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Coexpression cluster:C1098: Difference between revisions

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|ontology_enrichment_disease=DOID:2531!3.74e-16!51;DOID:0060083!3.74e-16!51;DOID:1240!7.58e-15!39;DOID:14566!9.27e-13!239;DOID:162!1.82e-12!235;DOID:8692!4.98e-12!31;DOID:0050686!1.38e-08!137
|ontology_enrichment_disease=DOID:2531!3.74e-16!51;DOID:0060083!3.74e-16!51;DOID:1240!7.58e-15!39;DOID:14566!9.27e-13!239;DOID:162!1.82e-12!235;DOID:8692!4.98e-12!31;DOID:0050686!1.38e-08!137
|ontology_enrichment_uberon=UBERON:0001049!2.07e-10!57;UBERON:0005068!2.07e-10!57;UBERON:0006241!2.07e-10!57;UBERON:0007135!2.07e-10!57;UBERON:0003080!1.07e-09!42;UBERON:0001017!1.12e-09!82;UBERON:0007023!1.18e-09!115;UBERON:0002346!1.38e-09!90;UBERON:0005743!1.39e-09!86;UBERON:0002780!1.51e-09!41;UBERON:0001890!1.51e-09!41;UBERON:0006240!1.51e-09!41;UBERON:0000073!3.47e-09!94;UBERON:0001016!3.47e-09!94;UBERON:0003075!1.40e-08!86;UBERON:0007284!1.40e-08!86;UBERON:0002616!1.60e-08!59;UBERON:0002020!1.33e-07!34;UBERON:0003528!1.33e-07!34;UBERON:0003056!1.60e-07!61;UBERON:0002791!6.47e-07!33;UBERON:0000955!8.24e-07!69;UBERON:0006238!8.24e-07!69;UBERON:0001893!9.66e-07!34
|ontology_enrichment_uberon=UBERON:0001049!2.07e-10!57;UBERON:0005068!2.07e-10!57;UBERON:0006241!2.07e-10!57;UBERON:0007135!2.07e-10!57;UBERON:0003080!1.07e-09!42;UBERON:0001017!1.12e-09!82;UBERON:0007023!1.18e-09!115;UBERON:0002346!1.38e-09!90;UBERON:0005743!1.39e-09!86;UBERON:0002780!1.51e-09!41;UBERON:0001890!1.51e-09!41;UBERON:0006240!1.51e-09!41;UBERON:0000073!3.47e-09!94;UBERON:0001016!3.47e-09!94;UBERON:0003075!1.40e-08!86;UBERON:0007284!1.40e-08!86;UBERON:0002616!1.60e-08!59;UBERON:0002020!1.33e-07!34;UBERON:0003528!1.33e-07!34;UBERON:0003056!1.60e-07!61;UBERON:0002791!6.47e-07!33;UBERON:0000955!8.24e-07!69;UBERON:0006238!8.24e-07!69;UBERON:0001893!9.66e-07!34
|tf_chipseq_enrich=IRF3#3661;3:17.6182320793086:0.000497999438667357:0.00440096153113726!MAFF#23764;3:21.1182586837294:0.000293010169114186:0.00310803260736507!MAFK#7975;3:10.1627749266862:0.00244557310713952:0.0137689061852585!NFYA#4800;3:6.90959276243645:0.00727972723713068:0.0301235164990171!NFYB#4801;3:6.28492247007617:0.00947376901248262:0.0356976210230066!PBX3#5090;3:8.21794225752905:0.00447320658280844:0.0211679756366983!SP2#6668;3:9.80757393519174:0.00270718466508561:0.014887876322304
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}}
}}

Revision as of 12:37, 5 September 2012


Full id: C1098_acute_teratocarcinoma_myelodysplastic_colon_adult_Mast_merkel



Phase1 CAGE Peaks

Hg19::chrX:80370321..80370336,-p@chrX:80370321..80370336
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Hg19::chrX:80370650..80370666,-p@chrX:80370650..80370666
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Hg19::chrX:80371754..80371768,-p@chrX:80371754..80371768
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Hg19::chrX:80373952..80373966,-p@chrX:80373952..80373966
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Hg19::chrX:80373978..80373996,-p@chrX:80373978..80373996
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Hg19::chrX:80377100..80377111,-p5@HMGN5
Hg19::chrX:80377118..80377149,-p1@HMGN5
Hg19::chrX:80377162..80377180,-p2@HMGN5


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
neural tube2.07e-1057
neural rod2.07e-1057
future spinal cord2.07e-1057
neural keel2.07e-1057
anterior neural tube1.07e-0942
central nervous system1.12e-0982
adult organism1.18e-09115
neurectoderm1.38e-0990
regional part of forebrain1.51e-0941
forebrain1.51e-0941
future forebrain1.51e-0941
regional part of nervous system3.47e-0994
nervous system3.47e-0994
neural plate1.40e-0886
presumptive neural plate1.40e-0886
regional part of brain1.60e-0859
gray matter1.33e-0734
brain grey matter1.33e-0734
pre-chordal neural plate1.60e-0761
regional part of telencephalon6.47e-0733
brain8.24e-0769
future brain8.24e-0769
telencephalon9.66e-0734
Disease
Ontology termp-valuen
hematologic cancer3.74e-1651
immune system cancer3.74e-1651
leukemia7.58e-1539
disease of cellular proliferation9.27e-13239
cancer1.82e-12235
myeloid leukemia4.98e-1231
organ system cancer1.38e-08137


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
IRF3#3661317.61823207930860.0004979994386673570.00440096153113726
MAFF#23764321.11825868372940.0002930101691141860.00310803260736507
MAFK#7975310.16277492668620.002445573107139520.0137689061852585
NFYA#480036.909592762436450.007279727237130680.0301235164990171
NFYB#480136.284922470076170.009473769012482620.0356976210230066
PBX3#509038.217942257529050.004473206582808440.0211679756366983
SP2#666839.807573935191740.002707184665085610.014887876322304



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.