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Coexpression cluster:C4418: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!4.94e-39!86;UBERON:0000073!5.45e-39!94;UBERON:0001016!5.45e-39!94;UBERON:0001017!2.64e-36!82;UBERON:0003075!5.79e-36!86;UBERON:0007284!5.79e-36!86;UBERON:0001049!2.24e-35!57;UBERON:0005068!2.24e-35!57;UBERON:0006241!2.24e-35!57;UBERON:0007135!2.24e-35!57;UBERON:0002346!5.85e-33!90;UBERON:0007023!4.03e-31!115;UBERON:0004121!4.85e-30!169;UBERON:0000955!5.32e-29!69;UBERON:0006238!5.32e-29!69;UBERON:0002616!7.25e-29!59;UBERON:0000924!2.21e-28!173;UBERON:0006601!2.21e-28!173;UBERON:0002020!1.85e-26!34;UBERON:0003528!1.85e-26!34;UBERON:0001893!2.30e-26!34;UBERON:0002780!1.04e-25!41;UBERON:0001890!1.04e-25!41;UBERON:0006240!1.04e-25!41;UBERON:0002791!1.47e-25!33;UBERON:0003080!1.11e-24!42;UBERON:0001869!1.62e-24!32;UBERON:0003056!2.62e-23!61;UBERON:0000033!2.02e-21!123;UBERON:0000153!9.91e-21!129;UBERON:0007811!9.91e-21!129;UBERON:0000956!5.98e-19!25;UBERON:0000203!5.98e-19!25;UBERON:0002619!2.24e-18!22;UBERON:0001950!6.30e-17!20;UBERON:0004111!6.76e-13!241;UBERON:0003076!9.11e-12!15;UBERON:0003057!9.11e-12!15;UBERON:0000025!1.59e-11!194;UBERON:0000483!4.85e-11!309;UBERON:0000119!1.43e-10!312;UBERON:0004732!4.56e-10!13;UBERON:0000477!5.26e-10!286;UBERON:0004733!3.65e-09!12;UBERON:0002028!3.65e-09!12;UBERON:0007277!3.65e-09!12;UBERON:0000064!3.89e-09!219;UBERON:0002308!5.48e-09!9;UBERON:0000125!5.48e-09!9;UBERON:0000468!7.13e-09!659;UBERON:0002420!1.97e-08!9;UBERON:0007245!1.97e-08!9;UBERON:0010009!1.97e-08!9;UBERON:0010011!1.97e-08!9;UBERON:0000454!1.97e-08!9;UBERON:0000922!6.65e-08!612;UBERON:0000467!1.32e-07!625;UBERON:0000480!1.69e-07!626;UBERON:0009663!3.34e-07!7;UBERON:0000475!7.66e-07!365;UBERON:0002680!8.53e-07!9;UBERON:0001895!8.53e-07!9;UBERON:0010092!8.53e-07!9;UBERON:0001871!9.34e-07!7
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}}
}}

Revision as of 20:00, 8 August 2012


Full id: C4418_cerebellum_optic_smallcell_leiomyoma_Mesothelial_caudate_substantia



Phase1 CAGE Peaks

Hg19::chr4:44450814..44450832,-p1@KCTD8
Hg19::chr4:44450933..44450947,-p2@KCTD8
Hg19::chr7:143059752..143059755,-p11@FAM131B


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:0008076voltage-gated potassium channel complex0.0487975391498881
GO:0005249voltage-gated potassium channel activity0.0487975391498881
GO:0005267potassium channel activity0.0487975391498881
GO:0022843voltage-gated cation channel activity0.0487975391498881
GO:0006813potassium ion transport0.0487975391498881
GO:0005244voltage-gated ion channel activity0.0487975391498881
GO:0022832voltage-gated channel activity0.0487975391498881
GO:0005261cation channel activity0.0487975391498881
GO:0046873metal ion transmembrane transporter activity0.0487975391498881
GO:0022836gated channel activity0.0487975391498881
GO:0015672monovalent inorganic cation transport0.0487975391498881
GO:0005216ion channel activity0.0487975391498881
GO:0030001metal ion transport0.0487975391498881
GO:0022838substrate specific channel activity0.0487975391498881
GO:0015267channel activity0.0487975391498881
GO:0022803passive transmembrane transporter activity0.0487975391498881



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 system5.45e-3994
nervous system5.45e-3994
central nervous system2.64e-3682
neural plate5.79e-3686
presumptive neural plate5.79e-3686
neural tube2.24e-3557
neural rod2.24e-3557
future spinal cord2.24e-3557
neural keel2.24e-3557
neurectoderm5.85e-3390
adult organism4.03e-31115
ectoderm-derived structure4.85e-30169
brain5.32e-2969
future brain5.32e-2969
regional part of brain7.25e-2959
ectoderm2.21e-28173
presumptive ectoderm2.21e-28173
gray matter1.85e-2634
brain grey matter1.85e-2634
telencephalon2.30e-2634
regional part of forebrain1.04e-2541
forebrain1.04e-2541
future forebrain1.04e-2541
regional part of telencephalon1.47e-2533
anterior neural tube1.11e-2442
cerebral hemisphere1.62e-2432
pre-chordal neural plate2.62e-2361
head2.02e-21123
anterior region of body9.91e-21129
craniocervical region9.91e-21129
cerebral cortex5.98e-1925
pallium5.98e-1925
regional part of cerebral cortex2.24e-1822
neocortex6.30e-1720
anatomical conduit6.76e-13241
posterior neural tube9.11e-1215
chordal neural plate9.11e-1215
tube1.59e-11194
epithelium4.85e-11309
cell layer1.43e-10312
segmental subdivision of nervous system4.56e-1013
anatomical cluster5.26e-10286
segmental subdivision of hindbrain3.65e-0912
hindbrain3.65e-0912
presumptive hindbrain3.65e-0912
organ part3.89e-09219
nucleus of brain5.48e-099
neural nucleus5.48e-099
multi-cellular organism7.13e-09659
basal ganglion1.97e-089
nuclear complex of neuraxis1.97e-089
aggregate regional part of brain1.97e-089
collection of basal ganglia1.97e-089
cerebral subcortex1.97e-089
embryo6.65e-08612
anatomical system1.32e-07625
anatomical group1.69e-07626
telencephalic nucleus3.34e-077
organism subdivision7.66e-07365
regional part of metencephalon8.53e-079
metencephalon8.53e-079
future metencephalon8.53e-079
temporal lobe9.34e-077


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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