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Coexpression cluster:C447

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Full id: C447_Alveolar_Bronchial_Smooth_Renal_Tracheal_Keratocytes_Hepatic



Phase1 CAGE Peaks

  Short description
Hg19::chr11:62341318..62341402,- p1@EEF1G
Hg19::chr14:23299088..23299114,+ p1@MRPL52
Hg19::chr17:49230905..49231005,+ p1@NME1
p3@NME1-NME2
p3@NME2
Hg19::chr17:7210852..7210861,+ p5@EIF5A
Hg19::chr17:7210877..7210888,+ p4@EIF5A
Hg19::chr17:7210898..7210918,+ p2@EIF5A
Hg19::chr17:79670386..79670427,+ p2@MRPL12
p2@SLC25A10
Hg19::chr19:1438351..1438382,+ p2@RPS15
Hg19::chr19:1438383..1438409,+ p1@RPS15
Hg19::chr19:17970693..17970729,+ p1@RPL18A
Hg19::chr19:42364267..42364301,+ p2@RPS19
Hg19::chr19:5690266..5690296,+ p2@RPL36
Hg19::chr20:60962115..60962126,+ p2@RPS21
Hg19::chr22:24236562..24236621,+ p1@MIF
Hg19::chr22:30987849..30987904,- p1@PES1
Hg19::chr2:73461410..73461463,+ p1@CCT7
Hg19::chr3:23958612..23958630,+ p1@RPL15
Hg19::chr3:39448443..39448499,+ p@chr3:39448443..39448499
+
Hg19::chr3:52029945..52029956,- p3@RPL29
Hg19::chr3:52029958..52029974,- p2@RPL29
Hg19::chr5:177580855..177580927,- p1@NHP2
Hg19::chr9:132388423..132388477,+ p1@METTL11A


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


p.valueFDRnGenesnPathwayName
1.80279937805575e-143.08438677416343e-12792Ribosome (KEGG):03010
0.0004045066255997470.0284502993338489257Translation Factors (Wikipathways):WP107
1.94905957293108e-143.08438677416343e-12793Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
3.54069343756762e-172.24125894598031e-1410296Metabolism of proteins (Reactome):REACT_17015
8.42175523584154e-141.06619421285754e-117114Regulation of beta-cell development (Reactome):REACT_13698
1.23159185623497e-111.1137109214239e-098421Gene Expression (Reactome):REACT_71
1.0400835009089e-108.22966070094168e-097312Diabetes pathways (Reactome):REACT_15380
4.24738473644491e-134.48099089694938e-117143Influenza Infection (Reactome):REACT_6167
1.51898137154035e-154.80757604092522e-138138{RPS27A,138} (Static Module):NA



