Personal tools

Coexpression cluster:C3186: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 3: Line 3:
|gostat_on_coexpression_clusters=GO:0006510!ATP-dependent proteolysis!0.0153822753973291!164832$GO:0005246!calcium channel regulator activity!0.0153822753973291!9379$GO:0004176!ATP-dependent peptidase activity!0.0153822753973291!164832$GO:0007416!synaptogenesis!0.0188282299490645!9379$GO:0016247!channel regulator activity!0.0188282299490645!9379$GO:0050808!synapse organization and biogenesis!0.0188282299490645!9379$GO:0007269!neurotransmitter secretion!0.0188282299490645!9379$GO:0045055!regulated secretory pathway!0.0218247999485838!9379$GO:0003001!generation of a signal involved in cell-cell signaling!0.0251450577024572!9379$GO:0001505!regulation of neurotransmitter levels!0.0251450577024572!9379$GO:0043062!extracellular structure organization and biogenesis!0.0251450577024572!9379
|gostat_on_coexpression_clusters=GO:0006510!ATP-dependent proteolysis!0.0153822753973291!164832$GO:0005246!calcium channel regulator activity!0.0153822753973291!9379$GO:0004176!ATP-dependent peptidase activity!0.0153822753973291!164832$GO:0007416!synaptogenesis!0.0188282299490645!9379$GO:0016247!channel regulator activity!0.0188282299490645!9379$GO:0050808!synapse organization and biogenesis!0.0188282299490645!9379$GO:0007269!neurotransmitter secretion!0.0188282299490645!9379$GO:0045055!regulated secretory pathway!0.0218247999485838!9379$GO:0003001!generation of a signal involved in cell-cell signaling!0.0251450577024572!9379$GO:0001505!regulation of neurotransmitter levels!0.0251450577024572!9379$GO:0043062!extracellular structure organization and biogenesis!0.0251450577024572!9379
|id=C3186
|id=C3186
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.39e-46!115;UBERON:0001017!5.24e-43!82;UBERON:0001049!4.96e-42!57;UBERON:0005068!4.96e-42!57;UBERON:0006241!4.96e-42!57;UBERON:0007135!4.96e-42!57;UBERON:0000073!1.78e-41!94;UBERON:0001016!1.78e-41!94;UBERON:0005743!2.73e-41!86;UBERON:0000955!1.22e-36!69;UBERON:0006238!1.22e-36!69;UBERON:0002616!1.90e-35!59;UBERON:0002780!7.08e-34!41;UBERON:0001890!7.08e-34!41;UBERON:0006240!7.08e-34!41;UBERON:0003080!1.12e-32!42;UBERON:0003075!9.40e-32!86;UBERON:0007284!9.40e-32!86;UBERON:0002346!2.14e-31!90;UBERON:0002020!4.73e-30!34;UBERON:0003528!4.73e-30!34;UBERON:0001893!6.03e-30!34;UBERON:0002791!5.43e-29!33;UBERON:0001869!1.83e-28!32;UBERON:0002619!1.08e-23!22;UBERON:0001950!1.17e-21!20;UBERON:0000956!2.62e-21!25;UBERON:0000203!2.62e-21!25;UBERON:0003056!6.75e-21!61;UBERON:0000924!2.24e-19!173;UBERON:0006601!2.24e-19!173;UBERON:0004121!3.36e-19!169;UBERON:0000153!3.65e-17!129;UBERON:0007811!3.65e-17!129;UBERON:0000033!2.96e-16!123;UBERON:0002420!1.72e-10!9;UBERON:0007245!1.72e-10!9;UBERON:0010009!1.72e-10!9;UBERON:0010011!1.72e-10!9;UBERON:0000454!1.72e-10!9;UBERON:0003076!2.57e-10!15;UBERON:0003057!2.57e-10!15;UBERON:0002308!3.24e-10!9;UBERON:0000125!3.24e-10!9;UBERON:0001871!2.35e-09!7;UBERON:0009663!1.94e-08!7;UBERON:0004733!7.18e-08!12;UBERON:0002028!7.18e-08!12;UBERON:0007277!7.18e-08!12;UBERON:0000200!2.61e-07!6;UBERON:0004732!5.12e-07!13;UBERON:0000349!9.82e-07!5
}}
}}

Revision as of 14:33, 21 May 2012


Full id: C3186_putamen_cerebellum_acute_caudate_brain_amygdala_temporal



Phase1 CAGE Peaks

Hg19::chr11:64411156..64411192,-p5@NRXN2
Hg19::chr11:64411195..64411222,-p6@NRXN2
Hg19::chr2:100938957..100938968,-p4@LONRF2


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:0006510ATP-dependent proteolysis0.0153822753973291
GO:0005246calcium channel regulator activity0.0153822753973291
GO:0004176ATP-dependent peptidase activity0.0153822753973291
GO:0007416synaptogenesis0.0188282299490645
GO:0016247channel regulator activity0.0188282299490645
GO:0050808synapse organization and biogenesis0.0188282299490645
GO:0007269neurotransmitter secretion0.0188282299490645
GO:0045055regulated secretory pathway0.0218247999485838
GO:0003001generation of a signal involved in cell-cell signaling0.0251450577024572
GO:0001505regulation of neurotransmitter levels0.0251450577024572
GO:0043062extracellular structure organization and biogenesis0.0251450577024572



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 organism1.39e-46115
central nervous system5.24e-4382
neural tube4.96e-4257
neural rod4.96e-4257
future spinal cord4.96e-4257
neural keel4.96e-4257
regional part of nervous system1.78e-4194
nervous system1.78e-4194
brain1.22e-3669
future brain1.22e-3669
regional part of brain1.90e-3559
regional part of forebrain7.08e-3441
forebrain7.08e-3441
future forebrain7.08e-3441
anterior neural tube1.12e-3242
neural plate9.40e-3286
presumptive neural plate9.40e-3286
neurectoderm2.14e-3190
gray matter4.73e-3034
brain grey matter4.73e-3034
telencephalon6.03e-3034
regional part of telencephalon5.43e-2933
cerebral hemisphere1.83e-2832
regional part of cerebral cortex1.08e-2322
neocortex1.17e-2120
cerebral cortex2.62e-2125
pallium2.62e-2125
pre-chordal neural plate6.75e-2161
ectoderm2.24e-19173
presumptive ectoderm2.24e-19173
ectoderm-derived structure3.36e-19169
anterior region of body3.65e-17129
craniocervical region3.65e-17129
head2.96e-16123
basal ganglion1.72e-109
nuclear complex of neuraxis1.72e-109
aggregate regional part of brain1.72e-109
collection of basal ganglia1.72e-109
cerebral subcortex1.72e-109
posterior neural tube2.57e-1015
chordal neural plate2.57e-1015
nucleus of brain3.24e-109
neural nucleus3.24e-109
temporal lobe2.35e-097
telencephalic nucleus1.94e-087
segmental subdivision of hindbrain7.18e-0812
hindbrain7.18e-0812
presumptive hindbrain7.18e-0812
gyrus2.61e-076
segmental subdivision of nervous system5.12e-0713
limbic system9.82e-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.