matter2.21e-6134
telencephalon2.44e-6134
cerebral hemisphere7.82e-5832
regional part of telencephalon1.74e-5732
ecto-epithelium9.83e-56104
pre-chordal neural plate4.23e-5361
ectoderm-derived structure1.45e-47171
ectoderm1.45e-47171
presumptive ectoderm1.45e-47171
cerebral cortex7.15e-4525
pallium7.15e-4525
regional part of cerebral cortex6.08e-4422
adult organism2.49e-42114
structure with developmental contribution from neural crest3.39e-42132
neocortex1.22e-3920
organ system subdivision5.70e-31223
posterior neural tube2.96e-2115
chordal neural plate2.96e-2115
basal ganglion7.66e-189
nuclear complex of neuraxis7.66e-189
aggregate regional part of brain7.66e-189
collection of basal ganglia7.66e-189
cerebral subcortex7.66e-189
tube8.34e-18192
neural nucleus1.38e-179
nucleus of brain1.38e-179
anatomical cluster3.57e-16373
segmental subdivision of hindbrain7.67e-1612
hindbrain7.67e-1612
presumptive hindbrain7.67e-1612
organ part5.44e-15218
segmental subdivision of nervous system1.93e-1413
gyrus5.77e-146
telencephalic nucleus7.46e-147
anatomical conduit9.50e-13240
brainstem1.84e-126
epithelium6.69e-12306
limbic system8.45e-125
temporal lobe9.41e-126
cell layer1.25e-11309
occipital lobe1.27e-115
parietal lobe1.51e-115
regional part of metencephalon9.04e-119
metencephalon9.04e-119
future metencephalon9.04e-119
multi-tissue structure7.48e-09342
corpus striatum8.63e-094
striatum8.63e-094
ventral part of telencephalon8.63e-094
future corpus striatum8.63e-094
embryo1.23e-08592
regional part of diencephalon1.24e-084
frontal cortex9.36e-083
germ layer2.51e-07560
germ layer / neural crest2.51e-07560
embryonic tissue2.51e-07560
presumptive structure2.51e-07560
germ layer / neural crest derived structure2.51e-07560
epiblast (generic)2.51e-07560
diencephalon2.86e-077
future diencephalon2.86e-077
spinal cord3.05e-073
dorsal region element3.05e-073
dorsum3.05e-073
developing anatomical structure3.33e-07581
pons3.69e-073
embryonic structure3.93e-07564
medulla oblongata5.94e-073
myelencephalon5.94e-073
future myelencephalon5.94e-073
caudate-putamen6.58e-073
dorsal striatum6.58e-073


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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