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:0044249cellular biosynthetic process1.63536519439817e-12
GO:0033279ribosomal subunit2.59202003269642e-12
GO:0009058biosynthetic process8.6750274201438e-12
GO:0006412translation8.6750274201438e-12
GO:0005830cytosolic ribosome (sensu Eukaryota)2.4732840086186e-11
GO:0044445cytosolic part4.20728102009308e-11
GO:0009059macromolecule biosynthetic process8.32198503670861e-11
GO:0003735structural constituent of ribosome2.43550401320784e-10
GO:0005840ribosome4.71495388940078e-10
GO:0030529ribonucleoprotein complex5.71573379108332e-09
GO:0015934large ribosomal subunit1.81502338481676e-08
GO:0005829cytosol4.47144288756933e-08
GO:0032991macromolecular complex7.70890439572307e-07
GO:0043232intracellular non-membrane-bound organelle7.70890439572307e-07
GO:0043228non-membrane-bound organelle7.70890439572307e-07
GO:0044267cellular protein metabolic process1.78090254612308e-06
GO:0044260cellular macromolecule metabolic process1.94152835452668e-06
GO:0019538protein metabolic process2.6494594484899e-06
GO:0005737cytoplasm2.6494594484899e-06
GO:0044444cytoplasmic part2.91903608333342e-06
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)5.23508541645072e-06
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)7.62170201263084e-06
GO:0010467gene expression1.51581020644333e-05
GO:0003723RNA binding2.47431966682721e-05
GO:0044446intracellular organelle part0.000147606563219062
GO:0044422organelle part0.000147606563219062
GO:0005762mitochondrial large ribosomal subunit0.000178278722220159
GO:0000315organellar large ribosomal subunit0.000178278722220159
GO:0015935small ribosomal subunit0.000178278722220159
GO:0005515protein binding0.000207267769744039
GO:0044237cellular metabolic process0.000207267769744039
GO:0044238primary metabolic process0.000228281165093755
GO:0044424intracellular part0.000285289357924009
GO:0043233organelle lumen0.000339362993530787
GO:0031974membrane-enclosed lumen0.000339362993530787
GO:0005730nucleolus0.00036235080550322
GO:0043229intracellular organelle0.0011593666543526
GO:0043226organelle0.0011593666543526
GO:0000313organellar ribosome0.00152367751972329
GO:0005761mitochondrial ribosome0.00152367751972329
GO:0043170macromolecule metabolic process0.00155370022125681
GO:0005622intracellular0.00201124067833298
GO:0007000nucleolus organization and biogenesis0.0026693105552166
GO:0050178phenylpyruvate tautomerase activity0.0026693105552166
GO:0003676nucleic acid binding0.00282955004644999
GO:0051323metaphase0.0074936979378262
GO:0000089mitotic metaphase0.0074936979378262
GO:0005832chaperonin-containing T-complex0.00958180233340283
GO:0043030regulation of macrophage activation0.00958180233340283
GO:0032502developmental process0.0110492591165849
GO:0006390transcription from mitochondrial promoter0.0115051858477387
GO:0005759mitochondrial matrix0.0145227496622909
GO:0031980mitochondrial lumen0.0145227496622909
GO:0031981nuclear lumen0.0155820216738653
GO:0008135translation factor activity, nucleic acid binding0.0168141455663711
GO:0008283cell proliferation0.0185141408805772
GO:0042116macrophage activation0.0185141408805772
GO:0043022ribosome binding0.0192183727001798
GO:0001516prostaglandin biosynthetic process0.0192183727001798
GO:0046457prostanoid biosynthetic process0.0192183727001798
GO:0016862intramolecular oxidoreductase activity, interconverting keto- and enol-groups0.0192183727001798
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0221078039902013
GO:0006915apoptosis0.0243405685871074
GO:0012501programmed cell death0.0245085795362319
GO:0043234protein complex0.0261257076792559
GO:0016265death0.0263258028457658
GO:0008219cell death0.0263258028457658
GO:0048869cellular developmental process0.0263258028457658
GO:0030154cell differentiation0.0263258028457658
GO:0007566embryo implantation0.0272612887625557
GO:0043021ribonucleoprotein binding0.0272612887625557
GO:0006693prostaglandin metabolic process0.0272612887625557
GO:0006692prostanoid metabolic process0.0272612887625557
GO:0048522positive regulation of cellular process0.0276967443860152
GO:0022414reproductive process0.0276967443860152
GO:0050679positive regulation of epithelial cell proliferation0.0277197817017431
GO:0051272positive regulation of cell motility0.0314910633148022
GO:0040017positive regulation of locomotion0.0314910633148022
GO:0048518positive regulation of biological process0.0350683770571089
GO:0005853eukaryotic translation elongation factor 1 complex0.0350683770571089
GO:0044428nuclear part0.038465921753742
GO:0002274myeloid leukocyte activation0.038465921753742
GO:0019079viral genome replication0.0408006772958901
GO:0050678regulation of epithelial cell proliferation0.0416965439544594
GO:0015669gas transport0.0437543521028632
GO:0030218erythrocyte differentiation0.0437543521028632
GO:0046456icosanoid biosynthetic process0.0437543521028632
GO:0050673epithelial cell proliferation0.0437543521028632
GO:0046051UTP metabolic process0.0440157626532768
GO:0004550nucleoside diphosphate kinase activity0.0440157626532768
GO:0006228UTP biosynthetic process0.0440157626532768
GO:0009208pyrimidine ribonucleoside triphosphate metabolic process0.0440157626532768
GO:0046036CTP metabolic process0.0440157626532768
GO:0009209pyrimidine ribonucleoside triphosphate biosynthetic process0.0440157626532768
GO:0006241CTP biosynthetic process0.0440157626532768
GO:0048468cell development0.0440157626532768
GO:0046039GTP metabolic process0.0440157626532768
GO:0006183GTP biosynthetic process0.0440157626532768
GO:0006997nuclear organization and biogenesis0.0447395533592941
GO:0009220pyrimidine ribonucleotide biosynthetic process0.0466041472028266
GO:0009218pyrimidine ribonucleotide metabolic process0.047286560910938



