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Difference between revisions of "Coexpression cluster:C3538"

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|ontology_enrichment_uberon=UBERON:0000490!1.05e-10!138;UBERON:0004290!1.27e-10!70;UBERON:0000914!1.38e-10!83;UBERON:0002329!1.38e-10!83;UBERON:0003077!1.38e-10!83;UBERON:0003059!1.38e-10!83;UBERON:0007282!1.38e-10!83;UBERON:0009618!1.38e-10!83;UBERON:0007285!1.38e-10!83;UBERON:0000486!1.80e-10!82;UBERON:0003104!3.02e-10!238;UBERON:0009142!3.02e-10!238;UBERON:0005256!1.05e-09!143;UBERON:0001134!4.91e-09!61;UBERON:0002036!4.91e-09!61;UBERON:0003082!4.91e-09!61;UBERON:0002100!6.11e-09!216;UBERON:0002385!7.72e-08!63;UBERON:0001015!7.72e-08!63;UBERON:0000383!7.72e-08!63;UBERON:0002049!1.12e-07!79;UBERON:0007798!1.12e-07!79;UBERON:0003914!1.84e-07!118;UBERON:0001637!5.00e-07!42;UBERON:0003509!5.00e-07!42;UBERON:0004572!5.00e-07!42
 
|ontology_enrichment_uberon=UBERON:0000490!1.05e-10!138;UBERON:0004290!1.27e-10!70;UBERON:0000914!1.38e-10!83;UBERON:0002329!1.38e-10!83;UBERON:0003077!1.38e-10!83;UBERON:0003059!1.38e-10!83;UBERON:0007282!1.38e-10!83;UBERON:0009618!1.38e-10!83;UBERON:0007285!1.38e-10!83;UBERON:0000486!1.80e-10!82;UBERON:0003104!3.02e-10!238;UBERON:0009142!3.02e-10!238;UBERON:0005256!1.05e-09!143;UBERON:0001134!4.91e-09!61;UBERON:0002036!4.91e-09!61;UBERON:0003082!4.91e-09!61;UBERON:0002100!6.11e-09!216;UBERON:0002385!7.72e-08!63;UBERON:0001015!7.72e-08!63;UBERON:0000383!7.72e-08!63;UBERON:0002049!1.12e-07!79;UBERON:0007798!1.12e-07!79;UBERON:0003914!1.84e-07!118;UBERON:0001637!5.00e-07!42;UBERON:0003509!5.00e-07!42;UBERON:0004572!5.00e-07!42
 
|pathway_enrichment=3.23952687815502e-08;1.05948726550059e-05;3;92;Ribosome (KEGG):03010!3.34751110742684e-08;1.05948726550059e-05;3;93;Cytoplasmic Ribosomal Proteins (Wikipathways):WP477!1.1037505066909e-06;0.00011644567845589;3;296;Metabolism of proteins (Reactome):REACT_17015!6.2031341872007e-08;1.30886131349935e-05;3;114;Regulation of beta-cell development (Reactome):REACT_13698!3.18533613032144e-06;0.000252039721311684;3;421;Gene Expression (Reactome):REACT_71!1.29326205516739e-06;0.000116947840131565;3;312;Diabetes pathways (Reactome):REACT_15380!1.23098667822397e-07;1.55842913463155e-05;3;143;Influenza Infection (Reactome):REACT_6167!1.10547371417187e-07;1.55842913463155e-05;3;138;{RPS27A,138} (Static Module):NA
 
|pathway_enrichment=3.23952687815502e-08;1.05948726550059e-05;3;92;Ribosome (KEGG):03010!3.34751110742684e-08;1.05948726550059e-05;3;93;Cytoplasmic Ribosomal Proteins (Wikipathways):WP477!1.1037505066909e-06;0.00011644567845589;3;296;Metabolism of proteins (Reactome):REACT_17015!6.2031341872007e-08;1.30886131349935e-05;3;114;Regulation of beta-cell development (Reactome):REACT_13698!3.18533613032144e-06;0.000252039721311684;3;421;Gene Expression (Reactome):REACT_71!1.29326205516739e-06;0.000116947840131565;3;312;Diabetes pathways (Reactome):REACT_15380!1.23098667822397e-07;1.55842913463155e-05;3;143;Influenza Infection (Reactome):REACT_6167!1.10547371417187e-07;1.55842913463155e-05;3;138;{RPS27A,138} (Static Module):NA
 +
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324682851513938!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461300995705857!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.000627318133236668!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.0043341692450175!KAT2A#2648;1:205.363333333333:0.00486154522073778:0.0227530773609067!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186263337455966!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293993785736637!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.026920251712695!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00881081094282167!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484033284896721!RXRA#6256;2:13.3830780927555:0.00719643442946573:0.0298249371182131!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276104957752262!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370672859627738!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246058534509359!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154672529988785!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00541808247528257!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328716314110035!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.0038853153331239!ZZZ3#26009;1:79.8044041450777:0.012478437908258:0.0451587226411364
 
