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Coexpression cluster:C2217: Difference between revisions

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|full_id=C2217_mature_skeletal_neuroepithelioma_neuroectodermal_argyrophil_breast_left
|full_id=C2217_mature_skeletal_neuroepithelioma_neuroectodermal_argyrophil_breast_left
|id=C2217
|id=C2217
|ontology_enrichment_celltype=CL:0000136!1.12e-07!15
|ontology_enrichment_celltype=CL:0000136!6.89e-09!15
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.81e-47!115;UBERON:0001049!2.17e-30!57;UBERON:0005068!2.17e-30!57;UBERON:0006241!2.17e-30!57;UBERON:0007135!2.17e-30!57;UBERON:0001017!5.71e-30!82;UBERON:0005743!8.59e-30!86;UBERON:0002346!3.76e-28!90;UBERON:0000073!1.41e-27!94;UBERON:0001016!1.41e-27!94;UBERON:0002616!3.69e-26!59;UBERON:0003075!9.86e-26!86;UBERON:0007284!9.86e-26!86;UBERON:0000955!5.70e-24!69;UBERON:0006238!5.70e-24!69;UBERON:0003080!1.82e-23!42;UBERON:0002780!1.19e-22!41;UBERON:0001890!1.19e-22!41;UBERON:0006240!1.19e-22!41;UBERON:0001893!1.16e-21!34;UBERON:0002020!1.60e-21!34;UBERON:0003528!1.60e-21!34;UBERON:0002791!4.99e-21!33;UBERON:0001869!1.25e-20!32;UBERON:0003056!8.63e-18!61;UBERON:0000924!2.97e-17!173;UBERON:0006601!2.97e-17!173;UBERON:0000956!1.08e-15!25;UBERON:0000203!1.08e-15!25;UBERON:0004121!1.58e-15!169;UBERON:0002619!2.44e-15!22;UBERON:0001950!3.80e-14!20;UBERON:0000153!8.43e-14!129;UBERON:0007811!8.43e-14!129;UBERON:0000033!2.68e-13!123;UBERON:0000468!3.30e-09!659;UBERON:0000475!3.63e-09!365;UBERON:0000062!3.82e-09!511;UBERON:0000025!7.03e-09!194;UBERON:0004111!2.08e-08!241;UBERON:0000922!2.31e-08!612;UBERON:0000481!4.54e-08!347;UBERON:0003076!4.70e-08!15;UBERON:0003057!4.70e-08!15;UBERON:0002420!1.15e-07!9;UBERON:0007245!1.15e-07!9;UBERON:0010009!1.15e-07!9;UBERON:0010011!1.15e-07!9;UBERON:0000454!1.15e-07!9;UBERON:0000064!1.57e-07!219;UBERON:0002308!2.60e-07!9;UBERON:0000125!2.60e-07!9;UBERON:0004732!8.78e-07!13
|ontology_enrichment_uberon=UBERON:0007023!1.22e-57!114;UBERON:0001049!6.71e-33!56;UBERON:0005068!6.71e-33!56;UBERON:0006241!6.71e-33!56;UBERON:0007135!6.71e-33!56;UBERON:0001017!4.88e-31!81;UBERON:0000073!1.13e-30!53;UBERON:0002616!1.13e-30!53;UBERON:0001016!1.25e-29!89;UBERON:0001893!5.33e-28!34;UBERON:0003528!7.52e-28!34;UBERON:0002020!7.52e-28!34;UBERON:0001869!1.32e-26!32;UBERON:0002791!1.77e-26!32;UBERON:0002346!4.22e-26!86;UBERON:0002780!4.66e-26!41;UBERON:0001890!4.66e-26!41;UBERON:0003080!4.66e-26!41;UBERON:0006240!4.66e-26!41;UBERON:0000955!1.56e-23!68;UBERON:0006238!1.56e-23!68;UBERON:0003075!3.22e-23!82;UBERON:0007284!3.22e-23!82;UBERON:0000956!2.50e-20!25;UBERON:0000203!2.50e-20!25;UBERON:0002619!1.32e-19!22;UBERON:0011216!1.19e-18!223;UBERON:0001950!3.96e-18!20;UBERON:0010371!1.81e-17!104;UBERON:0004121!4.41e-17!171;UBERON:0000924!4.41e-17!171;UBERON:0006601!4.41e-17!171;UBERON:0003056!7.92e-16!61;UBERON:0010314!1.95e-14!132;UBERON:0000477!1.58e-13!373;UBERON:0000025!3.76e-12!192;UBERON:0004111!7.04e-11!240;UBERON:0000481!1.76e-10!342;UBERON:0000922!1.81e-09!592;UBERON:0002420!2.30e-09!9;UBERON:0007245!2.30e-09!9;UBERON:0010009!2.30e-09!9;UBERON:0010011!2.30e-09!9;UBERON:0000454!2.30e-09!9;UBERON:0000125!5.90e-09!9;UBERON:0002308!5.90e-09!9;UBERON:0000468!7.73e-09!656;UBERON:0000064!4.91e-08!218;UBERON:0003076!4.97e-08!15;UBERON:0003057!4.97e-08!15;UBERON:0000489!6.86e-08!31;UBERON:0003103!8.90e-08!68;UBERON:0005423!1.03e-07!581;UBERON:0009663!1.19e-07!7;UBERON:0000062!5.12e-07!503;UBERON:0001871!5.65e-07!6
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}}
}}

