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Coexpression cluster:C2172: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!3.21e-112!53;UBERON:0002616!3.21e-112!53;UBERON:0001049!4.58e-111!56;UBERON:0005068!4.58e-111!56;UBERON:0006241!4.58e-111!56;UBERON:0007135!4.58e-111!56;UBERON:0000955!2.58e-93!68;UBERON:0006238!2.58e-93!68;UBERON:0001017!1.14e-92!81;UBERON:0002780!2.63e-89!41;UBERON:0001890!2.63e-89!41;UBERON:0003080!2.63e-89!41;UBERON:0006240!2.63e-89!41;UBERON:0001893!1.28e-83!34;UBERON:0003528!1.32e-83!34;UBERON:0002020!1.32e-83!34;UBERON:0001016!1.40e-82!89;UBERON:0001869!1.84e-77!32;UBERON:0002791!6.04e-77!32;UBERON:0003075!1.08e-76!82;UBERON:0007284!1.08e-76!82;UBERON:0002619!8.70e-76!22;UBERON:0002346!1.05e-72!86;UBERON:0001950!1.80e-68!20;UBERON:0000956!2.35e-66!25;UBERON:0000203!2.35e-66!25;UBERON:0003056!2.24e-61!61;UBERON:0010371!1.67e-58!104;UBERON:0007023!7.02e-56!114;UBERON:0010314!9.16e-49!132;UBERON:0004121!1.45e-40!171;UBERON:0000924!1.45e-40!171;UBERON:0006601!1.45e-40!171;UBERON:0011216!3.24e-30!223;UBERON:0000025!9.82e-26!192;UBERON:0004733!8.70e-23!12;UBERON:0002028!8.70e-23!12;UBERON:0007277!8.70e-23!12;UBERON:0000200!1.30e-22!6;UBERON:0003076!4.78e-22!15;UBERON:0003057!4.78e-22!15;UBERON:0002298!3.74e-21!6;UBERON:0004732!6.62e-21!13;UBERON:0000349!1.15e-19!5;UBERON:0001872!1.80e-19!5;UBERON:0001871!3.78e-19!6;UBERON:0002021!4.93e-19!5;UBERON:0002420!6.58e-19!9;UBERON:0007245!6.58e-19!9;UBERON:0010009!6.58e-19!9;UBERON:0010011!6.58e-19!9;UBERON:0000454!6.58e-19!9;UBERON:0004111!1.29e-18!240;UBERON:0000125!2.20e-18!9;UBERON:0002308!2.20e-18!9;UBERON:0000064!1.81e-15!218;UBERON:0000477!9.96e-15!373;UBERON:0000483!3.15e-14!306;UBERON:0002680!4.88e-14!9;UBERON:0001895!4.88e-14!9;UBERON:0010092!4.88e-14!9;UBERON:0000119!5.43e-14!309;UBERON:0000481!1.82e-12!342;UBERON:0009663!2.52e-12!7;UBERON:0001870!2.76e-12!3;UBERON:0000988!1.35e-11!3;UBERON:0001896!2.69e-11!3;UBERON:0005290!2.69e-11!3;UBERON:0010096!2.69e-11!3;UBERON:0001876!5.37e-09!2;UBERON:0001954!7.02e-09!2;UBERON:0003022!7.02e-09!2;UBERON:0002421!7.02e-09!2;UBERON:0002600!7.02e-09!2;UBERON:0000369!9.58e-09!4;UBERON:0002435!9.58e-09!4;UBERON:0000204!9.58e-09!4;UBERON:0010082!9.58e-09!4;UBERON:0002771!1.24e-08!2;UBERON:0002702!1.50e-08!2;UBERON:0001894!2.35e-08!7;UBERON:0006222!2.35e-08!7;UBERON:0001897!2.81e-08!2;UBERON:0002148!2.81e-08!2;UBERON:0006331!2.81e-08!2;UBERON:0009662!2.81e-08!2;UBERON:0010225!2.81e-08!2;UBERON:0002360!5.80e-08!2;UBERON:0000094!5.80e-08!2;UBERON:0010743!5.80e-08!2;UBERON:0000062!1.87e-07!503
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}}
}}

