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|gostat_on_coexpression_clusters=GO:0005843!cytosolic small ribosomal subunit (sensu Eukaryota)!7.194409102925e-05!6222;6208$GO:0005830!cytosolic ribosome (sensu Eukaryota)!0.000177936588775551!6222;6208$GO:0015935!small ribosomal subunit!0.000310347059341862!6222;6208$GO:0044445!cytosolic part!0.000575648910173879!6222;6208$GO:0033279!ribosomal subunit!0.000622361272308287!6222;6208$GO:0042257!ribosomal subunit assembly!0.000622361272308287!6208$GO:0000028!ribosomal small subunit assembly and maintenance!0.000622361272308287!6208$GO:0042274!ribosomal small subunit biogenesis and assembly!0.000968103285525504!6208$GO:0030490!maturation of SSU-rRNA!0.000968103285525504!6208$GO:0005829!cytosol!0.00206506472197114!6222;6208$GO:0042255!ribosome assembly!0.00277209174988996!6208$GO:0003735!structural constituent of ribosome!0.00323014220823884!6222;6208$GO:0005840!ribosome!0.00355109640920681!6222;6208$GO:0003723!RNA binding!0.00436735624453293!6222;6208$GO:0030529!ribonucleoprotein complex!0.00553112840447372!6222;6208$GO:0006412!translation!0.00583360297203652!6222;6208$GO:0009059!macromolecule biosynthetic process!0.00870856932178837!6222;6208$GO:0019843!rRNA binding!0.00870856932178837!6222$GO:0044249!cellular biosynthetic process!0.0126687003930597!6222;6208$GO:0006364!rRNA processing!0.0153350836109307!6208$GO:0016072!rRNA metabolic process!0.0153350836109307!6208$GO:0009058!biosynthetic process!0.0175449323810289!6222;6208$GO:0042254!ribosome biogenesis and assembly!0.0209909472866491!6208$GO:0043234!protein complex!0.0210206369465923!6222;6208$GO:0043232!intracellular non-membrane-bound organelle!0.0210206369465923!6222;6208$GO:0043228!non-membrane-bound organelle!0.0210206369465923!6222;6208$GO:0022618!protein-RNA complex assembly!0.0223825016040295!6208$GO:0045892!negative regulation of transcription, DNA-dependent!0.0314909289356775!6208$GO:0032991!macromolecular complex!0.0333293770674674!6222;6208$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0341701770605187!6208$GO:0044446!intracellular organelle part!0.0341701770605187!6222;6208$GO:0044422!organelle part!0.0341701770605187!6222;6208$GO:0016481!negative regulation of transcription!0.0382526883561942!6208$GO:0044444!cytoplasmic part!0.0395208036809799!6222;6208$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0395208036809799!6208$GO:0031324!negative regulation of cellular metabolic process!0.0458487231224755!6208
|gostat_on_coexpression_clusters=GO:0005843!cytosolic small ribosomal subunit (sensu Eukaryota)!7.194409102925e-05!6222;6208$GO:0005830!cytosolic ribosome (sensu Eukaryota)!0.000177936588775551!6222;6208$GO:0015935!small ribosomal subunit!0.000310347059341862!6222;6208$GO:0044445!cytosolic part!0.000575648910173879!6222;6208$GO:0033279!ribosomal subunit!0.000622361272308287!6222;6208$GO:0042257!ribosomal subunit assembly!0.000622361272308287!6208$GO:0000028!ribosomal small subunit assembly and maintenance!0.000622361272308287!6208$GO:0042274!ribosomal small subunit biogenesis and assembly!0.000968103285525504!6208$GO:0030490!maturation of SSU-rRNA!0.000968103285525504!6208$GO:0005829!cytosol!0.00206506472197114!6222;6208$GO:0042255!ribosome assembly!0.00277209174988996!6208$GO:0003735!structural constituent of ribosome!0.00323014220823884!6222;6208$GO:0005840!ribosome!0.00355109640920681!6222;6208$GO:0003723!RNA binding!0.00436735624453293!6222;6208$GO:0030529!ribonucleoprotein complex!0.00553112840447372!6222;6208$GO:0006412!translation!0.00583360297203652!6222;6208$GO:0009059!macromolecule biosynthetic process!0.00870856932178837!6222;6208$GO:0019843!rRNA binding!0.00870856932178837!6222$GO:0044249!cellular biosynthetic process!0.0126687003930597!6222;6208$GO:0006364!rRNA processing!0.0153350836109307!6208$GO:0016072!rRNA metabolic process!0.0153350836109307!6208$GO:0009058!biosynthetic process!0.0175449323810289!6222;6208$GO:0042254!ribosome biogenesis and assembly!0.0209909472866491!6208$GO:0043234!protein complex!0.0210206369465923!6222;6208$GO:0043232!intracellular non-membrane-bound organelle!0.0210206369465923!6222;6208$GO:0043228!non-membrane-bound organelle!0.0210206369465923!6222;6208$GO:0022618!protein-RNA complex assembly!0.0223825016040295!6208$GO:0045892!negative regulation of transcription, DNA-dependent!0.0314909289356775!6208$GO:0032991!macromolecular complex!0.0333293770674674!6222;6208$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0341701770605187!6208$GO:0044446!intracellular organelle part!0.0341701770605187!6222;6208$GO:0044422!organelle part!0.0341701770605187!6222;6208$GO:0016481!negative regulation of transcription!0.0382526883561942!6208$GO:0044444!cytoplasmic part!0.0395208036809799!6222;6208$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0395208036809799!6208$GO:0031324!negative regulation of cellular metabolic process!0.0458487231224755!6208
|id=C4341
|id=C4341
|ontology_enrichment_celltype=CL:0000838!4.96e-16!52;CL:0000542!9.97e-16!53;CL:0000051!9.97e-16!53;CL:0000012!5.71e-12!682;CL:0000003!8.90e-12!722;CL:0000548!9.93e-11!679;CL:0000004!9.93e-11!679;CL:0000255!9.93e-11!679;CL:0000144!3.42e-10!625;CL:0000791!1.65e-09!18;CL:0000789!1.65e-09!18;CL:0002420!1.65e-09!18;CL:0002419!1.65e-09!18;CL:0000790!1.65e-09!18;CL:0000084!4.47e-09!25;CL:0000827!4.47e-09!25;CL:0002371!2.73e-08!591;CL:0000945!6.38e-08!24;CL:0000826!6.38e-08!24
|ontology_enrichment_disease=
|ontology_enrichment_uberon=
}}
}}

