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Coexpression cluster:C3238: Difference between revisions

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|full_id=C3238_Small_salivary_duodenum_temporal_Wilms_Neurons_Neural
|full_id=C3238_Small_salivary_duodenum_temporal_Wilms_Neurons_Neural
|id=C3238
|id=C3238
|ontology_enrichment_celltype=CL:0002368!8.30e-09!13;CL:0000540!1.02e-07!6;CL:0000031!1.02e-07!6;CL:0000404!1.02e-07!6;CL:0000047!1.22e-07!8
|ontology_enrichment_celltype=CL:0000047!1.09e-09!8;CL:0002368!1.66e-09!13;CL:0000540!3.16e-09!6;CL:0000031!3.16e-09!6;CL:0000404!3.16e-09!6;CL:0002322!4.58e-09!5
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.11e-44!94;UBERON:0001016!2.11e-44!94;UBERON:0001017!6.90e-44!82;UBERON:0005743!1.77e-42!86;UBERON:0001049!7.51e-40!57;UBERON:0005068!7.51e-40!57;UBERON:0006241!7.51e-40!57;UBERON:0007135!7.51e-40!57;UBERON:0007023!1.06e-34!115;UBERON:0000955!2.14e-33!69;UBERON:0006238!2.14e-33!69;UBERON:0002616!4.23e-33!59;UBERON:0002780!2.44e-31!41;UBERON:0001890!2.44e-31!41;UBERON:0006240!2.44e-31!41;UBERON:0002346!3.12e-31!90;UBERON:0003080!2.71e-30!42;UBERON:0003075!2.59e-29!86;UBERON:0007284!2.59e-29!86;UBERON:0001893!2.94e-24!34;UBERON:0002619!3.45e-24!22;UBERON:0002020!3.60e-24!34;UBERON:0003528!3.60e-24!34;UBERON:0000924!8.68e-24!173;UBERON:0006601!8.68e-24!173;UBERON:0002791!3.51e-23!33;UBERON:0001869!8.24e-23!32;UBERON:0001950!1.75e-22!20;UBERON:0004121!3.67e-22!169;UBERON:0003056!6.95e-22!61;UBERON:0000956!1.91e-20!25;UBERON:0000203!1.91e-20!25;UBERON:0000153!8.17e-20!129;UBERON:0007811!8.17e-20!129;UBERON:0000033!8.73e-20!123;UBERON:0000922!1.44e-10!612;UBERON:0003076!1.71e-10!15;UBERON:0003057!1.71e-10!15;UBERON:0004732!2.69e-09!13;UBERON:0001894!1.08e-08!7;UBERON:0006222!1.08e-08!7;UBERON:0004733!1.76e-08!12;UBERON:0002028!1.76e-08!12;UBERON:0007277!1.76e-08!12;UBERON:0000468!1.93e-08!659;UBERON:0000200!3.46e-08!6;UBERON:0002050!5.41e-08!605;UBERON:0005423!5.41e-08!605;UBERON:0001871!1.02e-07!7;UBERON:0000923!1.20e-07!604;UBERON:0005291!1.20e-07!604;UBERON:0006598!1.20e-07!604;UBERON:0002532!1.20e-07!604;UBERON:0001872!1.72e-07!5;UBERON:0002021!1.93e-07!5;UBERON:0003135!4.39e-07!11
|ontology_enrichment_uberon=UBERON:0001016!2.56e-43!89;UBERON:0001017!5.57e-43!81;UBERON:0000073!5.99e-35!53;UBERON:0002616!5.99e-35!53;UBERON:0002780!2.75e-34!41;UBERON:0001890!2.75e-34!41;UBERON:0003080!2.75e-34!41;UBERON:0006240!2.75e-34!41;UBERON:0000955!3.64e-34!68;UBERON:0006238!3.64e-34!68;UBERON:0001049!1.45e-32!56;UBERON:0005068!1.45e-32!56;UBERON:0006241!1.45e-32!56;UBERON:0007135!1.45e-32!56;UBERON:0001893!3.14e-28!34;UBERON:0003528!5.10e-28!34;UBERON:0002020!5.10e-28!34;UBERON:0001869!6.55e-28!32;UBERON:0002619!2.31e-26!22;UBERON:0001950!2.91e-26!20;UBERON:0003056!2.42e-25!61;UBERON:0002791!2.91e-25!32;UBERON:0002346!5.62e-25!86;UBERON:0004121!1.11e-24!171;UBERON:0000924!1.11e-24!171;UBERON:0006601!1.11e-24!171;UBERON:0003075!2.18e-23!82;UBERON:0007284!2.18e-23!82;UBERON:0000956!1.07e-22!25;UBERON:0000203!1.07e-22!25;UBERON:0011216!5.10e-21!223;UBERON:0007023!1.72e-18!114;UBERON:0010371!1.94e-17!104;UBERON:0010314!1.98e-14!132;UBERON:0001872!2.74e-11!5;UBERON:0000477!2.88e-11!373;UBERON:0000922!3.99e-10!592;UBERON:0000200!7.18e-09!6;UBERON:0002021!1.29e-07!5;UBERON:0005423!1.62e-07!581;UBERON:0001894!2.01e-07!7;UBERON:0006222!2.01e-07!7;UBERON:0001871!2.48e-07!6;UBERON:0002050!2.60e-07!564;UBERON:0000923!5.07e-07!560;UBERON:0010316!5.07e-07!560;UBERON:0005291!5.07e-07!560;UBERON:0006598!5.07e-07!560;UBERON:0010317!5.07e-07!560;UBERON:0002532!5.07e-07!560;UBERON:0000468!6.03e-07!656;UBERON:0000125!7.56e-07!9;UBERON:0002308!7.56e-07!9
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56,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 14:55, 19 October 2012


