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Coexpression cluster:C3421: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.45e-38!82;UBERON:0002780!2.87e-37!41;UBERON:0001890!2.87e-37!41;UBERON:0006240!2.87e-37!41;UBERON:0005743!6.45e-37!86;UBERON:0003080!5.07e-36!42;UBERON:0000955!6.65e-36!69;UBERON:0006238!6.65e-36!69;UBERON:0001893!1.85e-35!34;UBERON:0000073!4.30e-35!94;UBERON:0001016!4.30e-35!94;UBERON:0003056!1.37e-34!61;UBERON:0002791!1.95e-34!33;UBERON:0001869!4.02e-34!32;UBERON:0002020!7.54e-31!34;UBERON:0003528!7.54e-31!34;UBERON:0002616!1.36e-30!59;UBERON:0003075!1.16e-29!86;UBERON:0007284!1.16e-29!86;UBERON:0002346!2.21e-29!90;UBERON:0001049!5.08e-28!57;UBERON:0005068!5.08e-28!57;UBERON:0006241!5.08e-28!57;UBERON:0007135!5.08e-28!57;UBERON:0000153!1.18e-27!129;UBERON:0007811!1.18e-27!129;UBERON:0000956!1.99e-26!25;UBERON:0000203!1.99e-26!25;UBERON:0000033!9.22e-26!123;UBERON:0002619!5.18e-23!22;UBERON:0000924!6.58e-23!173;UBERON:0006601!6.58e-23!173;UBERON:0004121!9.93e-23!169;UBERON:0001950!8.95e-21!20;UBERON:0000475!1.74e-15!365;UBERON:0000025!7.59e-12!194;UBERON:0000483!2.70e-11!309;UBERON:0000119!6.40e-11!312;UBERON:0002420!1.13e-10!9;UBERON:0007245!1.13e-10!9;UBERON:0010009!1.13e-10!9;UBERON:0010011!1.13e-10!9;UBERON:0000454!1.13e-10!9;UBERON:0007023!1.41e-10!115;UBERON:0009663!1.55e-08!7;UBERON:0000477!2.95e-08!286;UBERON:0000064!6.65e-08!219;UBERON:0000200!7.66e-08!6;UBERON:0001871!9.33e-08!7;UBERON:0004111!1.53e-07!241;UBERON:0000481!2.73e-07!347;UBERON:0000349!4.04e-07!5;UBERON:0000467!9.07e-07!625
|ontology_enrichment_uberon=UBERON:0001017!2.45e-38!82;UBERON:0002780!2.87e-37!41;UBERON:0001890!2.87e-37!41;UBERON:0006240!2.87e-37!41;UBERON:0005743!6.45e-37!86;UBERON:0003080!5.07e-36!42;UBERON:0000955!6.65e-36!69;UBERON:0006238!6.65e-36!69;UBERON:0001893!1.85e-35!34;UBERON:0000073!4.30e-35!94;UBERON:0001016!4.30e-35!94;UBERON:0003056!1.37e-34!61;UBERON:0002791!1.95e-34!33;UBERON:0001869!4.02e-34!32;UBERON:0002020!7.54e-31!34;UBERON:0003528!7.54e-31!34;UBERON:0002616!1.36e-30!59;UBERON:0003075!1.16e-29!86;UBERON:0007284!1.16e-29!86;UBERON:0002346!2.21e-29!90;UBERON:0001049!5.08e-28!57;UBERON:0005068!5.08e-28!57;UBERON:0006241!5.08e-28!57;UBERON:0007135!5.08e-28!57;UBERON:0000153!1.18e-27!129;UBERON:0007811!1.18e-27!129;UBERON:0000956!1.99e-26!25;UBERON:0000203!1.99e-26!25;UBERON:0000033!9.22e-26!123;UBERON:0002619!5.18e-23!22;UBERON:0000924!6.58e-23!173;UBERON:0006601!6.58e-23!173;UBERON:0004121!9.93e-23!169;UBERON:0001950!8.95e-21!20;UBERON:0000475!1.74e-15!365;UBERON:0000025!7.59e-12!194;UBERON:0000483!2.70e-11!309;UBERON:0000119!6.40e-11!312;UBERON:0002420!1.13e-10!9;UBERON:0007245!1.13e-10!9;UBERON:0010009!1.13e-10!9;UBERON:0010011!1.13e-10!9;UBERON:0000454!1.13e-10!9;UBERON:0007023!1.41e-10!115;UBERON:0009663!1.55e-08!7;UBERON:0000477!2.95e-08!286;UBERON:0000064!6.65e-08!219;UBERON:0000200!7.66e-08!6;UBERON:0001871!9.33e-08!7;UBERON:0004111!1.53e-07!241;UBERON:0000481!2.73e-07!347;UBERON:0000349!4.04e-07!5;UBERON:0000467!9.07e-07!625
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}}
}}

Revision as of 19:09, 8 August 2012


Full id: C3421_Neural_caudate_medulloblastoma_Neurons_small_Astrocyte_putamen



Phase1 CAGE Peaks

Hg19::chr14:29236997..29237007,+p11@FOXG1
Hg19::chr14:29237009..29237049,+p4@FOXG1
Hg19::chr14:29241984..29242013,+p1@C14orf23


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>


Uber Anatomy
Ontology termp-valuen
central nervous system2.45e-3882
regional part of forebrain2.87e-3741
forebrain2.87e-3741
future forebrain2.87e-3741
anterior neural tube5.07e-3642
brain6.65e-3669
future brain6.65e-3669
telencephalon1.85e-3534
regional part of nervous system4.30e-3594
nervous system4.30e-3594
pre-chordal neural plate1.37e-3461
regional part of telencephalon1.95e-3433
cerebral hemisphere4.02e-3432
gray matter7.54e-3134
brain grey matter7.54e-3134
regional part of brain1.36e-3059
neural plate1.16e-2986
presumptive neural plate1.16e-2986
neurectoderm2.21e-2990
neural tube5.08e-2857
neural rod5.08e-2857
future spinal cord5.08e-2857
neural keel5.08e-2857
anterior region of body1.18e-27129
craniocervical region1.18e-27129
cerebral cortex1.99e-2625
pallium1.99e-2625
head9.22e-26123
regional part of cerebral cortex5.18e-2322
ectoderm6.58e-23173
presumptive ectoderm6.58e-23173
ectoderm-derived structure9.93e-23169
neocortex8.95e-2120
organism subdivision1.74e-15365
tube7.59e-12194
epithelium2.70e-11309
cell layer6.40e-11312
basal ganglion1.13e-109
nuclear complex of neuraxis1.13e-109
aggregate regional part of brain1.13e-109
collection of basal ganglia1.13e-109
cerebral subcortex1.13e-109
adult organism1.41e-10115
telencephalic nucleus1.55e-087
anatomical cluster2.95e-08286
organ part6.65e-08219
gyrus7.66e-086
temporal lobe9.33e-087
anatomical conduit1.53e-07241
multi-tissue structure2.73e-07347
limbic system4.04e-075
anatomical system9.07e-07625


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.