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Difference between revisions of "Coexpression cluster:C1437"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0000914!4.15e-23!83;UBERON:0002329!4.15e-23!83;UBERON:0003077!4.15e-23!83;UBERON:0003059!4.15e-23!83;UBERON:0007282!4.15e-23!83;UBERON:0009618!4.15e-23!83;UBERON:0007285!4.15e-23!83;UBERON:0004290!2.44e-22!70;UBERON:0002049!1.23e-21!79;UBERON:0007798!1.23e-21!79;UBERON:0000486!1.79e-20!82;UBERON:0004872!3.35e-20!84;UBERON:0004535!5.25e-19!110;UBERON:0001134!7.59e-19!61;UBERON:0002036!7.59e-19!61;UBERON:0003082!7.59e-19!61;UBERON:0000055!3.44e-18!69;UBERON:0001009!3.89e-18!113;UBERON:0002385!1.02e-17!63;UBERON:0001015!1.02e-17!63;UBERON:0000383!1.02e-17!63;UBERON:0001981!3.65e-17!60;UBERON:0007500!3.65e-17!60;UBERON:0004537!3.65e-17!60;UBERON:0006965!3.65e-17!60;UBERON:0005256!6.55e-17!143;UBERON:0003914!6.95e-16!118;UBERON:0003081!9.08e-16!216;UBERON:0001637!1.74e-15!42;UBERON:0003509!1.74e-15!42;UBERON:0004572!1.74e-15!42;UBERON:0002204!8.07e-13!167;UBERON:0000926!2.04e-12!448;UBERON:0004120!2.04e-12!448;UBERON:0006603!2.04e-12!448;UBERON:0004573!7.24e-12!33;UBERON:0004571!7.24e-12!33;UBERON:0000490!1.34e-11!138;UBERON:0002100!3.95e-10!216;UBERON:0000468!1.72e-08!659;UBERON:0000353!2.26e-07!17;UBERON:0004211!3.30e-07!16;UBERON:0001285!3.30e-07!16;UBERON:0007684!3.30e-07!16;UBERON:0003220!3.30e-07!16;UBERON:0004208!3.30e-07!16;UBERON:0002050!4.62e-07!605;UBERON:0005423!4.62e-07!605;UBERON:0000923!6.30e-07!604;UBERON:0005291!6.30e-07!604;UBERON:0006598!6.30e-07!604;UBERON:0002532!6.30e-07!604;UBERON:0006555!6.99e-07!17;UBERON:0005103!6.99e-07!17;UBERON:0000083!6.99e-07!17;UBERON:0009201!6.99e-07!17;UBERON:0004819!6.99e-07!17;UBERON:0006553!6.99e-07!17;UBERON:0003074!6.99e-07!17;UBERON:0003060!6.99e-07!17;UBERON:0001013!8.09e-07!14
 