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 cell3.07e-38679
eukaryotic cell3.07e-38679
embryonic cell1.23e-33248
mesodermal cell4.59e-25119
epithelial cell5.70e-23254
non-terminally differentiated cell7.67e-22180
native cell1.05e-21722
somatic cell1.13e-20591
contractile cell6.24e-1959
muscle precursor cell1.55e-1757
myoblast1.55e-1757
multi-potent skeletal muscle stem cell1.55e-1757
electrically responsive cell1.83e-1760
electrically active cell1.83e-1760
muscle cell4.36e-1754
smooth muscle cell6.20e-1542
smooth muscle myoblast6.20e-1542
vascular associated smooth muscle cell3.89e-1232
squamous epithelial cell2.28e-0962
lining cell3.46e-0857
barrier cell3.46e-0857
meso-epithelial cell2.95e-0744
epithelial cell of nephron3.04e-0716
blood vessel endothelial cell4.12e-0718
embryonic blood vessel endothelial progenitor cell4.12e-0718
endothelial cell4.60e-0735
Uber Anatomy
Ontology termp-valuen
multilaminar epithelium3.61e-1982
dermomyotome7.06e-1970
somite2.03e-1883
paraxial mesoderm2.03e-1883
presomitic mesoderm2.03e-1883
presumptive segmental plate2.03e-1883
trunk paraxial mesoderm2.03e-1883
presumptive paraxial mesoderm2.03e-1883
trunk mesenchyme1.17e-17143
mesenchyme2.19e-16238
entire embryonic mesenchyme2.19e-16238
unilaminar epithelium2.39e-16138
epithelial tube6.82e-16118
vasculature6.97e-1679
vascular system6.97e-1679
trunk2.23e-15216
skeletal muscle tissue2.52e-1561
striated muscle tissue2.52e-1561
myotome2.52e-1561
vessel1.50e-1469
blood vessel2.75e-1460
epithelial tube open at both ends2.75e-1460
blood vasculature2.75e-1460
vascular cord2.75e-1460
artery4.93e-1442
arterial blood vessel4.93e-1442
arterial system4.93e-1442
muscle tissue9.83e-1463
musculature9.83e-1463
musculature of body9.83e-1463
splanchnic layer of lateral plate mesoderm4.70e-1384
cell layer5.51e-10312
systemic artery6.14e-1033
systemic arterial system6.14e-1033
epithelium2.00e-09309
cardiovascular system6.94e-09110
circulatory system3.12e-08113
simple squamous epithelium1.36e-0722
multi-tissue structure1.59e-07347
nephron epithelium3.04e-0716
nephron3.04e-0716
uriniferous tubule3.04e-0716
metanephric mesenchyme3.04e-0716
nephrogenic mesenchyme3.04e-0716
endothelium4.12e-0718
blood vessel endothelium4.12e-0718
cardiovascular system endothelium4.12e-0718
squamous epithelium9.58e-0725
Disease
Ontology termp-valuen
disease of cellular proliferation1.09e-08239
cancer3.45e-08235


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.