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}}
 
}}

Revision as of 03:53, 5 September 2012


Full id: C3538_iPS_Mallassezderived_Bronchial_HES3GFP_acute_chronic_hepatocellular



Phase1 CAGE Peaks

  Short description
Hg19::chr16:18801619..18801630,- p2@RPS15A
Hg19::chr2:55459808..55459860,+ p1@RPS27A
Hg19::chr3:197677089..197677100,+ p2@RPL35A


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
3.23952687815502e-081.05948726550059e-05392Ribosome (KEGG):03010
3.34751110742684e-081.05948726550059e-05393Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.1037505066909e-060.000116445678455893296Metabolism of proteins (Reactome):REACT_17015
6.2031341872007e-081.30886131349935e-053114Regulation of beta-cell development (Reactome):REACT_13698
3.18533613032144e-060.0002520397213116843421Gene Expression (Reactome):REACT_71
1.29326205516739e-060.0001169478401315653312Diabetes pathways (Reactome):REACT_15380
1.23098667822397e-071.55842913463155e-053143Influenza Infection (Reactome):REACT_6167
1.10547371417187e-071.55842913463155e-053138{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:0005830cytosolic ribosome (sensu Eukaryota)0.00204574031208939
GO:0044445cytosolic part0.00417978982585916
GO:0033279ribosomal subunit0.00417978982585916
GO:0008582regulation of synaptic growth at neuromuscular junction0.00417978982585916
GO:0051124synaptic growth at neuromuscular junction0.00417978982585916
GO:0042062long-term strengthening of neuromuscular junction0.00417978982585916
GO:0050806positive regulation of synaptic transmission0.0106074249154712
GO:0051971positive regulation of transmission of nerve impulse0.0106074249154712
GO:0031646positive regulation of neurological process0.0106074249154712
GO:0005829cytosol0.0106074249154712
GO:0007528neuromuscular junction development0.0106074249154712
GO:0030433ER-associated protein catabolic process0.0106074249154712
GO:0006515misfolded or incompletely synthesized protein catabolic process0.0106074249154712
GO:0048167regulation of synaptic plasticity0.0125334643717844
GO:0050804regulation of synaptic transmission0.0125334643717844
GO:0003735structural constituent of ribosome0.0125334643717844
GO:0051969regulation of transmission of nerve impulse0.0125334643717844
GO:0050803regulation of synapse structure and activity0.0125334643717844
GO:0005840ribosome0.0136205233382194
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.0136205233382194
GO:0000049tRNA binding0.0136205233382194
GO:0031644regulation of neurological process0.0136205233382194
GO:0007416synaptogenesis0.0136205233382194
GO:0003723RNA binding0.014385426350698
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0164385508748134
GO:0048589developmental growth0.0164385508748134
GO:0030529ribonucleoprotein complex0.0164385508748134
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.0164385508748134
GO:0050808synapse organization and biogenesis0.0164385508748134
GO:0006412translation0.0164385508748134
GO:0048741skeletal muscle fiber development0.0164385508748134
GO:0048747muscle fiber development0.0164385508748134
GO:0010467gene expression0.0177973724591936
GO:0044267cellular protein metabolic process0.0185390426406863
GO:0044260cellular macromolecule metabolic process0.0187151417405112
GO:0007411axon guidance0.0194746956104163
GO:0019538protein metabolic process0.019669226711609
GO:0007519skeletal muscle development0.0220666113673117
GO:0009059macromolecule biosynthetic process0.0224279650682972
GO:0016567protein ubiquitination0.022836552979904
GO:0032446protein modification by small protein conjugation0.0234975929219407
GO:0043062extracellular structure organization and biogenesis0.025018250826649
GO:0014706striated muscle development0.0255970539033313
GO:0015934large ribosomal subunit0.0296229750907722
GO:0044249cellular biosynthetic process0.0296229750907722
GO:0007409axonogenesis0.0303299924990499
GO:0048667neuron morphogenesis during differentiation0.0303299924990499
GO:0048812neurite morphogenesis0.0303299924990499
GO:0015935small ribosomal subunit0.0303299924990499
GO:0005737cytoplasm0.0303299924990499
GO:0000904cellular morphogenesis during differentiation0.03086667314336
GO:0031175neurite development0.0324268433209433
GO:0048666neuron development0.0362723634105823
GO:0009058biosynthetic process0.0390181141743141
GO:0007517muscle development0.0390181141743141
GO:0040008regulation of growth0.0430991616255652
GO:0032990cell part morphogenesis0.0430991616255652
GO:0048858cell projection morphogenesis0.0430991616255652
GO:0030030cell projection organization and biogenesis0.0430991616255652
GO:0030182neuron differentiation0.0433450960231335
GO:0005515protein binding0.0433450960231335
GO:0016477cell migration0.0463453531660582
GO:0043232intracellular non-membrane-bound organelle0.0463453531660582
GO:0043228non-membrane-bound organelle0.0463453531660582
GO:0048699generation of neurons0.046355984662957
GO:0022008neurogenesis0.0484043620897308
GO:0051239regulation of multicellular organismal process0.0484043620897308
GO:0045941positive regulation of transcription0.0484043620897308
GO:0006511ubiquitin-dependent protein catabolic process0.0484043620897308
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0484043620897308
GO:0019941modification-dependent protein catabolic process0.0484043620897308
GO:0043632modification-dependent macromolecule catabolic process0.0484043620897308
GO:0051603proteolysis involved in cellular protein catabolic process0.0484043620897308
GO:0007268synaptic transmission0.0484043620897308
GO:0044257cellular protein catabolic process0.0484043620897308



