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Difference between revisions of "Coexpression cluster:C2276"

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|full_id=C2276_anaplastic_pituitary_locus_skeletal_tongue_diaphragm_neuroblastoma
 
|full_id=C2276_anaplastic_pituitary_locus_skeletal_tongue_diaphragm_neuroblastoma
 
|id=C2276
 
|id=C2276
|ontology_enrichment_celltype=
+
|ontology_enrichment_celltype=CL:0002322!6.11e-09!5
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!5.90e-23!94;UBERON:0001016!5.90e-23!94;UBERON:0001017!1.67e-21!82;UBERON:0007023!2.36e-21!115;UBERON:0005743!1.63e-20!86;UBERON:0001049!8.40e-20!57;UBERON:0005068!8.40e-20!57;UBERON:0006241!8.40e-20!57;UBERON:0007135!8.40e-20!57;UBERON:0002616!9.08e-18!59;UBERON:0000955!7.84e-16!69;UBERON:0006238!7.84e-16!69;UBERON:0002780!5.11e-15!41;UBERON:0001890!5.11e-15!41;UBERON:0006240!5.11e-15!41;UBERON:0002020!8.03e-15!34;UBERON:0003528!8.03e-15!34;UBERON:0003080!2.21e-14!42;UBERON:0001893!2.41e-14!34;UBERON:0002791!9.15e-14!33;UBERON:0001869!4.54e-13!32;UBERON:0003075!1.42e-12!86;UBERON:0007284!1.42e-12!86;UBERON:0002346!8.67e-12!90;UBERON:0000956!5.77e-10!25;UBERON:0000203!5.77e-10!25;UBERON:0004121!6.88e-10!169;UBERON:0000924!1.67e-09!173;UBERON:0006601!1.67e-09!173;UBERON:0003056!4.02e-09!61;UBERON:0001950!4.58e-09!20;UBERON:0002619!4.58e-09!22;UBERON:0000153!1.65e-08!129;UBERON:0007811!1.65e-08!129;UBERON:0000033!3.45e-08!123
+
|ontology_enrichment_uberon=UBERON:0002298!1.91e-17!6;UBERON:0001049!9.94e-17!56;UBERON:0005068!9.94e-17!56;UBERON:0006241!9.94e-17!56;UBERON:0007135!9.94e-17!56;UBERON:0007023!3.24e-16!114;UBERON:0001016!2.33e-15!89;UBERON:0000073!1.96e-14!53;UBERON:0002616!1.96e-14!53;UBERON:0000125!1.62e-13!9;UBERON:0002308!1.62e-13!9;UBERON:0001017!1.96e-13!81;UBERON:0003075!6.75e-12!82;UBERON:0007284!6.75e-12!82;UBERON:0011216!2.60e-11!223;UBERON:0004121!3.25e-11!171;UBERON:0000924!3.25e-11!171;UBERON:0006601!3.25e-11!171;UBERON:0002346!4.51e-11!86;UBERON:0003076!4.59e-11!15;UBERON:0003057!4.59e-11!15;UBERON:0010371!4.24e-10!104;UBERON:0000955!5.60e-10!68;UBERON:0006238!5.60e-10!68;UBERON:0002420!1.11e-09!9;UBERON:0007245!1.11e-09!9;UBERON:0010009!1.11e-09!9;UBERON:0010011!1.11e-09!9;UBERON:0000454!1.11e-09!9;UBERON:0001896!1.26e-09!3;UBERON:0005290!1.26e-09!3;UBERON:0010096!1.26e-09!3;UBERON:0000988!1.58e-09!3;UBERON:0009663!1.00e-08!7;UBERON:0002780!1.35e-08!41;UBERON:0001890!1.35e-08!41;UBERON:0003080!1.35e-08!41;UBERON:0006240!1.35e-08!41;UBERON:0004733!2.77e-08!12;UBERON:0002028!2.77e-08!12;UBERON:0007277!2.77e-08!12;UBERON:0010314!3.95e-08!132;UBERON:0003528!5.78e-08!34;UBERON:0002020!5.78e-08!34;UBERON:0004732!1.40e-07!13;UBERON:0001893!1.52e-07!34;UBERON:0000007!3.36e-07!2;UBERON:0002148!4.36e-07!2;UBERON:0006331!4.36e-07!2;UBERON:0009662!4.36e-07!2
 
|tf_chipseq_enrich=BCL3#602;2:17.2735514018692:0.00483449420807607:0.0226732112172642
 
|tf_chipseq_enrich=BCL3#602;2:17.2735514018692:0.00483449420807607:0.0226732112172642
 
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}}
 
}}

Revision as of 04:49, 19 October 2012


Full id: C2276_anaplastic_pituitary_locus_skeletal_tongue_diaphragm_neuroblastoma



Phase1 CAGE Peaks

  Short description
Hg19::chr14:101202516..101202528,+ p@chr14:101202516..101202528
+
Hg19::chr14:101202697..101202709,+ p@chr14:101202697..101202709
+
Hg19::chr14:101202716..101202736,+ p@chr14:101202716..101202736
+
Hg19::chr4:72052646..72052664,+ p5@SLC4A4


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
embryonic stem cell6.11e-095
Uber Anatomy
Ontology termp-valuen
brainstem1.91e-176
neural tube9.94e-1756
neural rod9.94e-1756
future spinal cord9.94e-1756
neural keel9.94e-1756
adult organism3.24e-16114
nervous system2.33e-1589
regional part of nervous system1.96e-1453
regional part of brain1.96e-1453
neural nucleus1.62e-139
nucleus of brain1.62e-139
central nervous system1.96e-1381
neural plate6.75e-1282
presumptive neural plate6.75e-1282
organ system subdivision2.60e-11223
ectoderm-derived structure3.25e-11171
ectoderm3.25e-11171
presumptive ectoderm3.25e-11171
neurectoderm4.51e-1186
posterior neural tube4.59e-1115
chordal neural plate4.59e-1115
ecto-epithelium4.24e-10104
brain5.60e-1068
future brain5.60e-1068
basal ganglion1.11e-099
nuclear complex of neuraxis1.11e-099
aggregate regional part of brain1.11e-099
collection of basal ganglia1.11e-099
cerebral subcortex1.11e-099
medulla oblongata1.26e-093
myelencephalon1.26e-093
future myelencephalon1.26e-093
pons1.58e-093
telencephalic nucleus1.00e-087
regional part of forebrain1.35e-0841
forebrain1.35e-0841
anterior neural tube1.35e-0841
future forebrain1.35e-0841
segmental subdivision of hindbrain2.77e-0812
hindbrain2.77e-0812
presumptive hindbrain2.77e-0812
structure with developmental contribution from neural crest3.95e-08132
brain grey matter5.78e-0834
gray matter5.78e-0834
segmental subdivision of nervous system1.40e-0713
telencephalon1.52e-0734
pituitary gland3.36e-072
locus ceruleus4.36e-072
brainstem nucleus4.36e-072
hindbrain nucleus4.36e-072


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCL3#602217.27355140186920.004834494208076070.0226732112172642



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.