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Coexpression cluster:C3355: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 19:06, 8 August 2012


Full id: C3355_cerebellum_Neural_occipital_small_parietal_Neurons_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr13:113656022..113656041,+p9@MCF2L
Hg19::chr13:113656047..113656064,+p13@MCF2L
Hg19::chr8:62200509..62200590,+p1@CLVS1


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

GO IDGO nameFDR corrected p-value
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0332038149063935
GO:0035023regulation of Rho protein signal transduction0.0332038149063935
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0332038149063935
GO:0007266Rho protein signal transduction0.0332038149063935
GO:0005085guanyl-nucleotide exchange factor activity0.0372071117390792
GO:0046578regulation of Ras protein signal transduction0.0372071117390792
GO:0007265Ras protein signal transduction0.0372071117390792
GO:0005083small GTPase regulator activity0.0372071117390792
GO:0051056regulation of small GTPase mediated signal transduction0.0372071117390792
GO:0030695GTPase regulator activity0.049452490286118



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
neural cell1.82e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system3.90e-5882
neural tube2.81e-5757
neural rod2.81e-5757
future spinal cord2.81e-5757
neural keel2.81e-5757
regional part of nervous system5.95e-5794
nervous system5.95e-5794
regional part of brain1.74e-4959
brain2.37e-4969
future brain2.37e-4969
neural plate6.93e-4686
presumptive neural plate6.93e-4686
neurectoderm2.19e-4590
adult organism3.49e-45115
regional part of forebrain9.52e-4541
forebrain9.52e-4541
future forebrain9.52e-4541
anterior neural tube2.79e-4342
telencephalon5.63e-3734
gray matter5.96e-3734
brain grey matter5.96e-3734
regional part of telencephalon6.56e-3633
cerebral hemisphere3.79e-3532
ectoderm7.01e-35173
presumptive ectoderm7.01e-35173
pre-chordal neural plate1.07e-3461
ectoderm-derived structure1.23e-34169
anterior region of body2.27e-31129
craniocervical region2.27e-31129
head2.70e-30123
cerebral cortex9.63e-2825
pallium9.63e-2825
regional part of cerebral cortex1.42e-2522
neocortex1.62e-2320
tube2.22e-15194
organ part2.30e-15219
posterior neural tube1.40e-1415
chordal neural plate1.40e-1415
epithelium4.90e-13309
multi-tissue structure6.27e-13347
anatomical conduit6.38e-13241
organism subdivision7.80e-13365
cell layer1.28e-12312
segmental subdivision of nervous system1.41e-1213
anatomical cluster4.57e-12286
segmental subdivision of hindbrain7.48e-1212
hindbrain7.48e-1212
presumptive hindbrain7.48e-1212
basal ganglion1.39e-109
nuclear complex of neuraxis1.39e-109
aggregate regional part of brain1.39e-109
collection of basal ganglia1.39e-109
cerebral subcortex1.39e-109
embryo1.39e-10612
nucleus of brain1.52e-109
neural nucleus1.52e-109
temporal lobe1.31e-097
organ3.70e-09511
regional part of metencephalon4.46e-099
metencephalon4.46e-099
future metencephalon4.46e-099
diencephalon4.79e-097
future diencephalon4.79e-097
telencephalic nucleus1.21e-087
germ layer1.67e-08604
embryonic tissue1.67e-08604
presumptive structure1.67e-08604
epiblast (generic)1.67e-08604
multi-cellular organism1.74e-08659
embryonic structure2.04e-08605
developing anatomical structure2.04e-08605
gyrus5.07e-086
anatomical system1.41e-07625
anatomical group1.70e-07626
parietal lobe5.60e-075
brainstem6.40e-078
occipital lobe7.25e-075


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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