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Coexpression cluster:C1375: Difference between revisions

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|ontology_enrichment_disease=DOID:162!2.89e-35!235;DOID:14566!2.32e-33!239;DOID:0050687!7.59e-33!143;DOID:305!1.06e-23!106;DOID:0050686!8.03e-11!137;DOID:299!6.98e-09!25;DOID:3095!3.79e-07!22;DOID:2994!3.79e-07!22
|ontology_enrichment_disease=DOID:162!2.89e-35!235;DOID:14566!2.32e-33!239;DOID:0050687!7.59e-33!143;DOID:305!1.06e-23!106;DOID:0050686!8.03e-11!137;DOID:299!6.98e-09!25;DOID:3095!3.79e-07!22;DOID:2994!3.79e-07!22
|ontology_enrichment_uberon=UBERON:0001017!3.08e-38!82;UBERON:0005743!3.89e-37!86;UBERON:0000073!4.77e-37!94;UBERON:0001016!4.77e-37!94;UBERON:0000955!5.87e-30!69;UBERON:0006238!5.87e-30!69;UBERON:0002346!5.51e-27!90;UBERON:0002616!3.48e-25!59;UBERON:0001049!7.54e-25!57;UBERON:0005068!7.54e-25!57;UBERON:0006241!7.54e-25!57;UBERON:0007135!7.54e-25!57;UBERON:0003075!4.55e-24!86;UBERON:0007284!4.55e-24!86;UBERON:0000924!8.95e-24!173;UBERON:0006601!8.95e-24!173;UBERON:0004121!2.12e-21!169;UBERON:0000033!1.30e-17!123;UBERON:0000153!1.86e-16!129;UBERON:0007811!1.86e-16!129;UBERON:0002780!1.97e-16!41;UBERON:0001890!1.97e-16!41;UBERON:0006240!1.97e-16!41;UBERON:0003080!1.05e-15!42;UBERON:0003056!1.86e-15!61;UBERON:0001893!2.30e-14!34;UBERON:0002791!5.86e-14!33;UBERON:0002020!7.75e-14!34;UBERON:0003528!7.75e-14!34;UBERON:0001869!1.58e-13!32;UBERON:0000956!4.77e-12!25;UBERON:0000203!4.77e-12!25;UBERON:0003076!8.35e-11!15;UBERON:0003057!8.35e-11!15;UBERON:0002619!2.12e-10!22;UBERON:0004732!4.12e-10!13;UBERON:0004733!7.00e-10!12;UBERON:0002028!7.00e-10!12;UBERON:0007277!7.00e-10!12;UBERON:0001950!1.40e-09!20;UBERON:0002680!8.86e-08!9;UBERON:0001895!8.86e-08!9;UBERON:0010092!8.86e-08!9;UBERON:0002037!9.27e-07!6;UBERON:0006215!9.27e-07!6
|ontology_enrichment_uberon=UBERON:0001017!3.08e-38!82;UBERON:0005743!3.89e-37!86;UBERON:0000073!4.77e-37!94;UBERON:0001016!4.77e-37!94;UBERON:0000955!5.87e-30!69;UBERON:0006238!5.87e-30!69;UBERON:0002346!5.51e-27!90;UBERON:0002616!3.48e-25!59;UBERON:0001049!7.54e-25!57;UBERON:0005068!7.54e-25!57;UBERON:0006241!7.54e-25!57;UBERON:0007135!7.54e-25!57;UBERON:0003075!4.55e-24!86;UBERON:0007284!4.55e-24!86;UBERON:0000924!8.95e-24!173;UBERON:0006601!8.95e-24!173;UBERON:0004121!2.12e-21!169;UBERON:0000033!1.30e-17!123;UBERON:0000153!1.86e-16!129;UBERON:0007811!1.86e-16!129;UBERON:0002780!1.97e-16!41;UBERON:0001890!1.97e-16!41;UBERON:0006240!1.97e-16!41;UBERON:0003080!1.05e-15!42;UBERON:0003056!1.86e-15!61;UBERON:0001893!2.30e-14!34;UBERON:0002791!5.86e-14!33;UBERON:0002020!7.75e-14!34;UBERON:0003528!7.75e-14!34;UBERON:0001869!1.58e-13!32;UBERON:0000956!4.77e-12!25;UBERON:0000203!4.77e-12!25;UBERON:0003076!8.35e-11!15;UBERON:0003057!8.35e-11!15;UBERON:0002619!2.12e-10!22;UBERON:0004732!4.12e-10!13;UBERON:0004733!7.00e-10!12;UBERON:0002028!7.00e-10!12;UBERON:0007277!7.00e-10!12;UBERON:0001950!1.40e-09!20;UBERON:0002680!8.86e-08!9;UBERON:0001895!8.86e-08!9;UBERON:0010092!8.86e-08!9;UBERON:0002037!9.27e-07!6;UBERON:0006215!9.27e-07!6
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}}
}}

