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Coexpression cluster:C1179: Difference between revisions

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}}
}}

Revision as of 14:44, 26 November 2012


Full id: C1179_parietal_putamen_occipital_medial_caudate_hippocampus_amygdala



Phase1 CAGE Peaks

Hg19::chr12:87232771..87232788,-p2@ENST00000550014
Hg19::chr19:55946950..55946958,-p@chr19:55946950..55946958
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Hg19::chr2:166060606..166060607,-p6@SCN3A
Hg19::chr2:175708423..175708427,-p@chr2:175708423..175708427
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Hg19::chr3:116303353..116303355,-p@chr3:116303353..116303355
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Hg19::chr3:116818981..116818985,-p@chr3:116818981..116818985
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Hg19::chr3:116997189..116997193,-p@chr3:116997189..116997193
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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:0001518voltage-gated sodium channel complex0.0135994348286824
GO:0005248voltage-gated sodium channel activity0.0135994348286824
GO:0005272sodium channel activity0.023489932885906
GO:0031402sodium ion binding0.0296714941716708
GO:0006814sodium ion transport0.0427764040974921
GO:0031420alkali metal ion binding0.0443698732289336
GO:0022843voltage-gated cation channel activity0.0443698732289336
GO:0005244voltage-gated ion channel activity0.0443698732289336
GO:0022832voltage-gated channel activity0.0443698732289336
GO:0005261cation channel activity0.0479414419718199
GO:0046873metal ion transmembrane transporter activity0.0479414419718199
GO:0022836gated channel activity0.0479414419718199
GO:0015672monovalent inorganic cation transport0.0479414419718199
GO:0005216ion channel activity0.0479414419718199
GO:0030001metal ion transport0.0479414419718199
GO:0022838substrate specific channel activity0.0479414419718199
GO:0015267channel activity0.0479414419718199
GO:0022803passive transmembrane transporter activity0.0479414419718199



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 tube9.14e-9456
neural rod9.14e-9456
future spinal cord9.14e-9456
neural keel9.14e-9456
regional part of nervous system4.40e-8653
regional part of brain4.40e-8653
regional part of forebrain4.67e-7441
forebrain4.67e-7441
anterior neural tube4.67e-7441
future forebrain4.67e-7441
brain grey matter3.94e-7134
gray matter3.94e-7134
telencephalon1.76e-7034
central nervous system5.33e-6981
brain7.75e-6768
future brain7.75e-6768
nervous system3.02e-6689
regional part of telencephalon5.82e-6632
cerebral hemisphere6.58e-6632
neural plate3.96e-6382
presumptive neural plate3.96e-6382
neurectoderm1.26e-5986
regional part of cerebral cortex3.61e-5022
pre-chordal neural plate1.29e-4961
ecto-epithelium1.82e-49104
cerebral cortex6.75e-4825
pallium6.75e-4825
adult organism1.40e-47114
neocortex1.06e-4420
structure with developmental contribution from neural crest6.93e-40132
ectoderm-derived structure1.80e-31171
ectoderm1.80e-31171
presumptive ectoderm1.80e-31171
organ system subdivision4.82e-28223
basal ganglion7.35e-259
nuclear complex of neuraxis7.35e-259
aggregate regional part of brain7.35e-259
collection of basal ganglia7.35e-259
cerebral subcortex7.35e-259
neural nucleus1.31e-249
nucleus of brain1.31e-249
tube1.67e-24192
posterior neural tube5.57e-2015
chordal neural plate5.57e-2015
telencephalic nucleus1.39e-197
anatomical conduit6.00e-18240
gyrus8.44e-176
brainstem3.64e-166
limbic system7.04e-155
temporal lobe1.86e-146
parietal lobe4.23e-145
segmental subdivision of hindbrain2.48e-1312
hindbrain2.48e-1312
presumptive hindbrain2.48e-1312
anatomical cluster3.48e-13373
epithelium9.31e-13306
cell layer1.66e-12309
corpus striatum3.28e-124
striatum3.28e-124
ventral part of telencephalon3.28e-124
future corpus striatum3.28e-124
segmental subdivision of nervous system3.42e-1213
organ part3.56e-12218
multi-tissue structure6.04e-10342
caudate-putamen9.08e-103
dorsal striatum9.08e-103
frontal cortex9.35e-103
occipital lobe2.62e-095
spinal cord3.78e-093
dorsal region element3.78e-093
dorsum3.78e-093
pons5.69e-093
medulla oblongata6.88e-093
myelencephalon6.88e-093
future myelencephalon6.88e-093
embryonic structure1.01e-07564
regional part of metencephalon2.32e-079
metencephalon2.32e-079
future metencephalon2.32e-079
germ layer2.55e-07560
germ layer / neural crest2.55e-07560
embryonic tissue2.55e-07560
presumptive structure2.55e-07560
germ layer / neural crest derived structure2.55e-07560
epiblast (generic)2.55e-07560
middle frontal gyrus3.76e-072
embryo3.86e-07592
Ammon's horn3.87e-072
lobe parts of cerebral cortex3.87e-072
hippocampal formation3.87e-072
limbic lobe3.87e-072
developing anatomical structure4.97e-07581
amygdala5.78e-072
caudate nucleus5.95e-072
future caudate nucleus5.95e-072
middle temporal gyrus6.48e-072
dorsal plus ventral thalamus9.10e-072
thalamic complex9.10e-072


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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