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|full_id=C963_mesodermal_hippocampus_amygdala_medulla_thalamus_brain_corpus
|full_id=C963_mesodermal_hippocampus_amygdala_medulla_thalamus_brain_corpus
|id=C963
|id=C963
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.06e-63!115;UBERON:0001049!1.98e-52!57;UBERON:0005068!1.98e-52!57;UBERON:0006241!1.98e-52!57;UBERON:0007135!1.98e-52!57;UBERON:0001017!1.54e-45!82;UBERON:0003075!2.22e-44!86;UBERON:0007284!2.22e-44!86;UBERON:0005743!9.66e-44!86;UBERON:0002616!3.07e-43!59;UBERON:0002346!4.16e-41!90;UBERON:0000955!6.21e-41!69;UBERON:0006238!6.21e-41!69;UBERON:0000073!1.62e-39!94;UBERON:0001016!1.62e-39!94;UBERON:0003080!5.64e-39!42;UBERON:0002780!3.12e-38!41;UBERON:0001890!3.12e-38!41;UBERON:0006240!3.12e-38!41;UBERON:0000153!3.50e-33!129;UBERON:0007811!3.50e-33!129;UBERON:0001893!2.14e-32!34;UBERON:0002020!3.12e-32!34;UBERON:0003528!3.12e-32!34;UBERON:0002791!2.35e-31!33;UBERON:0000033!3.80e-31!123;UBERON:0003056!6.73e-31!61;UBERON:0001869!2.08e-30!32;UBERON:0004121!3.67e-28!169;UBERON:0000924!9.93e-27!173;UBERON:0006601!9.93e-27!173;UBERON:0000956!1.11e-23!25;UBERON:0000203!1.11e-23!25;UBERON:0002619!6.73e-23!22;UBERON:0001950!7.12e-21!20;UBERON:0003076!4.20e-14!15;UBERON:0003057!4.20e-14!15;UBERON:0004732!4.58e-12!13;UBERON:0000477!5.29e-12!286;UBERON:0004733!2.35e-11!12;UBERON:0002028!2.35e-11!12;UBERON:0007277!2.35e-11!12;UBERON:0004111!2.90e-11!241;UBERON:0000064!3.41e-11!219;UBERON:0000025!5.43e-11!194;UBERON:0002420!3.72e-10!9;UBERON:0007245!3.72e-10!9;UBERON:0010009!3.72e-10!9;UBERON:0010011!3.72e-10!9;UBERON:0000454!3.72e-10!9;UBERON:0002308!6.16e-10!9;UBERON:0000125!6.16e-10!9;UBERON:0000475!2.67e-09!365;UBERON:0000062!3.27e-09!511;UBERON:0002298!6.21e-09!8;UBERON:0001871!8.67e-09!7;UBERON:0002680!2.21e-08!9;UBERON:0001895!2.21e-08!9;UBERON:0010092!2.21e-08!9;UBERON:0000481!2.89e-08!347;UBERON:0009663!4.71e-08!7;UBERON:0000200!2.72e-07!6;UBERON:0001894!3.58e-07!7;UBERON:0006222!3.58e-07!7;UBERON:0000468!7.56e-07!659;UBERON:0000119!9.91e-07!312
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Revision as of 15:00, 21 May 2012


Full id: C963_mesodermal_hippocampus_amygdala_medulla_thalamus_brain_corpus



Phase1 CAGE Peaks

Hg19::chr9:87284248..87284254,+p27@NTRK2
Hg19::chr9:87284266..87284277,+p12@NTRK2
Hg19::chr9:87284438..87284450,+p16@NTRK2
Hg19::chr9:87284467..87284474,+p24@NTRK2
Hg19::chr9:87284530..87284552,+p6@NTRK2
Hg19::chr9:87284556..87284567,+p9@NTRK2
Hg19::chr9:87285257..87285270,+p19@NTRK2
Hg19::chr9:87285459..87285471,+p28@NTRK2
Hg19::chr9:87285630..87285643,+p15@NTRK2


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism7.06e-63115
neural tube1.98e-5257
neural rod1.98e-5257
future spinal cord1.98e-5257
neural keel1.98e-5257
central nervous system1.54e-4582
neural plate2.22e-4486
presumptive neural plate2.22e-4486
regional part of brain3.07e-4359
neurectoderm4.16e-4190
brain6.21e-4169
future brain6.21e-4169
regional part of nervous system1.62e-3994
nervous system1.62e-3994
anterior neural tube5.64e-3942
regional part of forebrain3.12e-3841
forebrain3.12e-3841
future forebrain3.12e-3841
anterior region of body3.50e-33129
craniocervical region3.50e-33129
telencephalon2.14e-3234
gray matter3.12e-3234
brain grey matter3.12e-3234
regional part of telencephalon2.35e-3133
head3.80e-31123
pre-chordal neural plate6.73e-3161
cerebral hemisphere2.08e-3032
ectoderm-derived structure3.67e-28169
ectoderm9.93e-27173
presumptive ectoderm9.93e-27173
cerebral cortex1.11e-2325
pallium1.11e-2325
regional part of cerebral cortex6.73e-2322
neocortex7.12e-2120
posterior neural tube4.20e-1415
chordal neural plate4.20e-1415
segmental subdivision of nervous system4.58e-1213
anatomical cluster5.29e-12286
segmental subdivision of hindbrain2.35e-1112
hindbrain2.35e-1112
presumptive hindbrain2.35e-1112
anatomical conduit2.90e-11241
organ part3.41e-11219
tube5.43e-11194
basal ganglion3.72e-109
nuclear complex of neuraxis3.72e-109
aggregate regional part of brain3.72e-109
collection of basal ganglia3.72e-109
cerebral subcortex3.72e-109
nucleus of brain6.16e-109
neural nucleus6.16e-109
organism subdivision2.67e-09365
organ3.27e-09511
brainstem6.21e-098
temporal lobe8.67e-097
regional part of metencephalon2.21e-089
metencephalon2.21e-089
future metencephalon2.21e-089
multi-tissue structure2.89e-08347
telencephalic nucleus4.71e-087
gyrus2.72e-076
diencephalon3.58e-077
future diencephalon3.58e-077
multi-cellular organism7.56e-07659
cell layer9.91e-07312


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.