Revision as of 13:16, 5 September 2012


Full id: C1375_cerebellum_Pericytes_extraskeletal_neuroblastoma_teratocarcinoma_neuroectodermal_H9



Phase1 CAGE Peaks

Hg19::chr13:100633838..100633854,-p@chr13:100633838..100633854
-
Hg19::chr13:100634004..100634025,+p2@ZIC2
Hg19::chr13:100634088..100634099,+p5@ZIC2
Hg19::chr13:100634111..100634118,+p8@ZIC2
Hg19::chr13:100634130..100634143,+p3@ZIC2
Hg19::chr3:147124697..147124729,+p@chr3:147124697..147124729
+


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>disease_data<br>


Cell Type
Ontology termp-valuen
neural cell4.01e-1125
neurectodermal cell5.44e-0959
neuronal stem cell5.35e-078
Uber Anatomy
Ontology termp-valuen
central nervous system3.08e-3882
regional part of nervous system4.77e-3794
nervous system4.77e-3794
brain5.87e-3069
future brain5.87e-3069
neurectoderm5.51e-2790
regional part of brain3.48e-2559
neural tube7.54e-2557
neural rod7.54e-2557
future spinal cord7.54e-2557
neural keel7.54e-2557
neural plate4.55e-2486
presumptive neural plate4.55e-2486
ectoderm8.95e-24173
presumptive ectoderm8.95e-24173
ectoderm-derived structure2.12e-21169
head1.30e-17123
anterior region of body1.86e-16129
craniocervical region1.86e-16129
regional part of forebrain1.97e-1641
forebrain1.97e-1641
future forebrain1.97e-1641
anterior neural tube1.05e-1542
pre-chordal neural plate1.86e-1561
telencephalon2.30e-1434
regional part of telencephalon5.86e-1433
gray matter7.75e-1434
brain grey matter7.75e-1434
cerebral hemisphere1.58e-1332
cerebral cortex4.77e-1225
pallium4.77e-1225
posterior neural tube8.35e-1115
chordal neural plate8.35e-1115
regional part of cerebral cortex2.12e-1022
segmental subdivision of nervous system4.12e-1013
segmental subdivision of hindbrain7.00e-1012
hindbrain7.00e-1012
presumptive hindbrain7.00e-1012
neocortex1.40e-0920
regional part of metencephalon8.86e-089
metencephalon8.86e-089
future metencephalon8.86e-089
cerebellum9.27e-076
rhombic lip9.27e-076
Disease
Ontology termp-valuen
cancer2.89e-35235
disease of cellular proliferation2.32e-33239
cell type cancer7.59e-33143
carcinoma1.06e-23106
organ system cancer8.03e-11137
adenocarcinoma6.98e-0925
germ cell and embryonal cancer3.79e-0722
germ cell cancer3.79e-0722


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)

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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
EGR1#195854.156815912341780.001617966818864440.010131840544153
HEY1#2346253.366759202588090.004423827045203030.0209485410462008
HMGN3#932445.452365148900390.002729616882333770.0149867762366763
TAF1#687252.785871904787740.01078636340290410.0397893828565943
TAF7#687959.52755783743662.84599232912077e-050.000599985048165209
ZBTB7A#5134156.126591089896580.0002476072821414750.00268897337418878
ZNF263#1012756.85153469750890.0001434607953814120.00186749370669815



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.