Full id: C3238_Small_salivary_duodenum_temporal_Wilms_Neurons_Neural



Phase1 CAGE Peaks

Hg19::chr12:111472591..111472630,+p@chr12:111472591..111472630
+
Hg19::chr12:111472632..111472643,+p@chr12:111472632..111472643
+
Hg19::chr12:111473432..111473437,+p@chr12:111473432..111473437
+


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
neuronal stem cell1.09e-098
respiratory epithelial cell1.66e-0913
neuron3.16e-096
neuroblast3.16e-096
electrically signaling cell3.16e-096
embryonic stem cell4.58e-095
Uber Anatomy
Ontology termp-valuen
nervous system2.56e-4389
central nervous system5.57e-4381
regional part of nervous system5.99e-3553
regional part of brain5.99e-3553
regional part of forebrain2.75e-3441
forebrain2.75e-3441
anterior neural tube2.75e-3441
future forebrain2.75e-3441
brain3.64e-3468
future brain3.64e-3468
neural tube1.45e-3256
neural rod1.45e-3256
future spinal cord1.45e-3256
neural keel1.45e-3256
telencephalon3.14e-2834
brain grey matter5.10e-2834
gray matter5.10e-2834
cerebral hemisphere6.55e-2832
regional part of cerebral cortex2.31e-2622
neocortex2.91e-2620
pre-chordal neural plate2.42e-2561
regional part of telencephalon2.91e-2532
neurectoderm5.62e-2586
ectoderm-derived structure1.11e-24171
ectoderm1.11e-24171
presumptive ectoderm1.11e-24171
neural plate2.18e-2382
presumptive neural plate2.18e-2382
cerebral cortex1.07e-2225
pallium1.07e-2225
organ system subdivision5.10e-21223
adult organism1.72e-18114
ecto-epithelium1.94e-17104
structure with developmental contribution from neural crest1.98e-14132
parietal lobe2.74e-115
anatomical cluster2.88e-11373
embryo3.99e-10592
gyrus7.18e-096
occipital lobe1.29e-075
developing anatomical structure1.62e-07581
diencephalon2.01e-077
future diencephalon2.01e-077
temporal lobe2.48e-076
embryonic structure2.60e-07564
germ layer5.07e-07560
germ layer / neural crest5.07e-07560
embryonic tissue5.07e-07560
presumptive structure5.07e-07560
germ layer / neural crest derived structure5.07e-07560
epiblast (generic)5.07e-07560
multi-cellular organism6.03e-07656
neural nucleus7.56e-079
nucleus of brain7.56e-079


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.

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