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Coexpression cluster:C2077: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!2.79e-82!56;UBERON:0005068!2.79e-82!56;UBERON:0006241!2.79e-82!56;UBERON:0007135!2.79e-82!56;UBERON:0000073!3.45e-78!53;UBERON:0002616!3.45e-78!53;UBERON:0001017!4.49e-73!81;UBERON:0000955!1.39e-72!68;UBERON:0006238!1.39e-72!68;UBERON:0003528!3.56e-71!34;UBERON:0002020!3.56e-71!34;UBERON:0001016!2.45e-68!89;UBERON:0002346!7.70e-66!86;UBERON:0001893!2.12e-65!34;UBERON:0002791!8.78e-65!32;UBERON:0001869!1.72e-64!32;UBERON:0003075!6.41e-63!82;UBERON:0007284!6.41e-63!82;UBERON:0002780!3.68e-62!41;UBERON:0001890!3.68e-62!41;UBERON:0003080!3.68e-62!41;UBERON:0006240!3.68e-62!41;UBERON:0002619!3.40e-50!22;UBERON:0010371!4.02e-50!104;UBERON:0003056!8.95e-46!61;UBERON:0000956!8.30e-44!25;UBERON:0000203!8.30e-44!25;UBERON:0001950!1.21e-43!20;UBERON:0004121!1.18e-39!171;UBERON:0000924!1.18e-39!171;UBERON:0006601!1.18e-39!171;UBERON:0007023!2.43e-38!114;UBERON:0010314!1.87e-37!132;UBERON:0000125!6.75e-30!9;UBERON:0002308!6.75e-30!9;UBERON:0011216!8.76e-24!223;UBERON:0002420!1.18e-23!9;UBERON:0007245!1.18e-23!9;UBERON:0010009!1.18e-23!9;UBERON:0010011!1.18e-23!9;UBERON:0000454!1.18e-23!9;UBERON:0009663!2.10e-23!7;UBERON:0003076!3.23e-20!15;UBERON:0003057!3.23e-20!15;UBERON:0000200!4.72e-20!6;UBERON:0002298!8.05e-20!6;UBERON:0000025!8.99e-20!192;UBERON:0004732!1.91e-19!13;UBERON:0001872!1.05e-16!5;UBERON:0004733!1.74e-16!12;UBERON:0002028!1.74e-16!12;UBERON:0007277!1.74e-16!12;UBERON:0000064!4.22e-14!218;UBERON:0004111!7.42e-14!240;UBERON:0000369!8.65e-14!4;UBERON:0002435!8.65e-14!4;UBERON:0000204!8.65e-14!4;UBERON:0010082!8.65e-14!4;UBERON:0001871!1.76e-12!6;UBERON:0000477!4.33e-12!373;UBERON:0000349!8.40e-12!5;UBERON:0000483!4.63e-11!306;UBERON:0001870!4.64e-11!3;UBERON:0000988!6.51e-11!3;UBERON:0005383!6.51e-11!3;UBERON:0005382!6.51e-11!3;UBERON:0000119!7.45e-11!309;UBERON:0001896!1.23e-10!3;UBERON:0005290!1.23e-10!3;UBERON:0010096!1.23e-10!3;UBERON:0002680!4.94e-09!9;UBERON:0001895!4.94e-09!9;UBERON:0010092!4.94e-09!9;UBERON:0001954!1.75e-08!2;UBERON:0003022!1.75e-08!2;UBERON:0002421!1.75e-08!2;UBERON:0002600!1.75e-08!2;UBERON:0002771!2.59e-08!2;UBERON:0001875!2.88e-08!2;UBERON:0006514!2.88e-08!2;UBERON:0002148!3.32e-08!2;UBERON:0006331!3.32e-08!2;UBERON:0009662!3.32e-08!2;UBERON:0000481!3.60e-08!342;UBERON:0002702!3.82e-08!2;UBERON:0001873!7.36e-08!2;UBERON:0010122!7.36e-08!2;UBERON:0000062!1.07e-07!503;UBERON:0002021!3.18e-07!5
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}}
}}

