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Coexpression cluster:C4396: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 19:59, 8 August 2012


Full id: C4396_glioblastoma_medial_amygdala_insula_olfactory_brain_parietal



Phase1 CAGE Peaks

Hg19::chr4:176734117..176734124,-p30@GPM6A
Hg19::chr4:176734149..176734174,-p12@GPM6A
Hg19::chr4:176734191..176734204,-p21@GPM6A


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 cell6.43e-108
neural cell3.68e-0825
Uber Anatomy
Ontology termp-valuen
central nervous system1.57e-10382
neural tube5.25e-9557
neural rod5.25e-9557
future spinal cord5.25e-9557
neural keel5.25e-9557
regional part of nervous system1.99e-9194
nervous system1.99e-9194
telencephalon1.25e-8534
cerebral hemisphere1.39e-8532
gray matter2.40e-8534
brain grey matter2.40e-8534
brain1.20e-8469
future brain1.20e-8469
regional part of brain6.81e-8359
regional part of telencephalon1.94e-8233
regional part of forebrain2.26e-7941
forebrain2.26e-7941
future forebrain2.26e-7941
anterior neural tube2.57e-7742
neural plate2.49e-7286
presumptive neural plate2.49e-7286
neurectoderm1.19e-6890
regional part of cerebral cortex1.01e-6722
cerebral cortex1.79e-6425
pallium1.79e-6425
neocortex1.30e-6120
pre-chordal neural plate4.95e-5461
ectoderm-derived structure3.69e-48169
head7.76e-48123
adult organism2.56e-47115
ectoderm8.78e-47173
presumptive ectoderm8.78e-47173
anterior region of body4.03e-45129
craniocervical region4.03e-45129
tube1.48e-24194
basal ganglion1.75e-229
nuclear complex of neuraxis1.75e-229
aggregate regional part of brain1.75e-229
collection of basal ganglia1.75e-229
cerebral subcortex1.75e-229
nucleus of brain1.11e-219
neural nucleus1.11e-219
gyrus5.32e-216
temporal lobe7.25e-217
posterior neural tube2.70e-1815
chordal neural plate2.70e-1815
anatomical conduit1.23e-17241
parietal lobe2.09e-175
limbic system4.34e-175
occipital lobe8.67e-175
telencephalic nucleus2.85e-167
organ part4.75e-16219
segmental subdivision of hindbrain5.88e-1512
hindbrain5.88e-1512
presumptive hindbrain5.88e-1512
anatomical cluster4.12e-14286
epithelium7.53e-14309
segmental subdivision of nervous system1.04e-1313
corpus striatum1.20e-134
striatum1.20e-134
ventral part of telencephalon1.20e-134
future corpus striatum1.20e-134
cell layer1.31e-13312
regional part of metencephalon9.87e-129
metencephalon9.87e-129
future metencephalon9.87e-129
organism subdivision1.07e-11365
middle temporal gyrus1.51e-113
caudate-putamen1.26e-103
dorsal striatum1.26e-103
pons7.58e-103
brainstem2.67e-098
frontal cortex2.99e-082
amygdala4.22e-082
Ammon's horn1.16e-072
lobe parts of cerebral cortex1.16e-072
hippocampal formation1.16e-072
limbic lobe1.16e-072
caudate nucleus1.72e-072
future caudate nucleus1.72e-072
meninx2.23e-072
membrane organ2.23e-072
future meninx2.23e-072
locus ceruleus3.62e-072
hindbrain nucleus3.62e-072
globus pallidus3.74e-072
pallidum3.74e-072
organ3.95e-07511
multi-tissue structure4.24e-07347
germ layer9.21e-07604
embryonic tissue9.21e-07604
presumptive structure9.21e-07604
epiblast (generic)9.21e-07604
embryonic structure9.94e-07605
developing anatomical structure9.94e-07605


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.