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Coexpression cluster:C685

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Full id: C685_Alveolar_Mesenchymal_Renal_Smooth_Hepatic_Fibroblast_Keratocytes



Phase1 CAGE Peaks

  Short description
Hg19::chr11:1968548..1968589,+ p1@MRPL23
Hg19::chr11:57508973..57509018,+ p3@C11orf31
Hg19::chr16:1359622..1359697,+ p1@UBE2I
Hg19::chr19:13885252..13885293,+ p1@C19orf53
Hg19::chr19:17970677..17970686,+ p2@RPL18A
Hg19::chr19:18043810..18043835,+ p1@CCDC124
Hg19::chr19:2427539..2427591,- p1@TIMM13
Hg19::chr19:45582497..45582551,+ p1@GEMIN7
Hg19::chr19:6361517..6361640,+ p1@CLPP
Hg19::chr1:54665832..54665877,+ p1@MRPL37
Hg19::chr3:49059510..49059579,+ p1@NDUFAF3
Hg19::chr7:44163126..44163155,- p1@POLD2


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0031974membrane-enclosed lumen0.000193512463740142
GO:0043233organelle lumen0.000193512463740142
GO:0000313organellar ribosome0.00299085559287461
GO:0005761mitochondrial ribosome0.00299085559287461
GO:0005739mitochondrion0.00299085559287461
GO:0030529ribonucleoprotein complex0.00411426777240149
GO:0044446intracellular organelle part0.00435327555541477
GO:0044422organelle part0.00435327555541477
GO:0043398HLH domain binding0.00526904509596138
GO:0015934large ribosomal subunit0.00578115676195091
GO:0016604nuclear body0.00578115676195091
GO:0044429mitochondrial part0.00595076123775477
GO:0043229intracellular organelle0.00840756935025863
GO:0043226organelle0.00840756935025863
GO:0008462endopeptidase Clp activity0.00948204782553061
GO:0003735structural constituent of ribosome0.0100779420613185
GO:0031980mitochondrial lumen0.0100779420613185
GO:0005759mitochondrial matrix0.0100779420613185
GO:0005840ribosome0.0109967187094474
GO:0033279ribosomal subunit0.0123026770219084
GO:0042719mitochondrial intermembrane space protein transporter complex0.0123026770219084
GO:0045039protein import into mitochondrial inner membrane0.0123026770219084
GO:0032991macromolecular complex0.0123026770219084
GO:0043231intracellular membrane-bound organelle0.0123026770219084
GO:0043227membrane-bound organelle0.0123026770219084
GO:0007007inner mitochondrial membrane organization and biogenesis0.0145791802178139
GO:0000387spliceosomal snRNP biogenesis0.0157922524412481
GO:0044424intracellular part0.0170194352354491
GO:0006412translation0.0197456222733237
GO:0000795synaptonemal complex0.0197456222733237
GO:0043681protein import into mitochondrion0.0197456222733237
GO:0044444cytoplasmic part0.0197456222733237
GO:0000315organellar large ribosomal subunit0.0202899870466734
GO:0005762mitochondrial large ribosomal subunit0.0202899870466734
GO:0005744mitochondrial inner membrane presequence translocase complex0.0202899870466734
GO:0016605PML body0.0210389911498501
GO:0043232intracellular non-membrane-bound organelle0.0227072814930335
GO:0043228non-membrane-bound organelle0.0227072814930335
GO:0005737cytoplasm0.0235427243499324
GO:0007006mitochondrial membrane organization and biogenesis0.0236577228278529
GO:0006626protein targeting to mitochondrion0.0253827994317314
GO:0044451nucleoplasm part0.02547497433364
GO:0009059macromolecule biosynthetic process0.0276297379577305
GO:0005758mitochondrial intermembrane space0.029801120846867
GO:0043170macromolecule metabolic process0.029801120846867
GO:0005654nucleoplasm0.0303935112857104
GO:0031970organelle envelope lumen0.0305183546678942
GO:0000794condensed nuclear chromosome0.0305183546678942
GO:0044267cellular protein metabolic process0.0307394584809551
GO:0044260cellular macromolecule metabolic process0.0318604052842707
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.0356935228895277
GO:0019538protein metabolic process0.0356935228895277
GO:0044249cellular biosynthetic process0.0405523371864651
GO:0006839mitochondrial transport0.0413585107437134
GO:0003887DNA-directed DNA polymerase activity0.0413585107437134
GO:0005622intracellular0.0413585107437134
GO:0008430selenium binding0.0413585107437134
GO:0031981nuclear lumen0.0415450125925671
GO:0000793condensed chromosome0.0415450125925671
GO:0007059chromosome segregation0.0463138328989554
GO:0044237cellular metabolic process0.0482158782953958
GO:0044454nuclear chromosome part0.0498887043556976
GO:0065002intracellular protein transport across a membrane0.0498887043556976
GO:0000398nuclear mRNA splicing, via spliceosome0.0498887043556976
GO:0000375RNA splicing, via transesterification reactions0.0498887043556976
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0498887043556976



