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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C900_CD4_thymus_Hodgkin_CD8_CD34_chronic_CD133
|full_id=C900_CD4_thymus_Hodgkin_CD8_CD34_chronic_CD133
|gostat_on_coexpression_clusters=GO:0021542!dentate gyrus development!0.00788803686016357!51176$GO:0021766!hippocampus development!0.00788803686016357!51176$GO:0048341!paraxial mesoderm formation!0.00788803686016357!51176$GO:0048340!paraxial mesoderm morphogenesis!0.00788803686016357!51176$GO:0048339!paraxial mesoderm development!0.00788803686016357!51176$GO:0021543!pallium development!0.00788803686016357!51176$GO:0021761!limbic system development!0.00788803686016357!51176$GO:0045843!negative regulation of striated muscle development!0.00788803686016357!51176$GO:0008301!DNA bending activity!0.00832491294628465!51176$GO:0021537!telencephalon development!0.00832491294628465!51176$GO:0016202!regulation of striated muscle development!0.00832491294628465!51176$GO:0030879!mammary gland development!0.00832491294628465!51176$GO:0001890!placenta development!0.00832491294628465!51176$GO:0001707!mesoderm formation!0.00832491294628465!51176$GO:0048332!mesoderm morphogenesis!0.00832491294628465!51176$GO:0001704!formation of primary germ layer!0.00832491294628465!51176$GO:0001756!somitogenesis!0.00832491294628465!51176$GO:0042475!odontogenesis of dentine-containing teeth!0.00832491294628465!51176$GO:0042476!odontogenesis!0.00925727956560874!51176$GO:0007369!gastrulation!0.00925727956560874!51176$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.00925727956560874!51176$GO:0035282!segmentation!0.00925727956560874!51176$GO:0030111!regulation of Wnt receptor signaling pathway!0.00925727956560874!51176$GO:0030326!embryonic limb morphogenesis!0.0100597509018366!51176$GO:0035113!embryonic appendage morphogenesis!0.0100597509018366!51176$GO:0060173!limb development!0.0100597509018366!51176$GO:0035107!appendage morphogenesis!0.0100597509018366!51176$GO:0035108!limb morphogenesis!0.0100597509018366!51176$GO:0048736!appendage development!0.0100597509018366!51176$GO:0007498!mesoderm development!0.0113327103941029!51176$GO:0030900!forebrain development!0.0113327103941029!51176$GO:0048732!gland development!0.0113327103941029!51176$GO:0009952!anterior/posterior pattern formation!0.013137632697009!51176$GO:0048729!tissue morphogenesis!0.0166883415293181!51176$GO:0003002!regionalization!0.0191898420490159!51176$GO:0014706!striated muscle development!0.0191898420490159!51176$GO:0048598!embryonic morphogenesis!0.0191898420490159!51176$GO:0009792!embryonic development ending in birth or egg hatching!0.0191898420490159!51176$GO:0043009!chordate embryonic development!0.0191898420490159!51176$GO:0003682!chromatin binding!0.023232030545665!51176$GO:0007389!pattern specification process!0.0238101401826761!51176$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0238101401826761!51176$GO:0007420!brain development!0.0248709738339615!51176$GO:0045944!positive regulation of transcription from RNA polymerase II promoter!0.0248709738339615!51176$GO:0016055!Wnt receptor signaling pathway!0.0253657508702202!51176$GO:0048646!anatomical structure formation!0.0261802979410705!51176$GO:0007517!muscle development!0.0287971716144891!51176$GO:0045892!negative regulation of transcription, DNA-dependent!0.0332640668261998!51176$GO:0005667!transcription factor complex!0.0337053528466996!51176$GO:0032991!macromolecular complex!0.0343816716168921!92906;51176$GO:0045893!positive regulation of transcription, DNA-dependent!0.0343816716168921!51176$GO:0007417!central nervous system development!0.0348583904248288!51176$GO:0009790!embryonic development!0.0348583904248288!51176$GO:0016070!RNA metabolic process!0.0371124061293968!92906;51176$GO:0006397!mRNA processing!0.0384558457409892!92906$GO:0003702!RNA polymerase II transcription factor activity!0.0384558457409892!51176$GO:0045941!positive regulation of transcription!0.0384558457409892!51176$GO:0045935!positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0387433320914088!51176$GO:0016481!negative regulation of transcription!0.0387433320914088!51176$GO:0009888!tissue development!0.0397803929901879!51176$GO:0016563!transcription activator activity!0.0397803929901879!51176$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0403994266050121!51176$GO:0016071!mRNA metabolic process!0.0426102447334929!92906$GO:0009887!organ morphogenesis!0.0440615929370697!51176$GO:0031325!positive regulation of cellular metabolic process!0.0440615929370697!51176$GO:0031324!negative regulation of cellular metabolic process!0.0452854709956637!51176$GO:0009893!positive regulation of metabolic process!0.0457736471972898!51176$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.048768482251992!51176$GO:0009892!negative regulation of metabolic process!0.0493319114072623!51176$GO:0010467!gene expression!0.0493319114072623!92906;51176$GO:0044451!nucleoplasm part!0.049888598166981!51176
|id=C900
|id=C900
}}
}}

