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Coexpression cluster:C2060: Difference between revisions

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}}
}}

Revision as of 15:16, 26 November 2012


Full id: C2060_cerebellum_Neural_parietal_Neurons_brain_maxillary_occipital



Phase1 CAGE Peaks

Hg19::chr10:47023421..47023433,-p@chr10:47023421..47023433
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Hg19::chr5:20471939..20471943,-p@chr5:20471939..20471943
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Hg19::chr7:137039191..137039196,-p1@ENST00000438969
Hg19::chrX:10644728..10644748,-p@chrX:10644728..10644748
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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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
neuronal stem cell2.22e-118
Uber Anatomy
Ontology termp-valuen
neural tube2.02e-7756
neural rod2.02e-7756
future spinal cord2.02e-7756
neural keel2.02e-7756
regional part of nervous system2.09e-7653
regional part of brain2.09e-7653
central nervous system2.09e-7681
nervous system2.66e-6889
brain6.50e-6268
future brain6.50e-6268
neural plate2.83e-5182
presumptive neural plate2.83e-5182
regional part of forebrain3.89e-5041
forebrain3.89e-5041
anterior neural tube3.89e-5041
future forebrain3.89e-5041
telencephalon2.52e-4934
neurectoderm1.23e-4886
cerebral hemisphere4.01e-4732
brain grey matter2.76e-4434
gray matter2.76e-4434
regional part of telencephalon5.65e-4232
cerebral cortex8.57e-4225
pallium8.57e-4225
regional part of cerebral cortex1.85e-4122
neocortex2.57e-3920
ecto-epithelium2.97e-39104
structure with developmental contribution from neural crest2.05e-34132
adult organism4.87e-33114
ectoderm-derived structure5.01e-33171
ectoderm5.01e-33171
presumptive ectoderm5.01e-33171
pre-chordal neural plate1.80e-3261
segmental subdivision of hindbrain4.42e-2812
hindbrain4.42e-2812
presumptive hindbrain4.42e-2812
posterior neural tube5.66e-2815
chordal neural plate5.66e-2815
segmental subdivision of nervous system7.92e-2613
organ system subdivision1.73e-25223
brainstem3.43e-226
gyrus3.05e-216
temporal lobe4.44e-196
tube1.54e-18192
medulla oblongata6.14e-173
myelencephalon6.14e-173
future myelencephalon6.14e-173
regional part of metencephalon3.25e-159
metencephalon3.25e-159
future metencephalon3.25e-159
anatomical conduit1.32e-13240
anatomical cluster1.29e-12373
middle temporal gyrus1.18e-112
organ part9.36e-11218
occipital lobe4.91e-105
epithelium2.41e-09306
cell layer3.41e-09309
cerebellum3.77e-096
rhombic lip3.77e-096
caudate-putamen3.95e-083
dorsal striatum3.95e-083
pons6.05e-083
frontal cortex7.20e-083
multi-tissue structure1.07e-07342
olfactory region6.43e-071
primary subdivision of skull6.43e-071
cranium6.43e-071
neurocranium6.43e-071
chondrocranium6.43e-071
cartilaginous neurocranium6.43e-071
head paraxial mesoderm6.43e-071


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.