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
animal cell2.19e-28679
eukaryotic cell2.19e-28679
embryonic cell1.57e-27248
mesodermal cell1.01e-22119
non-terminally differentiated cell5.32e-22180
contractile cell3.84e-1859
somatic cell1.45e-17591
native cell1.76e-15722
muscle cell2.50e-1554
electrically responsive cell3.21e-1560
electrically active cell3.21e-1560
muscle precursor cell3.35e-1557
myoblast3.35e-1557
multi-potent skeletal muscle stem cell3.35e-1557
epithelial cell1.26e-14254
smooth muscle cell4.01e-1342
smooth muscle myoblast4.01e-1342
vascular associated smooth muscle cell2.42e-1032
lining cell7.29e-0857
barrier cell7.29e-0857
meso-epithelial cell1.00e-0744
epithelial cell of nephron1.21e-0716
endothelial cell3.09e-0735
ectodermal cell4.02e-0771
blood vessel endothelial cell5.32e-0718
embryonic blood vessel endothelial progenitor cell5.32e-0718
kidney cortical cell9.84e-0713
renal cortical epithelial cell9.84e-0713
Uber Anatomy
Ontology termp-valuen
dermomyotome3.68e-1870
somite4.37e-1883
paraxial mesoderm4.37e-1883
presomitic mesoderm4.37e-1883
presumptive segmental plate4.37e-1883
trunk paraxial mesoderm4.37e-1883
presumptive paraxial mesoderm4.37e-1883
multilaminar epithelium8.95e-1882
trunk mesenchyme1.89e-16143
mesenchyme9.17e-15238
entire embryonic mesenchyme9.17e-15238
skeletal muscle tissue1.30e-1461
striated muscle tissue1.30e-1461
myotome1.30e-1461
unilaminar epithelium1.75e-14138
epithelial tube6.35e-14118
vasculature1.00e-1379
vascular system1.00e-1379
muscle tissue4.17e-1363
musculature4.17e-1363
musculature of body4.17e-1363
trunk1.09e-12216
splanchnic layer of lateral plate mesoderm2.23e-1284
vessel3.27e-1269
blood vessel7.32e-1260
epithelial tube open at both ends7.32e-1260
blood vasculature7.32e-1260
vascular cord7.32e-1260
artery5.79e-1142
arterial blood vessel5.79e-1142
arterial system5.79e-1142
cell layer1.43e-09312
epithelium5.43e-09309
cardiovascular system3.79e-08110
circulatory system4.23e-08113
multi-tissue structure7.42e-08347
nephron epithelium1.21e-0716
nephron1.21e-0716
uriniferous tubule1.21e-0716
metanephric mesenchyme1.21e-0716
nephrogenic mesenchyme1.21e-0716
systemic artery1.75e-0733
systemic arterial system1.75e-0733
endothelium5.32e-0718
blood vessel endothelium5.32e-0718
cardiovascular system endothelium5.32e-0718
parenchyma5.60e-0717
cortex of kidney9.84e-0713
renal parenchyma9.84e-0713
Disease
Ontology termp-valuen
hematologic cancer5.59e-0751
immune system cancer5.59e-0751


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.