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Coexpression cluster:C3658: Difference between revisions

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|full_id=C3658_anaplastic_granulocyte_spinal_CD34_seminal_pineal_merkel
|full_id=C3658_anaplastic_granulocyte_spinal_CD34_seminal_pineal_merkel
|id=C3658
|id=C3658
|ontology_enrichment_celltype=CL:0000542!2.78e-12!53;CL:0000051!2.78e-12!53;CL:0000838!4.51e-12!52;CL:0000791!2.14e-07!18;CL:0000789!2.14e-07!18;CL:0002420!2.14e-07!18;CL:0002419!2.14e-07!18;CL:0000790!2.14e-07!18;CL:0000084!2.81e-07!25;CL:0000827!2.81e-07!25
|ontology_enrichment_celltype=CL:0000542!1.47e-11!53;CL:0000051!1.47e-11!53;CL:0000838!2.34e-11!52;CL:0002242!2.50e-10!55;CL:0000791!1.62e-07!18;CL:0000789!1.62e-07!18;CL:0002420!1.62e-07!18;CL:0002419!1.62e-07!18;CL:0000790!1.62e-07!18;CL:0000084!2.99e-07!25;CL:0000827!2.99e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.94e-11!115;UBERON:0000073!2.25e-11!94;UBERON:0001016!2.25e-11!94;UBERON:0001017!3.43e-11!82;UBERON:0005743!5.96e-11!86;UBERON:0001049!1.41e-10!57;UBERON:0005068!1.41e-10!57;UBERON:0006241!1.41e-10!57;UBERON:0007135!1.41e-10!57;UBERON:0000955!1.72e-09!69;UBERON:0006238!1.72e-09!69;UBERON:0002616!3.16e-09!59;UBERON:0003075!4.39e-09!86;UBERON:0007284!4.39e-09!86;UBERON:0002346!3.06e-08!90;UBERON:0003080!3.38e-07!42;UBERON:0002780!5.31e-07!41;UBERON:0001890!5.31e-07!41;UBERON:0006240!5.31e-07!41
|ontology_enrichment_uberon=UBERON:0007023!9.20e-12!114;UBERON:0001016!1.51e-11!89;UBERON:0001017!6.40e-11!81;UBERON:0001049!2.87e-10!56;UBERON:0005068!2.87e-10!56;UBERON:0006241!2.87e-10!56;UBERON:0007135!2.87e-10!56;UBERON:0003075!3.09e-09!82;UBERON:0007284!3.09e-09!82;UBERON:0000955!3.64e-09!68;UBERON:0006238!3.64e-09!68;UBERON:0000073!5.08e-09!53;UBERON:0002616!5.08e-09!53;UBERON:0002346!2.78e-08!86;UBERON:0002780!4.62e-07!41;UBERON:0001890!4.62e-07!41;UBERON:0003080!4.62e-07!41;UBERON:0006240!4.62e-07!41;UBERON:0003056!8.33e-07!61
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324945520585546!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321744861528351!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320269322693434!JUN#3725;3:12.5128291923363:0.000510331399272625:0.004437843547763!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156577851310072!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186334767718161!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294170705691144!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308615866296967!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276347753452308!USF1#7391;3:6.36149927720796:0.0038840405729056:0.019006902511184!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421284063767658!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140023042301801!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010930212247945
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324945520585546!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321744861528351!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320269322693434!JUN#3725;3:12.5128291923363:0.000510331399272625:0.004437843547763!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156577851310072!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186334767718161!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294170705691144!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308615866296967!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276347753452308!USF1#7391;3:6.36149927720796:0.0038840405729056:0.019006902511184!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421284063767658!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140023042301801!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010930212247945
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}}
}}

Revision as of 15:17, 19 October 2012


Full id: C3658_anaplastic_granulocyte_spinal_CD34_seminal_pineal_merkel



Phase1 CAGE Peaks

Hg19::chr17:55333876..55333939,+p1@MSI2
Hg19::chr17:55333945..55333971,+p4@MSI2
Hg19::chr17:55333997..55334044,+p2@MSI2


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
lymphocyte1.47e-1153
common lymphoid progenitor1.47e-1153
lymphoid lineage restricted progenitor cell2.34e-1152
nucleate cell2.50e-1055
mature alpha-beta T cell1.62e-0718
alpha-beta T cell1.62e-0718
immature T cell1.62e-0718
mature T cell1.62e-0718
immature alpha-beta T cell1.62e-0718
T cell2.99e-0725
pro-T cell2.99e-0725
Uber Anatomy
Ontology termp-valuen
adult organism9.20e-12114
nervous system1.51e-1189
central nervous system6.40e-1181
neural tube2.87e-1056
neural rod2.87e-1056
future spinal cord2.87e-1056
neural keel2.87e-1056
neural plate3.09e-0982
presumptive neural plate3.09e-0982
brain3.64e-0968
future brain3.64e-0968
regional part of nervous system5.08e-0953
regional part of brain5.08e-0953
neurectoderm2.78e-0886
regional part of forebrain4.62e-0741
forebrain4.62e-0741
anterior neural tube4.62e-0741
future forebrain4.62e-0741
pre-chordal neural plate8.33e-0761


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#186934.907389214879320.008460985347239390.0324945520585546
E2F6#187635.017155731697390.00791769806886330.0321744861528351
EGR1#195834.988179094810140.008056488137383440.0320269322693434
JUN#3725312.51282919233630.0005103313992726250.004437843547763
JUND#372736.994663941871030.002921845042734990.0156577851310072
MAX#414936.452555509007120.003721913834265510.0186334767718161
MYC#460935.22228187160940.007020843755740150.0294170705691144
NR3C1#2908314.9730233311730.0002978331194675480.00308615866296967
SIN3A#2594235.408884726815140.006318961977991520.0276347753452308
USF1#739136.361499277207960.00388404057290560.019006902511184
USF2#7392312.99219738506960.0004558979393427810.00421284063767658
ZBTB7A#5134137.35190930787590.002516255860282270.0140023042301801
ZNF263#1012738.221841637010680.001799043925565870.010930212247945



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.