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Coexpression cluster:C3428: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!4.25e-87!57;UBERON:0005068!4.25e-87!57;UBERON:0006241!4.25e-87!57;UBERON:0007135!4.25e-87!57;UBERON:0001017!6.75e-73!82;UBERON:0002616!1.09e-72!59;UBERON:0005743!1.14e-71!86;UBERON:0000955!1.06e-68!69;UBERON:0006238!1.06e-68!69;UBERON:0000073!1.94e-68!94;UBERON:0001016!1.94e-68!94;UBERON:0002780!3.47e-68!41;UBERON:0001890!3.47e-68!41;UBERON:0006240!3.47e-68!41;UBERON:0003080!2.44e-66!42;UBERON:0003075!2.62e-66!86;UBERON:0007284!2.62e-66!86;UBERON:0001893!1.59e-65!34;UBERON:0002020!3.15e-65!34;UBERON:0003528!3.15e-65!34;UBERON:0002791!3.43e-63!33;UBERON:0002346!9.99e-63!90;UBERON:0001869!1.22e-61!32;UBERON:0003056!2.05e-50!61;UBERON:0000956!4.90e-46!25;UBERON:0000203!4.90e-46!25;UBERON:0002619!2.55e-44!22;UBERON:0007023!2.79e-41!115;UBERON:0001950!1.12e-39!20;UBERON:0000033!3.32e-38!123;UBERON:0000153!8.57e-36!129;UBERON:0007811!8.57e-36!129;UBERON:0004121!4.14e-33!169;UBERON:0000924!5.34e-32!173;UBERON:0006601!5.34e-32!173;UBERON:0002420!3.80e-21!9;UBERON:0007245!3.80e-21!9;UBERON:0010009!3.80e-21!9;UBERON:0010011!3.80e-21!9;UBERON:0000454!3.80e-21!9;UBERON:0003076!9.36e-21!15;UBERON:0003057!9.36e-21!15;UBERON:0002308!2.57e-20!9;UBERON:0000125!2.57e-20!9;UBERON:0000025!2.42e-18!194;UBERON:0009663!1.97e-16!7;UBERON:0000200!8.22e-16!6;UBERON:0001871!2.96e-15!7;UBERON:0004733!7.63e-15!12;UBERON:0002028!7.63e-15!12;UBERON:0007277!7.63e-15!12;UBERON:0004111!8.39e-14!241;UBERON:0004732!1.49e-13!13;UBERON:0000349!3.38e-13!5;UBERON:0002298!5.41e-13!8;UBERON:0001872!6.25e-13!5;UBERON:0000483!3.40e-12!309;UBERON:0000064!5.65e-12!219;UBERON:0000119!6.14e-12!312;UBERON:0000477!1.34e-11!286;UBERON:0000475!1.24e-10!365;UBERON:0000369!1.30e-10!4;UBERON:0002435!1.30e-10!4;UBERON:0000204!1.30e-10!4;UBERON:0010082!1.30e-10!4;UBERON:0002680!1.16e-09!9;UBERON:0001895!1.16e-09!9;UBERON:0010092!1.16e-09!9;UBERON:0002771!9.44e-09!3;UBERON:0005383!1.90e-08!3;UBERON:0005382!1.90e-08!3;UBERON:0002021!2.40e-08!5;UBERON:0002240!6.06e-08!3;UBERON:0000988!1.09e-07!3;UBERON:0006331!2.50e-07!3;UBERON:0001896!3.20e-07!3;UBERON:0005290!3.20e-07!3;UBERON:0010096!3.20e-07!3
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}}
}}

Revision as of 15:06, 19 October 2012


Full id: C3428_cerebellum_medial_hippocampus_amygdala_occipital_brain_olfactory



Phase1 CAGE Peaks

Hg19::chr14:51491727..51491730,-p@chr14:51491727..51491730
-
Hg19::chr20:10256173..10256180,+p7@SNAP25
Hg19::chr20:44688143..44688157,+p@chr20:44688143..44688157
+


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 tube1.76e-9256
neural rod1.76e-9256
future spinal cord1.76e-9256
neural keel1.76e-9256
regional part of nervous system1.03e-8653
regional part of brain1.03e-8653
central nervous system4.07e-7781
brain4.68e-7468
future brain4.68e-7468
telencephalon6.72e-7134
brain grey matter1.15e-7034
gray matter1.15e-7034
cerebral hemisphere2.00e-6932
nervous system8.14e-6989
regional part of forebrain8.73e-6941
forebrain8.73e-6941
anterior neural tube8.73e-6941
future forebrain8.73e-6941
neural plate6.74e-6582
presumptive neural plate6.74e-6582
regional part of telencephalon3.15e-6332
neurectoderm1.44e-6186
adult organism3.41e-57114
regional part of cerebral cortex7.89e-5522
ecto-epithelium1.02e-49104
pre-chordal neural plate3.00e-4861
cerebral cortex4.86e-4825
pallium4.86e-4825
neocortex1.23e-4620
structure with developmental contribution from neural crest1.27e-42132
ectoderm-derived structure1.18e-34171
ectoderm1.18e-34171
presumptive ectoderm1.18e-34171
gyrus1.91e-286
organ system subdivision8.05e-25223
basal ganglion1.26e-249
nuclear complex of neuraxis1.26e-249
aggregate regional part of brain1.26e-249
collection of basal ganglia1.26e-249
cerebral subcortex1.26e-249
neural nucleus6.39e-249
nucleus of brain6.39e-249
posterior neural tube1.70e-2315
chordal neural plate1.70e-2315
limbic system1.80e-235
tube4.98e-22192
corpus striatum1.20e-184
striatum1.20e-184
ventral part of telencephalon1.20e-184
future corpus striatum1.20e-184
segmental subdivision of hindbrain3.15e-1812
hindbrain3.15e-1812
presumptive hindbrain3.15e-1812
regional part of metencephalon3.95e-189
metencephalon3.95e-189
future metencephalon3.95e-189
anatomical conduit2.11e-17240
temporal lobe7.34e-176
segmental subdivision of nervous system9.40e-1713
telencephalic nucleus1.96e-167
frontal cortex7.27e-153
caudate-putamen1.53e-143
dorsal striatum1.53e-143
pons8.28e-143
anatomical cluster1.33e-13373
organ part1.70e-13218
brainstem3.31e-126
epithelium5.91e-12306
cell layer9.15e-12309
middle temporal gyrus7.77e-112
middle frontal gyrus1.19e-102
amygdala1.38e-102
Ammon's horn1.59e-102
lobe parts of cerebral cortex1.59e-102
hippocampal formation1.59e-102
limbic lobe1.59e-102
caudate nucleus2.42e-102
future caudate nucleus2.42e-102
multi-tissue structure6.70e-10342
locus ceruleus1.15e-092
brainstem nucleus1.15e-092
hindbrain nucleus1.15e-092
meninx1.21e-092
membrane organ1.21e-092
meningeal cluster1.21e-092
occipital lobe4.96e-095
parietal lobe6.88e-095
cerebellum6.08e-086
rhombic lip6.08e-086
organ3.41e-07503
spinal cord5.78e-073
dorsal region element5.78e-073
dorsum5.78e-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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