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Coexpression cluster:C2172: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.37e-79!57;UBERON:0005068!2.37e-79!57;UBERON:0006241!2.37e-79!57;UBERON:0007135!2.37e-79!57;UBERON:0002616!6.48e-67!59;UBERON:0001017!5.15e-66!82;UBERON:0005743!1.22e-64!86;UBERON:0000955!1.37e-64!69;UBERON:0006238!1.37e-64!69;UBERON:0002780!1.35e-62!41;UBERON:0001890!1.35e-62!41;UBERON:0006240!1.35e-62!41;UBERON:0003080!8.00e-61!42;UBERON:0000073!8.25e-59!94;UBERON:0001016!8.25e-59!94;UBERON:0003075!7.39e-58!86;UBERON:0007284!7.39e-58!86;UBERON:0001893!1.14e-54!34;UBERON:0002020!1.27e-54!34;UBERON:0003528!1.27e-54!34;UBERON:0002346!1.68e-54!90;UBERON:0002791!7.95e-53!33;UBERON:0001869!1.11e-51!32;UBERON:0007023!2.23e-44!115;UBERON:0003056!2.29e-40!61;UBERON:0000956!5.62e-40!25;UBERON:0000203!5.62e-40!25;UBERON:0002619!2.05e-39!22;UBERON:0001950!1.19e-35!20;UBERON:0000033!1.16e-33!123;UBERON:0000153!2.56e-31!129;UBERON:0007811!2.56e-31!129;UBERON:0004121!4.44e-27!169;UBERON:0000924!4.87e-26!173;UBERON:0006601!4.87e-26!173;UBERON:0000025!4.80e-21!194;UBERON:0003076!1.00e-18!15;UBERON:0003057!1.00e-18!15;UBERON:0002420!2.65e-16!9;UBERON:0007245!2.65e-16!9;UBERON:0010009!2.65e-16!9;UBERON:0010011!2.65e-16!9;UBERON:0000454!2.65e-16!9;UBERON:0002308!8.41e-16!9;UBERON:0000125!8.41e-16!9;UBERON:0004111!7.09e-15!241;UBERON:0004733!2.40e-14!12;UBERON:0002028!2.40e-14!12;UBERON:0007277!2.40e-14!12;UBERON:0004732!4.77e-13!13;UBERON:0000483!6.57e-13!309;UBERON:0000119!1.33e-12!312;UBERON:0009663!1.49e-12!7;UBERON:0000200!1.67e-12!6;UBERON:0001871!2.65e-12!7;UBERON:0000477!4.36e-11!286;UBERON:0000349!5.38e-11!5;UBERON:0002298!6.25e-11!8;UBERON:0001872!1.24e-10!5;UBERON:0002021!1.68e-10!5;UBERON:0000475!2.85e-10!365;UBERON:0002680!9.22e-10!9;UBERON:0001895!9.22e-10!9;UBERON:0010092!9.22e-10!9;UBERON:0001894!2.97e-09!7;UBERON:0006222!2.97e-09!7;UBERON:0000369!2.39e-08!4;UBERON:0002435!2.39e-08!4;UBERON:0000204!2.39e-08!4;UBERON:0010082!2.39e-08!4;UBERON:0000064!7.04e-08!219;UBERON:0000481!2.25e-07!347;UBERON:0002771!4.13e-07!3
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}}
}}

Revision as of 18:03, 8 August 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
neural tube2.37e-7957
neural rod2.37e-7957
future spinal cord2.37e-7957
neural keel2.37e-7957
regional part of brain6.48e-6759
central nervous system5.15e-6682
brain1.37e-6469
future brain1.37e-6469
regional part of forebrain1.35e-6241
forebrain1.35e-6241
future forebrain1.35e-6241
anterior neural tube8.00e-6142
regional part of nervous system8.25e-5994
nervous system8.25e-5994
neural plate7.39e-5886
presumptive neural plate7.39e-5886
telencephalon1.14e-5434
gray matter1.27e-5434
brain grey matter1.27e-5434
neurectoderm1.68e-5490
regional part of telencephalon7.95e-5333
cerebral hemisphere1.11e-5132
adult organism2.23e-44115
pre-chordal neural plate2.29e-4061
cerebral cortex5.62e-4025
pallium5.62e-4025
regional part of cerebral cortex2.05e-3922
neocortex1.19e-3520
head1.16e-33123
anterior region of body2.56e-31129
craniocervical region2.56e-31129
ectoderm-derived structure4.44e-27169
ectoderm4.87e-26173
presumptive ectoderm4.87e-26173
tube4.80e-21194
posterior neural tube1.00e-1815
chordal neural plate1.00e-1815
basal ganglion2.65e-169
nuclear complex of neuraxis2.65e-169
aggregate regional part of brain2.65e-169
collection of basal ganglia2.65e-169
cerebral subcortex2.65e-169
nucleus of brain8.41e-169
neural nucleus8.41e-169
anatomical conduit7.09e-15241
segmental subdivision of hindbrain2.40e-1412
hindbrain2.40e-1412
presumptive hindbrain2.40e-1412
segmental subdivision of nervous system4.77e-1313
epithelium6.57e-13309
cell layer1.33e-12312
telencephalic nucleus1.49e-127
gyrus1.67e-126
temporal lobe2.65e-127
anatomical cluster4.36e-11286
limbic system5.38e-115
brainstem6.25e-118
parietal lobe1.24e-105
occipital lobe1.68e-105
organism subdivision2.85e-10365
regional part of metencephalon9.22e-109
metencephalon9.22e-109
future metencephalon9.22e-109
diencephalon2.97e-097
future diencephalon2.97e-097
corpus striatum2.39e-084
striatum2.39e-084
ventral part of telencephalon2.39e-084
future corpus striatum2.39e-084
organ part7.04e-08219
multi-tissue structure2.25e-07347
middle temporal gyrus4.13e-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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