Personal tools

Coexpression cluster:C610: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.027549189648299,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.317748879753281,0.586608803072599,0.654804266211112,0.216542687324989,0.671326450193632,0.511763662169239,0.55157017142277,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0296885786825552,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0133047429825382,0,0,0,0,0,0,0,0,0,0,0,0,0.0344612179329091,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0256128589246175,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.769420236905995,0.23241382101223,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0386585674343867,0,0.0943522604903798,0,0,0,0.0395883422157288,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0580284054719272,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C610_melanoma_Melanocyte_migratory_mycosis_cerebellum_epithelioid_retina
|full_id=C610_melanoma_Melanocyte_migratory_mycosis_cerebellum_epithelioid_retina
|gostat_on_coexpression_clusters=GO:0004184!lysine carboxypeptidase activity!0.0190717246048572!1369$GO:0043034!costamere!0.0190717246048572!6840$GO:0008333!endosome to lysosome transport!0.0190717246048572!1130$GO:0007041!lysosomal transport!0.0223363955704967!1130$GO:0051693!actin filament capping!0.0223363955704967!6840$GO:0051016!barbed-end actin filament capping!0.0223363955704967!6840$GO:0030835!negative regulation of actin filament depolymerization!0.0223363955704967!6840$GO:0030834!regulation of actin filament depolymerization!0.0223363955704967!6840$GO:0030042!actin filament depolymerization!0.0223363955704967!6840$GO:0007034!vacuolar transport!0.0223363955704967!1130$GO:0051015!actin filament binding!0.0223363955704967!6840$GO:0016197!endosome transport!0.0223363955704967!1130$GO:0004182!carboxypeptidase A activity!0.0223363955704967!1369$GO:0008064!regulation of actin polymerization and/or depolymerization!0.0223363955704967!6840$GO:0051261!protein depolymerization!0.0223363955704967!6840$GO:0030832!regulation of actin filament length!0.0223363955704967!6840$GO:0032535!regulation of cellular component size!0.0223363955704967!6840$GO:0032956!regulation of actin cytoskeleton organization and biogenesis!0.0223363955704967!6840$GO:0004181!metallocarboxypeptidase activity!0.0223363955704967!1369$GO:0051129!negative regulation of cellular component organization and biogenesis!0.0223363955704967!6840$GO:0030016!myofibril!0.0223363955704967!6840$GO:0051493!regulation of cytoskeleton organization and biogenesis!0.0223363955704967!6840$GO:0033043!regulation of organelle organization and biogenesis!0.0223363955704967!6840$GO:0005856!cytoskeleton!0.0223363955704967!6840;1130$GO:0044449!contractile fiber part!0.0223363955704967!6840$GO:0008154!actin polymerization and/or depolymerization!0.0223363955704967!6840$GO:0043292!contractile fiber!0.022564953280771!6840$GO:0007519!skeletal muscle development!0.0227770052946295!6840$GO:0006968!cellular defense response!0.0231581945711703!1130$GO:0004180!carboxypeptidase