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Coexpression cluster:C3161

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Full id: C3161_skeletal_spinal_hippocampus_medulla_teratocarcinoma_skin_amygdala



Phase1 CAGE Peaks

Hg19::chr11:57003063..57003075,-p@chr11:57003063..57003075
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Hg19::chr11:57003843..57003857,-p@chr11:57003843..57003857
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Hg19::chr11:57003864..57003887,-p@chr11:57003864..57003887
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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


No GOStat results

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
adult organism9.64e-68115
neural tube7.46e-4657
neural rod7.46e-4657
future spinal cord7.46e-4657
neural keel7.46e-4657
central nervous system1.23e-4082
neural plate1.88e-3886
presumptive neural plate1.88e-3886
regional part of brain2.36e-3659
neurectoderm4.84e-3690
regional part of nervous system1.89e-3494
nervous system1.89e-3494
regional part of forebrain2.57e-3441
forebrain2.57e-3441
future forebrain2.57e-3441
brain6.35e-3469
future brain6.35e-3469
anterior neural tube2.85e-3342
gray matter1.34e-3234
brain grey matter1.34e-3234
telencephalon3.02e-3234
regional part of telencephalon4.70e-3133
cerebral hemisphere4.12e-2932
pre-chordal neural plate3.61e-2461
regional part of cerebral cortex2.37e-2322
anterior region of body6.74e-23129
craniocervical region6.74e-23129
cerebral cortex4.75e-2225
pallium4.75e-2225
ectoderm-derived structure2.08e-20169
head2.77e-20123
neocortex4.65e-2020
ectoderm1.51e-19173
presumptive ectoderm1.51e-19173
tube7.49e-17194
organ part4.36e-14219
anatomical cluster6.05e-14286
temporal lobe7.18e-147
anatomical conduit2.05e-13241
posterior neural tube2.30e-1315
chordal neural plate2.30e-1315
nucleus of brain3.55e-129
neural nucleus3.55e-129
basal ganglion3.94e-129
nuclear complex of neuraxis3.94e-129
aggregate regional part of brain3.94e-129
collection of basal ganglia3.94e-129
cerebral subcortex3.94e-129
epithelium1.94e-11309
cell layer3.79e-11312
brainstem4.71e-118
multi-tissue structure6.53e-11347
limbic system1.56e-095
organ1.96e-09511
embryo4.63e-09612
telencephalic nucleus4.74e-097
multi-cellular organism6.67e-09659
segmental subdivision of hindbrain1.05e-0812
hindbrain1.05e-0812
presumptive hindbrain1.05e-0812
segmental subdivision of nervous system6.67e-0813
organism subdivision8.05e-08365
corpus striatum2.24e-074
striatum2.24e-074
ventral part of telencephalon2.24e-074
future corpus striatum2.24e-074
gyrus2.51e-076
spinal cord4.35e-073
medulla oblongata6.11e-073
myelencephalon6.11e-073
future myelencephalon6.11e-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.