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


Uber Anatomy
Ontology termp-valuen
unilaminar epithelium1.05e-10138
dermomyotome1.27e-1070
somite1.38e-1083
paraxial mesoderm1.38e-1083
presomitic mesoderm1.38e-1083
presumptive segmental plate1.38e-1083
trunk paraxial mesoderm1.38e-1083
presumptive paraxial mesoderm1.38e-1083
multilaminar epithelium1.80e-1082
mesenchyme3.02e-10238
entire embryonic mesenchyme3.02e-10238
trunk mesenchyme1.05e-09143
skeletal muscle tissue4.91e-0961
striated muscle tissue4.91e-0961
myotome4.91e-0961
trunk6.11e-09216
muscle tissue7.72e-0863
musculature7.72e-0863
musculature of body7.72e-0863
vasculature1.12e-0779
vascular system1.12e-0779
epithelial tube1.84e-07118
artery5.00e-0742
arterial blood vessel5.00e-0742
arterial system5.00e-0742
Disease
Ontology termp-valuen
cancer7.90e-25235
disease of cellular proliferation9.34e-25239
cell type cancer1.81e-12143
carcinoma8.18e-12106
organ system cancer1.14e-11137
hematologic cancer1.82e-0751
immune system cancer1.82e-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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F1#186934.907389214879320.008460985347239390.0324682851513938
ELF1#199734.258097958807540.01295179875054610.0461300995705857
GTF2B#2959331.94382993432423.06634405746243e-050.000627318133236668
GTF2F1#2962312.73966087675770.0004835525047438590.0043341692450175
KAT2A#26481205.3633333333330.004861545220737780.0227530773609067
MAX#414936.452555509007120.003721913834265510.0186263337455966
MYC#460935.22228187160940.007020843755740150.0293993785736637
NFKB1#479035.488063424193840.006049381815655430.026920251712695
POU2F2#545239.106124057742520.001324165192682130.00881081094282167
RFX5#5993312.04791082719510.0005717246050312580.00484033284896721
RXRA#6256213.38307809275550.007196434429465730.0298249371182131
SIN3A#2594235.408884726815140.006318961977991520.0276104957752262
SIX5#147912211.3911435703060.009873820081429030.0370672859627738
SP1#666735.69838137814090.005403962701712170.0246058534509359
STAT1#6772320.70658749719920.0001125992441046670.00154672529988785
TAF7#6879311.43306940492390.0006690181981945830.00541808247528257
YY1#752834.911170749853860.008441455341808260.0328716314110035
ZNF143#7702313.50087655222790.0004062804962997170.0038853153331239
ZZZ3#26009179.80440414507770.0124784379082580.0451587226411364



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.