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Coexpression cluster:C3079: Difference between revisions

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}}
}}

Revision as of 15:54, 26 November 2012


Full id: C3079_caudate_parietal_amygdala_hippocampus_brain_occipital_medulla



Phase1 CAGE Peaks

Hg19::chr11:10715215..10715235,-p5@MRVI1
Hg19::chr11:10715449..10715466,-p12@MRVI1
Hg19::chr11:10715502..10715516,-p9@MRVI1


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 organism2.15e-60114
neural tube2.51e-4156
neural rod2.51e-4156
future spinal cord2.51e-4156
neural keel2.51e-4156
regional part of nervous system2.88e-3853
regional part of brain2.88e-3853
telencephalon1.78e-3334
brain grey matter1.82e-3334
gray matter1.82e-3334
regional part of forebrain3.12e-3241
forebrain3.12e-3241
anterior neural tube3.12e-3241
future forebrain3.12e-3241
regional part of telencephalon4.37e-3132
cerebral hemisphere4.64e-3132
neural plate6.95e-3182
presumptive neural plate6.95e-3182
brain1.24e-3068
future brain1.24e-3068
central nervous system1.83e-3081
neurectoderm1.25e-2886
nervous system4.74e-2789
structure with developmental contribution from neural crest4.02e-23132
cerebral cortex5.05e-2225
pallium5.05e-2225
regional part of cerebral cortex5.16e-2222
pre-chordal neural plate1.45e-2161
ecto-epithelium1.02e-20104
neocortex1.82e-1920
organ system subdivision7.38e-14223
ectoderm-derived structure1.56e-13171
ectoderm1.56e-13171
presumptive ectoderm1.56e-13171
basal ganglion2.56e-139
nuclear complex of neuraxis2.56e-139
aggregate regional part of brain2.56e-139
collection of basal ganglia2.56e-139
cerebral subcortex2.56e-139
neural nucleus3.25e-139
nucleus of brain3.25e-139
anatomical conduit1.50e-11240
tube3.10e-11192
telencephalic nucleus6.90e-117
organ1.08e-10503
organ part1.28e-10218
posterior neural tube4.15e-1015
chordal neural plate4.15e-1015
anatomical cluster2.29e-09373
gyrus6.55e-096
brainstem1.15e-086
multi-tissue structure3.74e-08342
limbic system5.40e-085
temporal lobe1.45e-076
segmental subdivision of hindbrain2.33e-0712
hindbrain2.33e-0712
presumptive hindbrain2.33e-0712
omentum2.35e-076
peritoneum2.35e-076
abdominal cavity2.35e-076
visceral peritoneum2.35e-076
cell layer2.85e-07309
corpus striatum5.50e-074
striatum5.50e-074
ventral part of telencephalon5.50e-074
future corpus striatum5.50e-074
epithelium7.92e-07306


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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