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Coexpression cluster:C1678

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Full id: C1678_medulla_spinal_locus_pons_corpus_globus_thalamus



Phase1 CAGE Peaks

Hg19::chr12:54765345..54765358,-p@chr12:54765345..54765358
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Hg19::chr14:62010202..62010207,-p@chr14:62010202..62010207
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Hg19::chr15:93616900..93616918,-p6@RGMA
Hg19::chr2:69741788..69741801,-p@chr2:69741788..69741801
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Hg19::chr2:69741832..69741847,-p@chr2:69741832..69741847
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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
neural tube2.76e-7956
neural rod2.76e-7956
future spinal cord2.76e-7956
neural keel2.76e-7956
regional part of nervous system9.15e-6853
regional part of brain9.15e-6853
central nervous system2.10e-5981
brain1.55e-5468
future brain1.55e-5468
nervous system6.92e-5389
adult organism2.08e-52114
neural plate2.89e-5282
presumptive neural plate2.89e-5282
neurectoderm1.53e-4986
brain grey matter7.67e-4934
gray matter7.67e-4934
regional part of forebrain8.16e-4941
forebrain8.16e-4941
anterior neural tube8.16e-4941
future forebrain8.16e-4941
telencephalon1.30e-4834
cerebral hemisphere1.94e-4132
regional part of telencephalon1.99e-4132
ecto-epithelium7.61e-40104
structure with developmental contribution from neural crest1.05e-36132
regional part of cerebral cortex1.44e-3622
neocortex1.31e-3420
cerebral cortex5.43e-3225
pallium5.43e-3225
posterior neural tube8.49e-3215
chordal neural plate8.49e-3215
pre-chordal neural plate2.09e-3161
brainstem5.08e-306
ectoderm-derived structure1.57e-24171
ectoderm1.57e-24171
presumptive ectoderm1.57e-24171
organ system subdivision1.15e-22223
tube2.14e-21192
segmental subdivision of hindbrain1.04e-1912
hindbrain1.04e-1912
presumptive hindbrain1.04e-1912
gyrus2.21e-196
neural nucleus1.33e-189
nucleus of brain1.33e-189
segmental subdivision of nervous system4.06e-1813
medulla oblongata5.36e-163
myelencephalon5.36e-163
future myelencephalon5.36e-163
spinal cord6.21e-163
dorsal region element6.21e-163
dorsum6.21e-163
pons8.34e-163
anatomical conduit1.13e-15240
anatomical cluster2.86e-13373
basal ganglion7.72e-139
nuclear complex of neuraxis7.72e-139
aggregate regional part of brain7.72e-139
collection of basal ganglia7.72e-139
cerebral subcortex7.72e-139
epithelium1.23e-11306
organ part1.26e-11218
cell layer1.89e-11309
locus ceruleus4.02e-112
brainstem nucleus4.02e-112
hindbrain nucleus4.02e-112
temporal lobe6.14e-116
telencephalic nucleus7.97e-117
middle temporal gyrus3.18e-102
limbic system4.77e-095
regional part of metencephalon4.78e-099
metencephalon4.78e-099
future metencephalon4.78e-099
occipital lobe5.04e-095
parietal lobe5.63e-095
multi-tissue structure1.22e-08342
frontal cortex3.18e-073
germ layer9.21e-07560
germ layer / neural crest9.21e-07560
embryonic tissue9.21e-07560
presumptive structure9.21e-07560
germ layer / neural crest derived structure9.21e-07560
epiblast (generic)9.21e-07560


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.