Revision as of 17:42, 18 May 2012


Full id: C900_CD4_thymus_Hodgkin_CD8_CD34_chronic_CD133



Phase1 CAGE Peaks

Hg19::chr13:30951074..30951122,-p1@LINC00426
Hg19::chr13:30951124..30951135,-p4@LINC00426
Hg19::chr13:30951150..30951161,-p5@LINC00426
Hg19::chr14:22309226..22309237,+p4@uc001wbx.2
p4@uc010tmg.1
Hg19::chr14:81425875..81425889,-p5@CEP128
Hg19::chr2:38830160..38830206,-p3@HNRPLL
Hg19::chr3:133209983..133210005,-p2@AK128281
Hg19::chr4:109087819..109087826,-p45@LEF1
Hg19::chr6:25042231..25042263,-p7@FAM65B


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

GO IDGO nameFDR corrected p-value
GO:0021542dentate gyrus development0.00788803686016357
GO:0021766hippocampus development0.00788803686016357
GO:0048341paraxial mesoderm formation0.00788803686016357
GO:0048340paraxial mesoderm morphogenesis0.00788803686016357
GO:0048339paraxial mesoderm development0.00788803686016357
GO:0021543pallium development0.00788803686016357
GO:0021761limbic system development0.00788803686016357
GO:0045843negative regulation of striated muscle development0.00788803686016357
GO:0008301DNA bending activity0.00832491294628465
GO:0021537telencephalon development0.00832491294628465
GO:0016202regulation of striated muscle development0.00832491294628465
GO:0030879mammary gland development0.00832491294628465
GO:0001890placenta development0.00832491294628465
GO:0001707mesoderm formation0.00832491294628465
GO:0048332mesoderm morphogenesis0.00832491294628465
GO:0001704formation of primary germ layer0.00832491294628465
GO:0001756somitogenesis0.00832491294628465
GO:0042475odontogenesis of dentine-containing teeth0.00832491294628465
GO:0042476odontogenesis0.00925727956560874
GO:0007369gastrulation0.00925727956560874
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.00925727956560874
GO:0035282segmentation0.00925727956560874
GO:0030111regulation of Wnt receptor signaling pathway0.00925727956560874
GO:0030326embryonic limb morphogenesis0.0100597509018366
GO:0035113embryonic appendage morphogenesis0.0100597509018366
GO:0060173limb development0.0100597509018366
GO:0035107appendage morphogenesis0.0100597509018366
GO:0035108limb morphogenesis0.0100597509018366
GO:0048736appendage development0.0100597509018366
GO:0007498mesoderm development0.0113327103941029
GO:0030900forebrain development0.0113327103941029
GO:0048732gland development0.0113327103941029
GO:0009952anterior/posterior pattern formation0.013137632697009
GO:0048729tissue morphogenesis0.0166883415293181
GO:0003002regionalization0.0191898420490159
GO:0014706striated muscle development0.0191898420490159
GO:0048598embryonic morphogenesis0.0191898420490159
GO:0009792embryonic development ending in birth or egg hatching0.0191898420490159
GO:0043009chordate embryonic development0.0191898420490159
GO:0003682chromatin binding0.023232030545665
GO:0007389pattern specification process0.0238101401826761
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0238101401826761
GO:0007420brain development0.0248709738339615
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0248709738339615
GO:0016055Wnt receptor signaling pathway0.0253657508702202
GO:0048646anatomical structure formation0.0261802979410705
GO:0007517muscle development0.0287971716144891
GO:0045892negative regulation of transcription, DNA-dependent0.0332640668261998
GO:0005667transcription factor complex0.0337053528466996
GO:0032991macromolecular complex0.0343816716168921
GO:0045893positive regulation of transcription, DNA-dependent0.0343816716168921
GO:0007417central nervous system development0.0348583904248288
GO:0009790embryonic development0.0348583904248288
GO:0016070RNA metabolic process0.0371124061293968
GO:0006397mRNA processing0.0384558457409892
GO:0003702RNA polymerase II transcription factor activity0.0384558457409892
GO:0045941positive regulation of transcription0.0384558457409892
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0387433320914088
GO:0016481negative regulation of transcription0.0387433320914088
GO:0009888tissue development0.0397803929901879
GO:0016563transcription activator activity0.0397803929901879
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0403994266050121
GO:0016071mRNA metabolic process0.0426102447334929
GO:0009887organ morphogenesis0.0440615929370697
GO:0031325positive regulation of cellular metabolic process0.0440615929370697
GO:0031324negative regulation of cellular metabolic process0.0452854709956637
GO:0009893positive regulation of metabolic process0.0457736471972898
GO:0006357regulation of transcription from RNA polymerase II promoter0.048768482251992
GO:0009892negative regulation of metabolic process0.0493319114072623
GO:0010467gene expression0.0493319114072623
GO:0044451nucleoplasm part0.049888598166981



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

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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

No analysis results for this cluster

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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