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Coexpression cluster:C891: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.15e-39!82;UBERON:0000073!6.98e-39!94;UBERON:0001016!6.98e-39!94;UBERON:0005743!2.66e-38!86;UBERON:0000955!6.54e-33!69;UBERON:0006238!6.54e-33!69;UBERON:0001049!1.16e-32!57;UBERON:0005068!1.16e-32!57;UBERON:0006241!1.16e-32!57;UBERON:0007135!1.16e-32!57;UBERON:0002616!3.27e-30!59;UBERON:0002346!1.27e-27!90;UBERON:0002780!6.47e-26!41;UBERON:0001890!6.47e-26!41;UBERON:0006240!6.47e-26!41;UBERON:0003075!7.91e-26!86;UBERON:0007284!7.91e-26!86;UBERON:0003080!8.33e-25!42;UBERON:0000924!1.30e-23!173;UBERON:0006601!1.30e-23!173;UBERON:0004121!4.89e-22!169;UBERON:0000033!5.05e-22!123;UBERON:0002020!5.34e-22!34;UBERON:0003528!5.34e-22!34;UBERON:0001893!6.35e-22!34;UBERON:0000153!9.41e-22!129;UBERON:0007811!9.41e-22!129;UBERON:0001869!1.14e-21!32;UBERON:0002791!3.51e-21!33;UBERON:0003056!4.27e-19!61;UBERON:0000475!1.09e-17!365;UBERON:0000956!2.44e-17!25;UBERON:0000203!2.44e-17!25;UBERON:0002619!3.96e-17!22;UBERON:0007023!5.13e-17!115;UBERON:0001950!1.58e-15!20;UBERON:0000468!1.61e-12!659;UBERON:0003076!6.38e-09!15;UBERON:0003057!6.38e-09!15;UBERON:0000481!7.36e-09!347;UBERON:0000467!1.47e-08!625;UBERON:0000025!1.67e-08!194;UBERON:0000480!2.01e-08!626;UBERON:0000483!1.22e-07!309;UBERON:0004733!1.43e-07!12;UBERON:0002028!1.43e-07!12;UBERON:0007277!1.43e-07!12;UBERON:0000922!1.93e-07!612;UBERON:0000119!2.15e-07!312
|ontology_enrichment_uberon=UBERON:0001017!2.15e-39!82;UBERON:0000073!6.98e-39!94;UBERON:0001016!6.98e-39!94;UBERON:0005743!2.66e-38!86;UBERON:0000955!6.54e-33!69;UBERON:0006238!6.54e-33!69;UBERON:0001049!1.16e-32!57;UBERON:0005068!1.16e-32!57;UBERON:0006241!1.16e-32!57;UBERON:0007135!1.16e-32!57;UBERON:0002616!3.27e-30!59;UBERON:0002346!1.27e-27!90;UBERON:0002780!6.47e-26!41;UBERON:0001890!6.47e-26!41;UBERON:0006240!6.47e-26!41;UBERON:0003075!7.91e-26!86;UBERON:0007284!7.91e-26!86;UBERON:0003080!8.33e-25!42;UBERON:0000924!1.30e-23!173;UBERON:0006601!1.30e-23!173;UBERON:0004121!4.89e-22!169;UBERON:0000033!5.05e-22!123;UBERON:0002020!5.34e-22!34;UBERON:0003528!5.34e-22!34;UBERON:0001893!6.35e-22!34;UBERON:0000153!9.41e-22!129;UBERON:0007811!9.41e-22!129;UBERON:0001869!1.14e-21!32;UBERON:0002791!3.51e-21!33;UBERON:0003056!4.27e-19!61;UBERON:0000475!1.09e-17!365;UBERON:0000956!2.44e-17!25;UBERON:0000203!2.44e-17!25;UBERON:0002619!3.96e-17!22;UBERON:0007023!5.13e-17!115;UBERON:0001950!1.58e-15!20;UBERON:0000468!1.61e-12!659;UBERON:0003076!6.38e-09!15;UBERON:0003057!6.38e-09!15;UBERON:0000481!7.36e-09!347;UBERON:0000467!1.47e-08!625;UBERON:0000025!1.67e-08!194;UBERON:0000480!2.01e-08!626;UBERON:0000483!1.22e-07!309;UBERON:0004733!1.43e-07!12;UBERON:0002028!1.43e-07!12;UBERON:0007277!1.43e-07!12;UBERON:0000922!1.93e-07!612;UBERON:0000119!2.15e-07!312
|tf_chipseq_enrich=CTCF#10664;6:3.57350424871668:0.00210388362937215:0.0121658547349537!TAF7#6879;4:5.08136417996618:0.0051419296120382:0.023905715222207
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}}
}}

Revision as of 12:03, 5 September 2012


Full id: C891_Fibroblast_occipital_mesothelioma_cholangiocellular_neuroblastoma_pineal_hippocampus



Phase1 CAGE Peaks

Hg19::chr12:130303291..130303304,-p@chr12:130303291..130303304
-
Hg19::chr5:167000419..167000430,+p@chr5:167000419..167000430
+
Hg19::chr5:167000441..167000460,+p@chr5:167000441..167000460
+
Hg19::chr5:167000581..167000611,+p6@ODZ2
Hg19::chr5:167000625..167000675,+p5@ODZ2
Hg19::chr5:167000685..167000706,+p11@ODZ2
Hg19::chr5:167000707..167000719,+p16@ODZ2
Hg19::chr5:167000959..167001019,+p2@ODZ2
Hg19::chr5:167148342..167148357,+p1@ENST00000517346


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
non-terminally differentiated cell5.95e-09180
neural cell1.47e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system2.15e-3982
regional part of nervous system6.98e-3994
nervous system6.98e-3994
brain6.54e-3369
future brain6.54e-3369
neural tube1.16e-3257
neural rod1.16e-3257
future spinal cord1.16e-3257
neural keel1.16e-3257
regional part of brain3.27e-3059
neurectoderm1.27e-2790
regional part of forebrain6.47e-2641
forebrain6.47e-2641
future forebrain6.47e-2641
neural plate7.91e-2686
presumptive neural plate7.91e-2686
anterior neural tube8.33e-2542
ectoderm1.30e-23173
presumptive ectoderm1.30e-23173
ectoderm-derived structure4.89e-22169
head5.05e-22123
gray matter5.34e-2234
brain grey matter5.34e-2234
telencephalon6.35e-2234
anterior region of body9.41e-22129
craniocervical region9.41e-22129
cerebral hemisphere1.14e-2132
regional part of telencephalon3.51e-2133
pre-chordal neural plate4.27e-1961
organism subdivision1.09e-17365
cerebral cortex2.44e-1725
pallium2.44e-1725
regional part of cerebral cortex3.96e-1722
adult organism5.13e-17115
neocortex1.58e-1520
multi-cellular organism1.61e-12659
posterior neural tube6.38e-0915
chordal neural plate6.38e-0915
multi-tissue structure7.36e-09347
anatomical system1.47e-08625
tube1.67e-08194
anatomical group2.01e-08626
epithelium1.22e-07309
segmental subdivision of hindbrain1.43e-0712
hindbrain1.43e-0712
presumptive hindbrain1.43e-0712
embryo1.93e-07612
cell layer2.15e-07312


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
CTCF#1066463.573504248716680.002103883629372150.0121658547349537
TAF7#687945.081364179966180.00514192961203820.023905715222207



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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