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Coexpression cluster:C2916: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.19e-37!115;UBERON:0001049!1.17e-27!57;UBERON:0005068!1.17e-27!57;UBERON:0006241!1.17e-27!57;UBERON:0007135!1.17e-27!57;UBERON:0001017!3.64e-26!82;UBERON:0005743!2.65e-25!86;UBERON:0000924!3.43e-24!173;UBERON:0006601!3.43e-24!173;UBERON:0002346!6.14e-24!90;UBERON:0000073!1.32e-23!94;UBERON:0001016!1.32e-23!94;UBERON:0002616!4.04e-23!59;UBERON:0000955!8.80e-23!69;UBERON:0006238!8.80e-23!69;UBERON:0003080!2.61e-22!42;UBERON:0002780!6.08e-22!41;UBERON:0001890!6.08e-22!41;UBERON:0006240!6.08e-22!41;UBERON:0004121!6.12e-22!169;UBERON:0003075!2.45e-21!86;UBERON:0007284!2.45e-21!86;UBERON:0000033!1.27e-20!123;UBERON:0000153!2.11e-20!129;UBERON:0007811!2.11e-20!129;UBERON:0001893!3.65e-19!34;UBERON:0002020!5.35e-19!34;UBERON:0003528!5.35e-19!34;UBERON:0002791!1.62e-18!33;UBERON:0001869!1.77e-18!32;UBERON:0003056!3.73e-16!61;UBERON:0000956!3.97e-15!25;UBERON:0000203!3.97e-15!25;UBERON:0002619!5.60e-15!22;UBERON:0000062!5.28e-14!511;UBERON:0001950!5.33e-14!20;UBERON:0000468!3.11e-12!659;UBERON:0000475!2.53e-10!365;UBERON:0000467!1.35e-08!625;UBERON:0000480!1.95e-08!626;UBERON:0000064!2.86e-08!219
|ontology_enrichment_uberon=UBERON:0001049!4.75e-48!56;UBERON:0005068!4.75e-48!56;UBERON:0006241!4.75e-48!56;UBERON:0007135!4.75e-48!56;UBERON:0001017!3.08e-46!81;UBERON:0000073!2.80e-44!53;UBERON:0002616!2.80e-44!53;UBERON:0001016!4.84e-44!89;UBERON:0000955!1.72e-40!68;UBERON:0006238!1.72e-40!68;UBERON:0002346!2.19e-40!86;UBERON:0002780!3.63e-35!41;UBERON:0001890!3.63e-35!41;UBERON:0003080!3.63e-35!41;UBERON:0006240!3.63e-35!41;UBERON:0003075!6.83e-35!82;UBERON:0007284!6.83e-35!82;UBERON:0001893!1.11e-32!34;UBERON:0001869!1.16e-32!32;UBERON:0007023!1.34e-32!114;UBERON:0003528!2.89e-32!34;UBERON:0002020!2.89e-32!34;UBERON:0002791!5.10e-30!32;UBERON:0004121!5.69e-30!171;UBERON:0000924!5.69e-30!171;UBERON:0006601!5.69e-30!171;UBERON:0001950!1.16e-29!20;UBERON:0002619!1.85e-29!22;UBERON:0010371!9.17e-27!104;UBERON:0000956!3.09e-25!25;UBERON:0000203!3.09e-25!25;UBERON:0003056!1.61e-23!61;UBERON:0010314!2.03e-23!132;UBERON:0011216!8.82e-19!223;UBERON:0003076!1.26e-13!15;UBERON:0003057!1.26e-13!15;UBERON:0000200!1.07e-10!6;UBERON:0004733!4.07e-10!12;UBERON:0002028!4.07e-10!12;UBERON:0007277!4.07e-10!12;UBERON:0002021!2.23e-09!5;UBERON:0004732!3.55e-09!13;UBERON:0002298!4.46e-09!6;UBERON:0001872!5.90e-09!5;UBERON:0001871!8.88e-09!6;UBERON:0000025!1.54e-08!192;UBERON:0000125!1.89e-08!9;UBERON:0002308!1.89e-08!9;UBERON:0000477!3.76e-08!373;UBERON:0000369!5.52e-08!4;UBERON:0002435!5.52e-08!4;UBERON:0000204!5.52e-08!4;UBERON:0010082!5.52e-08!4;UBERON:0004111!3.58e-07!240
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106825969137056!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.027996871236607
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106825969137056!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.027996871236607
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}}
}}

Revision as of 14:34, 19 October 2012


Full id: C2916_pineal_neuroectodermal_cerebellum_small_neuroepithelioma_thyroid_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr8:12809093..12809143,+p1@KIAA1456
Hg19::chr8:12809536..12809544,+p15@KIAA1456
Hg19::chr8:12809553..12809567,+p11@KIAA1456
Hg19::chr8:12809591..12809598,+p13@KIAA1456


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube4.75e-4856
neural rod4.75e-4856
future spinal cord4.75e-4856
neural keel4.75e-4856
central nervous system3.08e-4681
regional part of nervous system2.80e-4453
regional part of brain2.80e-4453
nervous system4.84e-4489
brain1.72e-4068
future brain1.72e-4068
neurectoderm2.19e-4086
regional part of forebrain3.63e-3541
forebrain3.63e-3541
anterior neural tube3.63e-3541
future forebrain3.63e-3541
neural plate6.83e-3582
presumptive neural plate6.83e-3582
telencephalon1.11e-3234
cerebral hemisphere1.16e-3232
adult organism1.34e-32114
brain grey matter2.89e-3234
gray matter2.89e-3234
regional part of telencephalon5.10e-3032
ectoderm-derived structure5.69e-30171
ectoderm5.69e-30171
presumptive ectoderm5.69e-30171
neocortex1.16e-2920
regional part of cerebral cortex1.85e-2922
ecto-epithelium9.17e-27104
cerebral cortex3.09e-2525
pallium3.09e-2525
pre-chordal neural plate1.61e-2361
structure with developmental contribution from neural crest2.03e-23132
organ system subdivision8.82e-19223
posterior neural tube1.26e-1315
chordal neural plate1.26e-1315
gyrus1.07e-106
segmental subdivision of hindbrain4.07e-1012
hindbrain4.07e-1012
presumptive hindbrain4.07e-1012
occipital lobe2.23e-095
segmental subdivision of nervous system3.55e-0913
brainstem4.46e-096
parietal lobe5.90e-095
temporal lobe8.88e-096
tube1.54e-08192
neural nucleus1.89e-089
nucleus of brain1.89e-089
anatomical cluster3.76e-08373
corpus striatum5.52e-084
striatum5.52e-084
ventral part of telencephalon5.52e-084
future corpus striatum5.52e-084
anatomical conduit3.58e-07240


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

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

TF#promotersEnrichmentp-valueq-value
E2F1#186944.907389214879320.001724022357361790.0106825969137056
ZNF263#1012736.166381227758010.006539814347975980.027996871236607



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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