Personal tools

Coexpression cluster:C2494: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C2494_brain_neuroblastoma_duodenum_occipital_temporal_parietal_small |id=C2494 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C2494_brain_neuroblastoma_duodenum_occipital_temporal_parietal_small
|full_id=C2494_brain_neuroblastoma_duodenum_occipital_temporal_parietal_small
|id=C2494
|id=C2494
|ontology_enrichment_celltype=CL:0000133!1.70e-14!59;CL:0002319!2.40e-11!25;CL:0000055!2.62e-10!180;CL:0000333!1.50e-09!41;CL:0000221!3.20e-09!71;CL:0000047!6.34e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!9.59e-44!94;UBERON:0001016!9.59e-44!94;UBERON:0005743!5.20e-42!86;UBERON:0001017!9.33e-41!82;UBERON:0002346!3.04e-34!90;UBERON:0001049!8.68e-34!57;UBERON:0005068!8.68e-34!57;UBERON:0006241!8.68e-34!57;UBERON:0007135!8.68e-34!57;UBERON:0003075!2.83e-33!86;UBERON:0007284!2.83e-33!86;UBERON:0000955!3.24e-32!69;UBERON:0006238!3.24e-32!69;UBERON:0000924!3.71e-29!173;UBERON:0006601!3.71e-29!173;UBERON:0002616!1.02e-28!59;UBERON:0004121!4.54e-28!169;UBERON:0003056!4.77e-26!61;UBERON:0002780!7.99e-26!41;UBERON:0001890!7.99e-26!41;UBERON:0006240!7.99e-26!41;UBERON:0003080!1.27e-25!42;UBERON:0001893!3.53e-22!34;UBERON:0002020!4.04e-22!34;UBERON:0003528!4.04e-22!34;UBERON:0002791!1.66e-21!33;UBERON:0001869!2.11e-21!32;UBERON:0000033!2.19e-21!123;UBERON:0000153!5.66e-21!129;UBERON:0007811!5.66e-21!129;UBERON:0000956!1.84e-17!25;UBERON:0000203!1.84e-17!25;UBERON:0007023!5.52e-17!115;UBERON:0002619!2.82e-16!22;UBERON:0001950!5.21e-15!20;UBERON:0000475!2.90e-13!365;UBERON:0000483!3.20e-11!309;UBERON:0000119!3.69e-11!312;UBERON:0000025!1.80e-10!194;UBERON:0000481!6.23e-10!347;UBERON:0003076!3.30e-09!15;UBERON:0003057!3.30e-09!15;UBERON:0004733!1.21e-07!12;UBERON:0002028!1.21e-07!12;UBERON:0007277!1.21e-07!12;UBERON:0000064!2.20e-07!219;UBERON:0000477!4.33e-07!286;UBERON:0004111!5.52e-07!241
}}
}}

Revision as of 14:24, 21 May 2012


Full id: C2494_brain_neuroblastoma_duodenum_occipital_temporal_parietal_small



Phase1 CAGE Peaks

Hg19::chr19:4474846..4474881,+p@chr19:4474846..4474881
+
Hg19::chr20:42875935..42875966,+p1@GDAP1L1
Hg19::chr6:3228944..3228955,+p2@uc003mvi.1
Hg19::chr6:33388013..33388053,+p4@SYNGAP1


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>


Cell Type
Ontology termp-valuen
neurectodermal cell1.70e-1459
neural cell2.40e-1125
non-terminally differentiated cell2.62e-10180
migratory neural crest cell1.50e-0941
ectodermal cell3.20e-0971
neuronal stem cell6.34e-078
Uber Anatomy
Ontology termp-valuen
regional part of nervous system9.59e-4494
nervous system9.59e-4494
central nervous system9.33e-4182
neurectoderm3.04e-3490
neural tube8.68e-3457
neural rod8.68e-3457
future spinal cord8.68e-3457
neural keel8.68e-3457
neural plate2.83e-3386
presumptive neural plate2.83e-3386
brain3.24e-3269
future brain3.24e-3269
ectoderm3.71e-29173
presumptive ectoderm3.71e-29173
regional part of brain1.02e-2859
ectoderm-derived structure4.54e-28169
pre-chordal neural plate4.77e-2661
regional part of forebrain7.99e-2641
forebrain7.99e-2641
future forebrain7.99e-2641
anterior neural tube1.27e-2542
telencephalon3.53e-2234
gray matter4.04e-2234
brain grey matter4.04e-2234
regional part of telencephalon1.66e-2133
cerebral hemisphere2.11e-2132
head2.19e-21123
anterior region of body5.66e-21129
craniocervical region5.66e-21129
cerebral cortex1.84e-1725
pallium1.84e-1725
adult organism5.52e-17115
regional part of cerebral cortex2.82e-1622
neocortex5.21e-1520
organism subdivision2.90e-13365
epithelium3.20e-11309
cell layer3.69e-11312
tube1.80e-10194
multi-tissue structure6.23e-10347
posterior neural tube3.30e-0915
chordal neural plate3.30e-0915
segmental subdivision of hindbrain1.21e-0712
hindbrain1.21e-0712
presumptive hindbrain1.21e-0712
organ part2.20e-07219
anatomical cluster4.33e-07286
anatomical conduit5.52e-07241


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.