Revision as of 15:16, 26 November 2012


Full id: C2077_optic_hippocampus_occipital_middle_amygdala_locus_medial



Phase1 CAGE Peaks

Hg19::chr10:83823278..83823283,+p@chr10:83823278..83823283
+
Hg19::chr11:83167654..83167665,-p43@DLG2
Hg19::chr13:84385839..84385842,-p@chr13:84385839..84385842
-
Hg19::chr5:132028817..132028824,-p@chr5:132028817..132028824
-


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 tube2.79e-8256
neural rod2.79e-8256
future spinal cord2.79e-8256
neural keel2.79e-8256
regional part of nervous system3.45e-7853
regional part of brain3.45e-7853
central nervous system4.49e-7381
brain1.39e-7268
future brain1.39e-7268
brain grey matter3.56e-7134
gray matter3.56e-7134
nervous system2.45e-6889
neurectoderm7.70e-6686
telencephalon2.12e-6534
regional part of telencephalon8.78e-6532
cerebral hemisphere1.72e-6432
neural plate6.41e-6382
presumptive neural plate6.41e-6382
regional part of forebrain3.68e-6241
forebrain3.68e-6241
anterior neural tube3.68e-6241
future forebrain3.68e-6241
regional part of cerebral cortex3.40e-5022
ecto-epithelium4.02e-50104
pre-chordal neural plate8.95e-4661
cerebral cortex8.30e-4425
pallium8.30e-4425
neocortex1.21e-4320
ectoderm-derived structure1.18e-39171
ectoderm1.18e-39171
presumptive ectoderm1.18e-39171
adult organism2.43e-38114
structure with developmental contribution from neural crest1.87e-37132
neural nucleus6.75e-309
nucleus of brain6.75e-309
organ system subdivision8.76e-24223
basal ganglion1.18e-239
nuclear complex of neuraxis1.18e-239
aggregate regional part of brain1.18e-239
collection of basal ganglia1.18e-239
cerebral subcortex1.18e-239
telencephalic nucleus2.10e-237
posterior neural tube3.23e-2015
chordal neural plate3.23e-2015
gyrus4.72e-206
brainstem8.05e-206
tube8.99e-20192
segmental subdivision of nervous system1.91e-1913
parietal lobe1.05e-165
segmental subdivision of hindbrain1.74e-1612
hindbrain1.74e-1612
presumptive hindbrain1.74e-1612
organ part4.22e-14218
anatomical conduit7.42e-14240
corpus striatum8.65e-144
striatum8.65e-144
ventral part of telencephalon8.65e-144
future corpus striatum8.65e-144
temporal lobe1.76e-126
anatomical cluster4.33e-12373
limbic system8.40e-125
epithelium4.63e-11306
frontal cortex4.64e-113
pons6.51e-113
caudate-putamen6.51e-113
dorsal striatum6.51e-113
cell layer7.45e-11309
medulla oblongata1.23e-103
myelencephalon1.23e-103
future myelencephalon1.23e-103
regional part of metencephalon4.94e-099
metencephalon4.94e-099
future metencephalon4.94e-099
Ammon's horn1.75e-082
lobe parts of cerebral cortex1.75e-082
hippocampal formation1.75e-082
limbic lobe1.75e-082
middle temporal gyrus2.59e-082
globus pallidus2.88e-082
pallidum2.88e-082
locus ceruleus3.32e-082
brainstem nucleus3.32e-082
hindbrain nucleus3.32e-082
multi-tissue structure3.60e-08342
middle frontal gyrus3.82e-082
caudate nucleus7.36e-082
future caudate nucleus7.36e-082
organ1.07e-07503
occipital lobe3.18e-075


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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