Revision as of 14:47, 21 May 2012


Full id: C4341_CD8_CD4_CD133_CD19_CD34_skeletal_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr3:61728802..61728813,-p1@RPL10AP6
Hg19::chr5:149829294..149829310,-p1@RPS14
Hg19::chr6:33239845..33239859,+p1@RPS18


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:0005843cytosolic small ribosomal subunit (sensu Eukaryota)7.194409102925e-05
GO:0005830cytosolic ribosome (sensu Eukaryota)0.000177936588775551
GO:0015935small ribosomal subunit0.000310347059341862
GO:0044445cytosolic part0.000575648910173879
GO:0033279ribosomal subunit0.000622361272308287
GO:0042257ribosomal subunit assembly0.000622361272308287
GO:0000028ribosomal small subunit assembly and maintenance0.000622361272308287
GO:0042274ribosomal small subunit biogenesis and assembly0.000968103285525504
GO:0030490maturation of SSU-rRNA0.000968103285525504
GO:0005829cytosol0.00206506472197114
GO:0042255ribosome assembly0.00277209174988996
GO:0003735structural constituent of ribosome0.00323014220823884
GO:0005840ribosome0.00355109640920681
GO:0003723RNA binding0.00436735624453293
GO:0030529ribonucleoprotein complex0.00553112840447372
GO:0006412translation0.00583360297203652
GO:0009059macromolecule biosynthetic process0.00870856932178837
GO:0019843rRNA binding0.00870856932178837
GO:0044249cellular biosynthetic process0.0126687003930597
GO:0006364rRNA processing0.0153350836109307
GO:0016072rRNA metabolic process0.0153350836109307
GO:0009058biosynthetic process0.0175449323810289
GO:0042254ribosome biogenesis and assembly0.0209909472866491
GO:0043234protein complex0.0210206369465923
GO:0043232intracellular non-membrane-bound organelle0.0210206369465923
GO:0043228non-membrane-bound organelle0.0210206369465923
GO:0022618protein-RNA complex assembly0.0223825016040295
GO:0045892negative regulation of transcription, DNA-dependent0.0314909289356775
GO:0032991macromolecular complex0.0333293770674674
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0341701770605187
GO:0044446intracellular organelle part0.0341701770605187
GO:0044422organelle part0.0341701770605187
GO:0016481negative regulation of transcription0.0382526883561942
GO:0044444cytoplasmic part0.0395208036809799
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0395208036809799
GO:0031324negative regulation of cellular metabolic process0.0458487231224755



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><br><br>


Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell4.96e-1652
lymphocyte9.97e-1653
common lymphoid progenitor9.97e-1653
native cell8.90e-12722
animal cell9.93e-11679
eukaryotic cell9.93e-11679
mature alpha-beta T cell1.65e-0918
alpha-beta T cell1.65e-0918
immature T cell1.65e-0918
mature T cell1.65e-0918
immature alpha-beta T cell1.65e-0918
T cell4.47e-0925
pro-T cell4.47e-0925
somatic cell2.73e-08591
lymphocyte of B lineage6.38e-0824
pro-B cell6.38e-0824


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.