Revision as of 12:12, 19 October 2012


Full id: C2217_mature_skeletal_neuroepithelioma_neuroectodermal_argyrophil_breast_left



Phase1 CAGE Peaks

Hg19::chr12:54982378..54982417,-p2@PPP1R1A
Hg19::chr12:54982420..54982461,-p1@PPP1R1A
Hg19::chr12:54982586..54982628,-p3@PPP1R1A
Hg19::chr12:54983026..54983043,-p@chr12:54983026..54983043
-


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
fat cell6.89e-0915
Uber Anatomy
Ontology termp-valuen
adult organism1.22e-57114
neural tube6.71e-3356
neural rod6.71e-3356
future spinal cord6.71e-3356
neural keel6.71e-3356
central nervous system4.88e-3181
regional part of nervous system1.13e-3053
regional part of brain1.13e-3053
nervous system1.25e-2989
telencephalon5.33e-2834
brain grey matter7.52e-2834
gray matter7.52e-2834
cerebral hemisphere1.32e-2632
regional part of telencephalon1.77e-2632
neurectoderm4.22e-2686
regional part of forebrain4.66e-2641
forebrain4.66e-2641
anterior neural tube4.66e-2641
future forebrain4.66e-2641
brain1.56e-2368
future brain1.56e-2368
neural plate3.22e-2382
presumptive neural plate3.22e-2382
cerebral cortex2.50e-2025
pallium2.50e-2025
regional part of cerebral cortex1.32e-1922
organ system subdivision1.19e-18223
neocortex3.96e-1820
ecto-epithelium1.81e-17104
ectoderm-derived structure4.41e-17171
ectoderm4.41e-17171
presumptive ectoderm4.41e-17171
pre-chordal neural plate7.92e-1661
structure with developmental contribution from neural crest1.95e-14132
anatomical cluster1.58e-13373
tube3.76e-12192
anatomical conduit7.04e-11240
multi-tissue structure1.76e-10342
embryo1.81e-09592
basal ganglion2.30e-099
nuclear complex of neuraxis2.30e-099
aggregate regional part of brain2.30e-099
collection of basal ganglia2.30e-099
cerebral subcortex2.30e-099
neural nucleus5.90e-099
nucleus of brain5.90e-099
multi-cellular organism7.73e-09656
organ part4.91e-08218
posterior neural tube4.97e-0815
chordal neural plate4.97e-0815
cavitated compound organ6.86e-0831
compound organ8.90e-0868
developing anatomical structure1.03e-07581
telencephalic nucleus1.19e-077
organ5.12e-07503
temporal lobe5.65e-076


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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