|ontology_enrichment_uberon=UBERON:0000914!4.15e-23!83;UBERON:0002329!4.15e-23!83;UBERON:0003077!4.15e-23!83;UBERON:0003059!4.15e-23!83;UBERON:0007282!4.15e-23!83;UBERON:0009618!4.15e-23!83;UBERON:0007285!4.15e-23!83;UBERON:0004290!2.44e-22!70;UBERON:0002049!1.23e-21!79;UBERON:0007798!1.23e-21!79;UBERON:0000486!1.79e-20!82;UBERON:0004872!3.35e-20!84;UBERON:0004535!5.25e-19!110;UBERON:0001134!7.59e-19!61;UBERON:0002036!7.59e-19!61;UBERON:0003082!7.59e-19!61;UBERON:0000055!3.44e-18!69;UBERON:0001009!3.89e-18!113;UBERON:0002385!1.02e-17!63;UBERON:0001015!1.02e-17!63;UBERON:0000383!1.02e-17!63;UBERON:0001981!3.65e-17!60;UBERON:0007500!3.65e-17!60;UBERON:0004537!3.65e-17!60;UBERON:0006965!3.65e-17!60;UBERON:0005256!6.55e-17!143;UBERON:0003914!6.95e-16!118;UBERON:0003081!9.08e-16!216;UBERON:0001637!1.74e-15!42;UBERON:0003509!1.74e-15!42;UBERON:0004572!1.74e-15!42;UBERON:0002204!8.07e-13!167;UBERON:0000926!2.04e-12!448;UBERON:0004120!2.04e-12!448;UBERON:0006603!2.04e-12!448;UBERON:0004573!7.24e-12!33;UBERON:0004571!7.24e-12!33;UBERON:0000490!1.34e-11!138;UBERON:0002100!3.95e-10!216;UBERON:0000468!1.72e-08!659;UBERON:0000353!2.26e-07!17;UBERON:0004211!3.30e-07!16;UBERON:0001285!3.30e-07!16;UBERON:0007684!3.30e-07!16;UBERON:0003220!3.30e-07!16;UBERON:0004208!3.30e-07!16;UBERON:0002050!4.62e-07!605;UBERON:0005423!4.62e-07!605;UBERON:0000923!6.30e-07!604;UBERON:0005291!6.30e-07!604;UBERON:0006598!6.30e-07!604;UBERON:0002532!6.30e-07!604;UBERON:0006555!6.99e-07!17;UBERON:0005103!6.99e-07!17;UBERON:0000083!6.99e-07!17;UBERON:0009201!6.99e-07!17;UBERON:0004819!6.99e-07!17;UBERON:0006553!6.99e-07!17;UBERON:0003074!6.99e-07!17;UBERON:0003060!6.99e-07!17;UBERON:0001013!8.09e-07!14
 +
|tf_chipseq_enrich=ATF3#467;3:11.2315872630044:0.00159345997118423:0.0100409898594491!CCNT2#905;4:4.22413438464176:0.00710980547887581:0.0296128005746086!EGR1#1958;5:4.15681591234178:0.00161796681886444:0.0101342711164318!ELF1#1997;6:4.25809795880754:0.000167722477628883:0.00205282641990893!ELK4#2005;3:8.11784082923401:0.00405611313418576:0.019408796830442!ETS1#2113;5:8.10730076850195:6.29183579217211e-05:0.00102754188944279!GABPB1#2553;4:4.71178922412145:0.00473005431155596:0.0222894979129447!MXI1#4601;4:6.6410477525062:0.00128851695803914:0.00863911039228667!NFKB1#4790;4:3.65870894946256:0.0120792728901523:0.0438341619657615!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380269059053913!SIN3A#25942;6:5.40888472681514:3.99207083571449e-05:0.000742789748817362!SP1#6667;4:3.7989209187606:0.0105224661679851:0.0389493476561472!SREBF1#6720;2:15.6686164801628:0.00641128316580946:0.0278913651249208!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00573211993726483!TAF7#6879;3:5.71653470246196:0.0109272937988966:0.0402140891878841!THAP1#55145;3:15.6845723014257:0.000602346980086485:0.00503187620006818!ZNF263#10127;4:5.48122775800712:0.00267560938060723:0.0147468451159026
 
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}}
 
}}

Revision as of 04:32, 5 September 2012


Full id: C1437_Mesenchymal_Osteoblast_Renal_Pericytes_Placental_Fibroblast_Nucleus



Phase1 CAGE Peaks

  Short description
Hg19::chr17:79791135..79791175,- p1@FAM195B
Hg19::chr19:507487..507508,+ p1@TPGS1
Hg19::chr1:36789194..36789256,- p1@FAM176B
Hg19::chr1:36789257..36789268,- p2@FAM176B
Hg19::chr3:49395753..49395769,- p3@GPX1
Hg19::chr6:144416737..144416766,- p2@SF3B5