Revision as of 15:20, 26 November 2012


Full id: C2172_amygdala_hippocampus_medial_cerebellum_parietal_insula_occipital



Phase1 CAGE Peaks

Hg19::chr11:85430299..85430311,-p13@SYTL2
Hg19::chr12:13720089..13720098,-p@chr12:13720089..13720098
-
Hg19::chr2:162565057..162565078,+p@chr2:162565057..162565078
+
Hg19::chr2:166096015..166096026,+p4@SCN2A


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:0042043neurexin binding0.0305870188632333
GO:0001518voltage-gated sodium channel complex0.0305870188632333
GO:0005248voltage-gated sodium channel activity0.0305870188632333
GO:0017137Rab GTPase binding0.0305870188632333
GO:0019897extrinsic to plasma membrane0.0337764427171738
GO:0005272sodium channel activity0.0337764427171738
GO:0044459plasma membrane part0.0337764427171738
GO:0017016Ras GTPase binding0.0337764427171738
GO:0048770pigment granule0.0337764427171738
GO:0042470melanosome0.0337764427171738
GO:0031267small GTPase binding0.0337764427171738
GO:0031402sodium ion binding0.0337764427171738
GO:0051020GTPase binding0.0337764427171738
GO:0019898extrinsic to membrane0.0345921258226974



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
regional part of nervous system3.21e-11253
regional part of brain3.21e-11253
neural tube4.58e-11156
neural rod4.58e-11156
future spinal cord4.58e-11156
neural keel4.58e-11156
brain2.58e-9368
future brain2.58e-9368
central nervous system1.14e-9281
regional part of forebrain2.63e-8941
forebrain2.63e-8941
anterior neural tube2.63e-8941
future forebrain2.63e-8941
telencephalon1.28e-8334
brain grey matter1.32e-8334
gray matter1.32e-8334
nervous system1.40e-8289
cerebral hemisphere1.84e-7732
regional part of telencephalon6.04e-7732
neural plate1.08e-7682
presumptive neural plate1.08e-7682
regional part of cerebral cortex8.70e-7622
neurectoderm1.05e-7286
neocortex1.80e-6820
cerebral cortex2.35e-6625
pallium2.35e-6625
pre-chordal neural plate2.24e-6161
ecto-epithelium1.67e-58104
adult organism7.02e-56114
structure with developmental contribution from neural crest9.16e-49132
ectoderm-derived structure1.45e-40171
ectoderm1.45e-40171
presumptive ectoderm1.45e-40171
organ system subdivision3.24e-30223
tube9.82e-26192
segmental subdivision of hindbrain8.70e-2312
hindbrain8.70e-2312
presumptive hindbrain8.70e-2312
gyrus1.30e-226
posterior neural tube4.78e-2215
chordal neural plate4.78e-2215
brainstem3.74e-216
segmental subdivision of nervous system6.62e-2113
limbic system1.15e-195
parietal lobe1.80e-195
temporal lobe3.78e-196
occipital lobe4.93e-195
basal ganglion6.58e-199
nuclear complex of neuraxis6.58e-199
aggregate regional part of brain6.58e-199
collection of basal ganglia6.58e-199
cerebral subcortex6.58e-199
anatomical conduit1.29e-18240
neural nucleus2.20e-189
nucleus of brain2.20e-189
organ part1.81e-15218
anatomical cluster9.96e-15373
epithelium3.15e-14306
regional part of metencephalon4.88e-149
metencephalon4.88e-149
future metencephalon4.88e-149
cell layer5.43e-14309
multi-tissue structure1.82e-12342
telencephalic nucleus2.52e-127
frontal cortex2.76e-123
pons1.35e-113
medulla oblongata2.69e-113
myelencephalon2.69e-113
future myelencephalon2.69e-113
amygdala5.37e-092
Ammon's horn7.02e-092
lobe parts of cerebral cortex7.02e-092
hippocampal formation7.02e-092
limbic lobe7.02e-092
corpus striatum9.58e-094
striatum9.58e-094
ventral part of telencephalon9.58e-094
future corpus striatum9.58e-094
middle temporal gyrus1.24e-082
middle frontal gyrus1.50e-082
diencephalon2.35e-087
future diencephalon2.35e-087
dorsal plus ventral thalamus2.81e-082
locus ceruleus2.81e-082
brainstem nucleus2.81e-082
hindbrain nucleus2.81e-082
thalamic complex2.81e-082
meninx5.80e-082
membrane organ5.80e-082
meningeal cluster5.80e-082
organ1.87e-07503


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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