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Coexpression cluster:C4134: Difference between revisions

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|tf_chipseq_enrich=PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268461534371988
|tf_chipseq_enrich=PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268461534371988
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}}
}}

Revision as of 16:34, 26 November 2012


Full id: C4134_nonsmall_cerebellum_medulloblastoma_small_gastrointestinal_eye_pons



Phase1 CAGE Peaks

Hg19::chr2:155554797..155554837,+p3@KCNJ3
Hg19::chr4:163084826..163084834,-p4@FSTL5
Hg19::chr4:163085107..163085118,-p2@FSTL5


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:0015467G-protein activated inward rectifier potassium channel activity0.00721139691311709
GO:0030315T-tubule0.00721139691311709
GO:0042383sarcolemma0.0153818225045911
GO:0005242inward rectifier potassium channel activity0.0187438363623487
GO:0009897external side of plasma membrane0.028826481240087



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
neural tube1.59e-7156
neural rod1.59e-7156
future spinal cord1.59e-7156
neural keel1.59e-7156
regional part of nervous system1.46e-6853
regional part of brain1.46e-6853
central nervous system2.42e-6281
brain9.02e-6068
future brain9.02e-6068
neurectoderm5.15e-5686
nervous system5.26e-5589
regional part of forebrain1.63e-5441
forebrain1.63e-5441
anterior neural tube1.63e-5441
future forebrain1.63e-5441
neural plate1.77e-5382
presumptive neural plate1.77e-5382
brain grey matter7.45e-4734
gray matter7.45e-4734
telencephalon2.11e-4634
cerebral hemisphere3.00e-4232
pre-chordal neural plate5.54e-4261
regional part of telencephalon6.29e-4232
ecto-epithelium6.77e-42104
regional part of cerebral cortex3.10e-3922
neocortex3.64e-3420
cerebral cortex4.34e-3425
pallium4.34e-3425
structure with developmental contribution from neural crest1.22e-30132
ectoderm-derived structure3.17e-30171
ectoderm3.17e-30171
presumptive ectoderm3.17e-30171
adult organism1.81e-28114
organ system subdivision9.28e-24223
tube1.27e-18192
posterior neural tube2.25e-1715
chordal neural plate2.25e-1715
gyrus2.82e-166
segmental subdivision of hindbrain1.15e-1412
hindbrain1.15e-1412
presumptive hindbrain1.15e-1412
neural nucleus5.14e-149
nucleus of brain5.14e-149
anatomical conduit2.02e-13240
segmental subdivision of nervous system2.04e-1313
anatomical cluster3.23e-12373
brainstem7.83e-126
regional part of metencephalon7.91e-129
metencephalon7.91e-129
future metencephalon7.91e-129
organ part7.10e-11218
epithelium4.23e-10306
basal ganglion5.26e-109
nuclear complex of neuraxis5.26e-109
aggregate regional part of brain5.26e-109
collection of basal ganglia5.26e-109
cerebral subcortex5.26e-109
cell layer6.88e-10309
pons1.23e-093
occipital lobe1.60e-095
temporal lobe2.11e-096
frontal cortex2.23e-093
diencephalon2.44e-097
future diencephalon2.44e-097
limbic system3.02e-095
telencephalic nucleus3.10e-097
parietal lobe5.28e-095
multi-tissue structure2.05e-08342
locus ceruleus5.58e-072
brainstem nucleus5.58e-072
hindbrain nucleus5.58e-072
Ammon's horn6.26e-072
lobe parts of cerebral cortex6.26e-072
hippocampal formation6.26e-072
limbic lobe6.26e-072
middle frontal gyrus8.83e-072
Disease
Ontology termp-valuen
lung small cell carcinoma4.81e-074


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
PBX3#5090214.60967512449610.006056122473217890.0268461534371988



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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