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Coexpression cluster:C3189

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Full id: C3189_Renal_Alveolar_Astrocyte_Hepatic_Smooth_Mesenchymal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr11:65625678..65625687,-p2@CFL1
Hg19::chr5:176900590..176900601,-p2@DBN1
Hg19::chr5:176900610..176900662,-p1@DBN1


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:0030036actin cytoskeleton organization and biogenesis0.00172691235919777
GO:0030029actin filament-based process0.00172691235919777
GO:0042641actomyosin0.00172691235919777
GO:0003779actin binding0.00364878926538013
GO:0050773regulation of dendrite development0.00395429430057747
GO:0005522profilin binding0.00395429430057747
GO:0008092cytoskeletal protein binding0.00395429430057747
GO:0007010cytoskeleton organization and biogenesis0.00447896764911961
GO:0048168regulation of neuronal synaptic plasticity0.00518012705880347
GO:0016358dendrite development0.00621587796210872
GO:0048167regulation of synaptic plasticity0.00753395387979974
GO:0050803regulation of synapse structure and activity0.0077691611814973
GO:0048468cell development0.00904072481948437
GO:0005856cytoskeleton0.0109284430475919
GO:0006996organelle organization and biogenesis0.0115741645968369
GO:0050767regulation of neurogenesis0.0115741645968369
GO:0030425dendrite0.0115741645968369
GO:0007015actin filament organization0.0117936203516336
GO:0016363nuclear matrix0.0118891572824671
GO:0048869cellular developmental process0.0118891572824671
GO:0030154cell differentiation0.0118891572824671
GO:0043005neuron projection0.0190520721847851
GO:0043232intracellular non-membrane-bound organelle0.027080640390655
GO:0043228non-membrane-bound organelle0.027080640390655
GO:0031175neurite development0.0279208040194611
GO:0048666neuron development0.0302942956279923
GO:0016043cellular component organization and biogenesis0.0302942956279923
GO:0032502developmental process0.0302942956279923
GO:0006916anti-apoptosis0.0302942956279923
GO:0007266Rho protein signal transduction0.0319002373737859
GO:0032990cell part morphogenesis0.0319002373737859
GO:0030030cell projection organization and biogenesis0.0319002373737859
GO:0048858cell projection morphogenesis0.0319002373737859
GO:0030182neuron differentiation0.0319002373737859
GO:0043066negative regulation of apoptosis0.0325078441224394
GO:0043069negative regulation of programmed cell death0.0325078441224394
GO:0050793regulation of developmental process0.0325078441224394
GO:0048699generation of neurons0.0325078441224394
GO:0044446intracellular organelle part0.0325078441224394
GO:0044422organelle part0.0325078441224394
GO:0022008neurogenesis0.0329789957614248
GO:0007268synaptic transmission0.0355079027878207
GO:0015629actin cytoskeleton0.0355079027878207
GO:0042995cell projection0.0366846410436107
GO:0019226transmission of nerve impulse0.0378081004023087
GO:0007265Ras protein signal transduction0.0483452356566323



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
non-terminally differentiated cell2.18e-39180
embryonic cell7.70e-33248
mesodermal cell6.54e-30119
contractile cell5.79e-2159
electrically responsive cell2.08e-1960
electrically active cell2.08e-1960
muscle precursor cell1.35e-1857
myoblast1.35e-1857
multi-potent skeletal muscle stem cell1.35e-1857
muscle cell4.46e-1854
smooth muscle cell2.38e-1642
smooth muscle myoblast2.38e-1642
fibroblast3.62e-1575
animal cell1.34e-14679
eukaryotic cell1.34e-14679
vascular associated smooth muscle cell2.17e-1332
somatic cell8.16e-13591
meso-epithelial cell1.22e-1044
lining cell1.43e-1057
barrier cell1.43e-1057
endothelial cell9.50e-1035
ectodermal cell4.19e-0971
epithelial cell of nephron6.84e-0916
endothelial cell of vascular tree1.27e-0824
blood vessel endothelial cell1.74e-0818
embryonic blood vessel endothelial progenitor cell1.74e-0818
neurectodermal cell1.80e-0859
epithelial cell1.20e-07254
kidney cell2.07e-0718
kidney epithelial cell2.07e-0718
kidney cortical cell3.03e-0713
renal cortical epithelial cell3.03e-0713
kidney tubule cell6.59e-0712
nephron tubule epithelial cell6.59e-0712
Uber Anatomy
Ontology termp-valuen
vasculature1.63e-2479
vascular system1.63e-2479
cell layer9.91e-24312
epithelium1.77e-22309
somite1.91e-2083
paraxial mesoderm1.91e-2083
presomitic mesoderm1.91e-2083
presumptive segmental plate1.91e-2083
trunk paraxial mesoderm1.91e-2083
presumptive paraxial mesoderm1.91e-2083
multilaminar epithelium5.83e-2082
organism subdivision6.66e-20365
dermomyotome1.10e-1970
trunk mesenchyme1.48e-19143
vessel1.70e-1969
epithelial tube3.48e-19118
blood vessel6.43e-1960
epithelial tube open at both ends6.43e-1960
blood vasculature6.43e-1960
vascular cord6.43e-1960
splanchnic layer of lateral plate mesoderm2.48e-1884
skeletal muscle tissue3.64e-1761
striated muscle tissue3.64e-1761
myotome3.64e-1761
artery7.57e-1742
arterial blood vessel7.57e-1742
arterial system7.57e-1742
unilaminar epithelium2.49e-16138
muscle tissue2.71e-1663
musculature2.71e-1663
musculature of body2.71e-1663
trunk4.52e-16216
cardiovascular system5.02e-15110
circulatory system5.62e-14113
multi-tissue structure6.22e-13347
systemic artery8.34e-1333
systemic arterial system8.34e-1333
multi-cellular organism7.26e-12659
tube1.68e-10194
anatomical cluster1.80e-10286
mesenchyme6.18e-10238
entire embryonic mesenchyme6.18e-10238
anatomical conduit1.81e-09241
nephron epithelium6.84e-0916
nephron6.84e-0916
uriniferous tubule6.84e-0916
metanephric mesenchyme6.84e-0916
nephrogenic mesenchyme6.84e-0916
endothelium1.74e-0818
blood vessel endothelium1.74e-0818
cardiovascular system endothelium1.74e-0818
simple squamous epithelium2.14e-0822
aorta2.57e-0821
aortic system2.57e-0821
excretory tube2.70e-0817
mesonephric epithelium2.70e-0817
mesonephric tubule2.70e-0817
nephric duct2.70e-0817
kidney epithelium2.70e-0817
renal duct2.70e-0817
mesonephric duct2.70e-0817


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.