activity!0.0231581945711703!1369$GO:0014706!striated muscle development!0.0270042522324104!6840$GO:0051128!regulation of cellular component organization and biogenesis!0.0297171835320079!6840$GO:0051248!negative regulation of protein metabolic process!0.0299657971946987!6840$GO:0008235!metalloexopeptidase activity!0.0327074740495181!1369$GO:0007517!muscle development!0.0466333195564237!6840$GO:0008238!exopeptidase activity!0.0492700420420545!1369$GO:0005768!endosome!0.0494677962577345!1130
|gostat_on_coexpression_clusters=GO:0004184!lysine carboxypeptidase activity!0.0190717246048572!1369$GO:0043034!costamere!0.0190717246048572!6840$GO:0008333!endosome to lysosome transport!0.0190717246048572!1130$GO:0007041!lysosomal transport!0.0223363955704967!1130$GO:0051693!actin filament capping!0.0223363955704967!6840$GO:0051016!barbed-end actin filament capping!0.0223363955704967!6840$GO:0030835!negative regulation of actin filament depolymerization!0.0223363955704967!6840$GO:0030834!regulation of actin filament depolymerization!0.0223363955704967!6840$GO:0030042!actin filament depolymerization!0.0223363955704967!6840$GO:0007034!vacuolar transport!0.0223363955704967!1130$GO:0051015!actin filament binding!0.0223363955704967!6840$GO:0016197!endosome transport!0.0223363955704967!1130$GO:0004182!carboxypeptidase A activity!0.0223363955704967!1369$GO:0008064!regulation of actin polymerization and/or depolymerization!0.0223363955704967!6840$GO:0051261!protein depolymerization!0.0223363955704967!6840$GO:0030832!regulation of actin filament length!0.0223363955704967!6840$GO:0032535!regulation of cellular component size!0.0223363955704967!6840$GO:0032956!regulation of actin cytoskeleton organization and biogenesis!0.0223363955704967!6840$GO:0004181!metallocarboxypeptidase activity!0.0223363955704967!1369$GO:0051129!negative regulation of cellular component organization and biogenesis!0.0223363955704967!6840$GO:0030016!myofibril!0.0223363955704967!6840$GO:0051493!regulation of cytoskeleton organization and biogenesis!0.0223363955704967!6840$GO:0033043!regulation of organelle organization and biogenesis!0.0223363955704967!6840$GO:0005856!cytoskeleton!0.0223363955704967!6840;1130$GO:0044449!contractile fiber part!0.0223363955704967!6840$GO:0008154!actin polymerization and/or depolymerization!0.0223363955704967!6840$GO:0043292!contractile fiber!0.022564953280771!6840$GO:0007519!skeletal muscle development!0.0227770052946295!6840$GO:0006968!cellular defense response!0.0231581945711703!1130$GO:0004180!carboxypeptidase activity!0.0231581945711703!1369$GO:0014706!striated muscle development!0.0270042522324104!6840$GO:0051128!regulation of cellular component organization and biogenesis!0.0297171835320079!6840$GO:0051248!negative regulation of protein metabolic process!0.0299657971946987!6840$GO:0008235!metalloexopeptidase activity!0.0327074740495181!1369$GO:0007517!muscle development!0.0466333195564237!6840$GO:0008238!exopeptidase activity!0.0492700420420545!1369$GO:0005768!endosome!0.0494677962577345!1130

