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Coexpression cluster:C3383: Difference between revisions

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|full_id=C3383_pineal_optic_corpus_substantia_thalamus_retinoblastoma_globus
|full_id=C3383_pineal_optic_corpus_substantia_thalamus_retinoblastoma_globus
|id=C3383
|id=C3383
|ontology_enrichment_celltype=CL:0002139!9.74e-09!24;CL:0000071!5.15e-07!18;CL:0002546!5.15e-07!18
|ontology_enrichment_celltype=CL:0002139!6.34e-08!24
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!6.61e-35!115;UBERON:0005743!5.15e-33!86;UBERON:0000073!1.16e-32!94;UBERON:0001016!1.16e-32!94;UBERON:0001017!5.04e-31!82;UBERON:0001049!1.80e-29!57;UBERON:0005068!1.80e-29!57;UBERON:0006241!1.80e-29!57;UBERON:0007135!1.80e-29!57;UBERON:0003075!1.73e-27!86;UBERON:0007284!1.73e-27!86;UBERON:0002346!3.04e-27!90;UBERON:0002616!1.42e-24!59;UBERON:0000955!6.57e-24!69;UBERON:0006238!6.57e-24!69;UBERON:0003080!1.05e-23!42;UBERON:0002780!2.08e-23!41;UBERON:0001890!2.08e-23!41;UBERON:0006240!2.08e-23!41;UBERON:0003056!4.78e-21!61;UBERON:0001893!1.07e-19!34;UBERON:0002020!1.08e-19!34;UBERON:0003528!1.08e-19!34;UBERON:0002791!4.51e-19!33;UBERON:0001869!2.72e-18!32;UBERON:0000025!3.61e-16!194;UBERON:0004111!9.01e-16!241;UBERON:0000924!2.22e-15!173;UBERON:0006601!2.22e-15!173;UBERON:0004121!3.45e-15!169;UBERON:0000033!1.82e-14!123;UBERON:0000153!2.98e-14!129;UBERON:0007811!2.98e-14!129;UBERON:0000956!3.03e-14!25;UBERON:0000203!3.03e-14!25;UBERON:0002619!3.16e-14!22;UBERON:0000477!3.35e-14!286;UBERON:0000468!1.10e-13!659;UBERON:0001950!4.48e-13!20;UBERON:0000922!7.28e-13!612;UBERON:0000467!3.25e-12!625;UBERON:0000480!3.91e-12!626;UBERON:0002050!1.48e-10!605;UBERON:0005423!1.48e-10!605;UBERON:0000923!2.12e-10!604;UBERON:0005291!2.12e-10!604;UBERON:0006598!2.12e-10!604;UBERON:0002532!2.12e-10!604;UBERON:0000119!6.29e-10!312;UBERON:0000483!9.13e-10!309;UBERON:0000062!2.40e-09!511;UBERON:0000064!6.15e-08!219;UBERON:0003076!5.03e-07!15;UBERON:0003057!5.03e-07!15;UBERON:0001986!5.15e-07!18;UBERON:0004638!5.15e-07!18;UBERON:0004852!5.15e-07!18;UBERON:0002308!5.97e-07!9;UBERON:0000125!5.97e-07!9;UBERON:0002420!9.50e-07!9;UBERON:0007245!9.50e-07!9;UBERON:0010009!9.50e-07!9;UBERON:0010011!9.50e-07!9;UBERON:0000454!9.50e-07!9
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}}
}}

Revision as of 15:03, 19 October 2012


Full id: C3383_pineal_optic_corpus_substantia_thalamus_retinoblastoma_globus



Phase1 CAGE Peaks

Hg19::chr13:51796497..51796517,+p1@FAM124A
Hg19::chr13:51796528..51796540,+p2@FAM124A
Hg19::chr13:51800146..51800150,+p@chr13:51800146..51800150
+


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
endothelial cell of vascular tree6.34e-0824
Uber Anatomy
Ontology termp-valuen
adult organism4.29e-42114
central nervous system8.34e-3381
nervous system1.53e-3289
neural tube6.57e-3156
neural rod6.57e-3156
future spinal cord6.57e-3156
neural keel6.57e-3156
neural plate4.62e-3082
presumptive neural plate4.62e-3082
neurectoderm6.31e-3086
regional part of nervous system1.59e-2853
regional part of brain1.59e-2853
regional part of forebrain1.06e-2641
forebrain1.06e-2641
anterior neural tube1.06e-2641
future forebrain1.06e-2641
pre-chordal neural plate3.57e-2661
brain2.21e-2468
future brain2.21e-2468
telencephalon2.29e-2234
brain grey matter2.40e-2234
gray matter2.40e-2234
regional part of telencephalon9.96e-2132
structure with developmental contribution from neural crest1.03e-20132
cerebral hemisphere1.17e-2032
ecto-epithelium1.08e-18104
ectoderm-derived structure1.67e-18171
ectoderm1.67e-18171
presumptive ectoderm1.67e-18171
anatomical cluster1.05e-16373
cerebral cortex1.32e-1525
pallium1.32e-1525
regional part of cerebral cortex2.26e-1522
organ system subdivision6.83e-15223
neocortex5.17e-1420
tube3.11e-12192
multi-cellular organism4.23e-12656
embryo1.28e-11592
anatomical conduit1.76e-11240
germ layer7.67e-11560
germ layer / neural crest7.67e-11560
embryonic tissue7.67e-11560
presumptive structure7.67e-11560
germ layer / neural crest derived structure7.67e-11560
epiblast (generic)7.67e-11560
embryonic structure1.37e-10564
anatomical system1.03e-09624
anatomical group1.41e-09625
developing anatomical structure1.50e-09581
neural nucleus2.63e-089
nucleus of brain2.63e-089
basal ganglion6.06e-089
nuclear complex of neuraxis6.06e-089
aggregate regional part of brain6.06e-089
collection of basal ganglia6.06e-089
cerebral subcortex6.06e-089
organ1.08e-07503
organ part2.20e-07218


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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