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Coexpression cluster:C3600: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 15:15, 19 October 2012


Full id: C3600_neuroectodermal_occipital_middle_parietal_medial_pituitary_olfactory



Phase1 CAGE Peaks

Hg19::chr16:88584331..88584360,-p@chr16:88584331..88584360
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Hg19::chr21:42035250..42035310,-p@chr21:42035250..42035310
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Hg19::chr5:132802985..132802999,-p@chr5:132802985..132802999
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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 tube2.33e-8856
neural rod2.33e-8856
future spinal cord2.33e-8856
neural keel2.33e-8856
regional part of nervous system5.72e-8053
regional part of brain5.72e-8053
central nervous system3.39e-7381
regional part of forebrain8.85e-7041
forebrain8.85e-7041
anterior neural tube8.85e-7041
future forebrain8.85e-7041
nervous system5.65e-6889
brain7.79e-6668
future brain7.79e-6668
neurectoderm8.09e-6686
brain grey matter1.29e-6434
gray matter1.29e-6434
telencephalon1.97e-6434
neural plate5.18e-6382
presumptive neural plate5.18e-6382
cerebral hemisphere4.04e-5932
regional part of telencephalon4.35e-5932
regional part of cerebral cortex2.75e-5122
neocortex5.95e-5120
pre-chordal neural plate2.98e-5061
ecto-epithelium9.80e-50104
cerebral cortex1.03e-4425
pallium1.03e-4425
structure with developmental contribution from neural crest6.01e-41132
ectoderm-derived structure2.03e-38171
ectoderm2.03e-38171
presumptive ectoderm2.03e-38171
adult organism5.68e-36114
organ system subdivision1.19e-26223
tube7.21e-22192
neural nucleus3.92e-219
nucleus of brain3.92e-219
gyrus3.70e-196
posterior neural tube6.15e-1915
chordal neural plate6.15e-1915
basal ganglion1.97e-169
nuclear complex of neuraxis1.97e-169
aggregate regional part of brain1.97e-169
collection of basal ganglia1.97e-169
cerebral subcortex1.97e-169
parietal lobe4.69e-165
occipital lobe7.25e-165
telencephalic nucleus1.13e-157
anatomical conduit2.76e-15240
anatomical cluster4.92e-14373
epithelium2.28e-13306
cell layer4.00e-13309
brainstem7.63e-136
segmental subdivision of hindbrain8.68e-1212
hindbrain8.68e-1212
presumptive hindbrain8.68e-1212
temporal lobe1.38e-116
organ part6.20e-11218
segmental subdivision of nervous system8.47e-1113
frontal cortex1.04e-103
spinal cord3.14e-103
dorsal region element3.14e-103
dorsum3.14e-103
pons4.71e-103
multi-tissue structure5.30e-10342
regional part of metencephalon1.75e-089
metencephalon1.75e-089
future metencephalon1.75e-089
corpus striatum6.65e-084
striatum6.65e-084
ventral part of telencephalon6.65e-084
future corpus striatum6.65e-084
middle frontal gyrus8.14e-082
gland of diencephalon8.78e-084
neuroendocrine gland8.78e-084
middle temporal gyrus8.98e-082
diencephalon1.80e-077
future diencephalon1.80e-077
pituitary gland1.82e-072
locus ceruleus3.01e-072
brainstem nucleus3.01e-072
hindbrain nucleus3.01e-072
germ layer3.88e-07560
germ layer / neural crest3.88e-07560
embryonic tissue3.88e-07560
presumptive structure3.88e-07560
germ layer / neural crest derived structure3.88e-07560
epiblast (generic)3.88e-07560
embryo4.25e-07592
globus pallidus5.09e-072
pallidum5.09e-072
embryonic structure5.44e-07564
developing anatomical structure6.21e-07581


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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