Revision as of 18:15, 12 September 2012


Full id: C610_melanoma_Melanocyte_migratory_mycosis_cerebellum_epithelioid_retina



Phase1 CAGE Peaks

Hg19::chr10:101825164..101825200,-p3@CPN1
Hg19::chr10:29811555..29811564,-p35@SVIL
Hg19::chr10:29811606..29811631,-p15@SVIL
Hg19::chr10:29811632..29811647,-p20@SVIL
Hg19::chr10:29811664..29811673,-p33@SVIL
Hg19::chr1:236046697..236046708,-p15@LYST
Hg19::chr1:236046717..236046726,-p17@LYST
Hg19::chr1:236046729..236046740,-p11@LYST
Hg19::chr1:236046799..236046806,-p18@LYST
Hg19::chr1:236046834..236046841,-p22@LYST
Hg19::chr1:236046843..236046855,-p8@LYST
Hg19::chr1:236046879..236046882,-p24@LYST
Hg19::chr1:236046891..236046902,-p12@LYST
Hg19::chr2:106227025..106227040,-p1@LOC285000


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:0004184lysine carboxypeptidase activity0.0190717246048572
GO:0043034costamere0.0190717246048572
GO:0008333endosome to lysosome transport0.0190717246048572
GO:0007041lysosomal transport0.0223363955704967
GO:0051693actin filament capping0.0223363955704967
GO:0051016barbed-end actin filament capping0.0223363955704967
GO:0030835negative regulation of actin filament depolymerization0.0223363955704967
GO:0030834regulation of actin filament depolymerization0.0223363955704967
GO:0030042actin filament depolymerization0.0223363955704967
GO:0007034vacuolar transport0.0223363955704967
GO:0051015actin filament binding0.0223363955704967
GO:0016197endosome transport0.0223363955704967
GO:0004182carboxypeptidase A activity0.0223363955704967
GO:0008064regulation of actin polymerization and/or depolymerization0.0223363955704967
GO:0051261protein depolymerization0.0223363955704967
GO:0030832regulation of actin filament length0.0223363955704967
GO:0032535regulation of cellular component size0.0223363955704967
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0223363955704967
GO:0004181metallocarboxypeptidase activity0.0223363955704967
GO:0051129negative regulation of cellular component organization and biogenesis0.0223363955704967
GO:0030016myofibril0.0223363955704967
GO:0051493regulation of cytoskeleton organization and biogenesis0.0223363955704967
GO:0033043regulation of organelle organization and biogenesis0.0223363955704967
GO:0005856cytoskeleton0.0223363955704967
GO:0044449contractile fiber part0.0223363955704967
GO:0008154actin polymerization and/or depolymerization0.0223363955704967
GO:0043292contractile fiber0.022564953280771
GO:0007519skeletal muscle development0.0227770052946295
GO:0006968cellular defense response0.0231581945711703
GO:0004180carboxypeptidase activity0.0231581945711703
GO:0014706striated muscle development0.0270042522324104
GO:0051128regulation of cellular component organization and biogenesis0.0297171835320079
GO:0051248negative regulation of protein metabolic process0.0299657971946987
GO:0008235metalloexopeptidase activity0.0327074740495181
GO:0007517muscle development0.0466333195564237
GO:0008238exopeptidase activity0.0492700420420545
GO:0005768endosome0.0494677962577345



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
neurecto-epithelial cell3.38e-0920
melanocyte9.54e-0810
melanoblast9.54e-0810
conventional dendritic cell2.39e-078
columnar/cuboidal epithelial cell2.47e-0727
pigment cell4.91e-0714
Uber Anatomy
Ontology termp-valuen
adult organism8.35e-23115
neural tube7.80e-1557
neural rod7.80e-1557
future spinal cord7.80e-1557
neural keel7.80e-1557
regional part of brain1.73e-1359
neural plate4.87e-1386
presumptive neural plate4.87e-1386
brain8.48e-1369
future brain8.48e-1369
neurectoderm1.62e-1290
central nervous system2.29e-1282
regional part of nervous system2.81e-1294
nervous system2.81e-1294
head1.32e-09123
anterior region of body1.52e-09129
craniocervical region1.52e-09129
posterior neural tube5.88e-0915
chordal neural plate5.88e-0915
pre-chordal neural plate2.73e-0861
anterior neural tube3.00e-0842
regional part of forebrain8.69e-0841
forebrain8.69e-0841
future forebrain8.69e-0841
ectoderm-derived structure1.24e-07169
segmental subdivision of nervous system1.49e-0713
ectoderm1.75e-07173
presumptive ectoderm1.75e-07173
gray matter2.34e-0734
brain grey matter2.34e-0734
telencephalon2.79e-0734
regional part of telencephalon8.33e-0733
segmental subdivision of hindbrain8.39e-0712
hindbrain8.39e-0712
presumptive hindbrain8.39e-0712


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
BATF#1053858.699214925822730.0001707317014125790.0020828230538288
EP300#203383.870823843556110.0002923517603882410.0031023090330408
JUND#372783.99695082392630.0002326701060612530.00255653163671028
MEF2A#420556.694011039158590.0005756168670652410.00485910523597047
PAX5#507983.811180303530190.0003264133745117030.0033288044547044
STAT3#677486.011122855516711.1795981756812e-050.000298729519568304
TFAP2A#702089.439219641739973.88124860065147e-071.88888034763951e-05
USF1#739183.635142444118830.0004558788878487240.00423627859845475
USF2#739287.424112791468342.41644431268328e-068.54915405055316e-05



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C610&oldid=2139968"