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|full_id=C1247_parietal_thalamus_hippocampus_olfactory_middle_amygdala_medial
|full_id=C1247_parietal_thalamus_hippocampus_olfactory_middle_amygdala_medial
|id=C1247
|id=C1247
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!9.97e-38!94;UBERON:0001016!9.97e-38!94;UBERON:0001049!2.03e-36!57;UBERON:0005068!2.03e-36!57;UBERON:0006241!2.03e-36!57;UBERON:0007135!2.03e-36!57;UBERON:0001017!2.10e-36!82;UBERON:0005743!1.32e-35!86;UBERON:0000955!4.61e-33!69;UBERON:0006238!4.61e-33!69;UBERON:0002780!9.18e-33!41;UBERON:0001890!9.18e-33!41;UBERON:0006240!9.18e-33!41;UBERON:0002346!2.34e-32!90;UBERON:0003075!5.29e-32!86;UBERON:0007284!5.29e-32!86;UBERON:0002616!8.60e-32!59;UBERON:0003080!1.85e-31!42;UBERON:0002020!3.57e-28!34;UBERON:0003528!3.57e-28!34;UBERON:0001893!7.32e-28!34;UBERON:0002791!3.97e-27!33;UBERON:0001869!1.55e-26!32;UBERON:0000924!1.58e-24!173;UBERON:0006601!1.58e-24!173;UBERON:0003056!6.12e-24!61;UBERON:0004121!6.71e-24!169;UBERON:0000033!8.28e-23!123;UBERON:0007023!1.13e-22!115;UBERON:0000153!2.17e-21!129;UBERON:0007811!2.17e-21!129;UBERON:0000956!5.51e-21!25;UBERON:0000203!5.51e-21!25;UBERON:0002619!1.22e-19!22;UBERON:0001950!5.88e-18!20;UBERON:0000475!4.01e-12!365;UBERON:0004111!9.82e-12!241;UBERON:0000025!2.47e-11!194;UBERON:0000477!8.66e-10!286;UBERON:0000483!1.33e-09!309;UBERON:0000119!2.36e-09!312;UBERON:0002420!1.14e-08!9;UBERON:0007245!1.14e-08!9;UBERON:0010009!1.14e-08!9;UBERON:0010011!1.14e-08!9;UBERON:0000454!1.14e-08!9;UBERON:0002308!1.34e-08!9;UBERON:0000125!1.34e-08!9;UBERON:0000468!6.17e-08!659;UBERON:0001871!7.83e-08!7;UBERON:0009663!5.10e-07!7;UBERON:0000922!6.86e-07!612
}}
}}

Revision as of 14:09, 21 May 2012


Full id: C1247_parietal_thalamus_hippocampus_olfactory_middle_amygdala_medial



Phase1 CAGE Peaks

Hg19::chr1:14819044..14819065,+p@chr1:14819044..14819065
+
Hg19::chr2:210526133..210526141,+p52@MAP2
Hg19::chr3:10369338..10369362,-p@chr3:10369338..10369362
-
Hg19::chr5:58148556..58148559,+p@chr5:58148556..58148559
+
Hg19::chr5:71502197..71502220,+p@chr5:71502197..71502220
+
Hg19::chr8:91969565..91969587,+p@chr8:91969565..91969587
+
Hg19::chr8:91969795..91969807,+p@chr8:91969795..91969807
+


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
regional part of nervous system9.97e-3894
nervous system9.97e-3894
neural tube2.03e-3657
neural rod2.03e-3657
future spinal cord2.03e-3657
neural keel2.03e-3657
central nervous system2.10e-3682
brain4.61e-3369
future brain4.61e-3369
regional part of forebrain9.18e-3341
forebrain9.18e-3341
future forebrain9.18e-3341
neurectoderm2.34e-3290
neural plate5.29e-3286
presumptive neural plate5.29e-3286
regional part of brain8.60e-3259
anterior neural tube1.85e-3142
gray matter3.57e-2834
brain grey matter3.57e-2834
telencephalon7.32e-2834
regional part of telencephalon3.97e-2733
cerebral hemisphere1.55e-2632
ectoderm1.58e-24173
presumptive ectoderm1.58e-24173
pre-chordal neural plate6.12e-2461
ectoderm-derived structure6.71e-24169
head8.28e-23123
adult organism1.13e-22115
anterior region of body2.17e-21129
craniocervical region2.17e-21129
cerebral cortex5.51e-2125
pallium5.51e-2125
regional part of cerebral cortex1.22e-1922
neocortex5.88e-1820
organism subdivision4.01e-12365
anatomical conduit9.82e-12241
tube2.47e-11194
anatomical cluster8.66e-10286
epithelium1.33e-09309
cell layer2.36e-09312
basal ganglion1.14e-089
nuclear complex of neuraxis1.14e-089
aggregate regional part of brain1.14e-089
collection of basal ganglia1.14e-089
cerebral subcortex1.14e-089
nucleus of brain1.34e-089
neural nucleus1.34e-089
multi-cellular organism6.17e-08659
temporal lobe7.83e-087
telencephalic nucleus5.10e-077
embryo6.86e-07612


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.