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:0010269response to selenium ion0.00356170431735566
GO:0033598mammary gland epithelial cell proliferation0.00356170431735566
GO:0033599regulation of mammary gland epithelial cell proliferation0.00356170431735566
GO:0008539proteasome inhibitor activity0.00356170431735566
GO:0043295glutathione binding0.00427398227263908
GO:0008631induction of apoptosis by oxidative stress0.00474879929383486
GO:0009650UV protection0.00610541935439425
GO:0030503regulation of cell redox homeostasis0.00712267470585477
GO:0043154negative regulation of caspase activity0.00712267470585477
GO:0042744hydrogen peroxide catabolic process0.00771577659443147
GO:0042743hydrogen peroxide metabolic process0.00771577659443147
GO:0001836release of cytochrome c from mitochondria0.00771577659443147
GO:0004602glutathione peroxidase activity0.0083782604577414
GO:0006749glutathione metabolic process0.0083782604577414
GO:0008637apoptotic mitochondrial changes0.0083782604577414
GO:0017124SH3 domain binding0.0083782604577414
GO:0042542response to hydrogen peroxide0.0083782604577414
GO:0000302response to reactive oxygen species0.0106811811903355
GO:0050678regulation of epithelial cell proliferation0.0111441033976822
GO:0009411response to UV0.0111441033976822
GO:0050673epithelial cell proliferation0.0111441033976822
GO:0010038response to metal ion0.0111441033976822
GO:0008629induction of apoptosis by intracellular signals0.0111441033976822
GO:0010035response to inorganic substance0.0123917946099916
GO:0006800oxygen and reactive oxygen species metabolic process0.0123917946099916
GO:0060047heart contraction0.0123917946099916
GO:0003015heart process0.0123917946099916
GO:0008430selenium binding0.0127113856780267
GO:0043281regulation of caspase activity0.0147255051928963
GO:0040029regulation of gene expression, epigenetic0.0149003678103095
GO:0004601peroxidase activity0.0149003678103095
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.0149003678103095
GO:0009416response to light stimulus0.0174643995027196
GO:0006790sulfur metabolic process0.0175880982868606
GO:0008632apoptotic program0.0175880982868606
GO:0007005mitochondrion organization and biogenesis0.0175880982868606
GO:0009314response to radiation0.0194166461393986
GO:0045454cell redox homeostasis0.0202138906401953
GO:0006979response to oxidative stress0.0218801128957829
GO:0019904protein domain specific binding0.0225752112702164
GO:0005681spliceosome0.0241013951022955
GO:0008015blood circulation0.0264440662770201
GO:0003013circulatory system process0.0264440662770201
GO:0009628response to abiotic stimulus0.0266486946639436
GO:0006916anti-apoptosis0.0268441119592487
GO:0042277peptide binding0.0315119562790315
GO:0006917induction of apoptosis0.0315119562790315
GO:0012502induction of programmed cell death0.0315119562790315
GO:0008380RNA splicing0.0320173688309457
GO:0043066negative regulation of apoptosis0.0320173688309457
GO:0043069negative regulation of programmed cell death0.0320173688309457
GO:0043065positive regulation of apoptosis0.0345455564991135
GO:0043068positive regulation of programmed cell death0.0345455564991135
GO:0006397mRNA processing0.0358691419109499
GO:0006732coenzyme metabolic process0.0371437391052508
GO:0051336regulation of hydrolase activity0.0388762339987535
GO:0016071mRNA metabolic process0.0419149300765837
GO:0051186cofactor metabolic process0.0419149300765837
GO:0019725cellular homeostasis0.0450273350297991
GO:0004857enzyme inhibitor activity0.0473285241774172



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


Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.91e-30180
mesodermal cell1.51e-27119
contractile cell3.58e-2359
somatic cell4.97e-23591
muscle precursor cell1.87e-2057
myoblast1.87e-2057
multi-potent skeletal muscle stem cell1.87e-2057
muscle cell2.42e-2054
electrically responsive cell9.40e-1960
electrically active cell9.40e-1960
smooth muscle cell2.94e-1742
smooth muscle myoblast2.94e-1742
vascular associated smooth muscle cell2.64e-1432
embryonic cell1.43e-12248
multi fate stem cell2.25e-12430
somatic stem cell1.46e-11436
meso-epithelial cell2.66e-1144
endothelial cell5.07e-1135
stem cell5.22e-11444
fibroblast5.60e-1175
animal cell9.26e-09679
eukaryotic cell9.26e-09679
lining cell4.52e-0857
barrier cell4.52e-0857
epithelial cell of nephron3.30e-0716
endothelial cell of vascular tree6.01e-0724
native cell7.85e-07722
cardiocyte9.10e-0716
Uber Anatomy
Ontology termp-valuen
somite4.15e-2383
paraxial mesoderm4.15e-2383
presomitic mesoderm4.15e-2383
presumptive segmental plate4.15e-2383
trunk paraxial mesoderm4.15e-2383
presumptive paraxial mesoderm4.15e-2383
dermomyotome2.44e-2270
vasculature1.23e-2179
vascular system1.23e-2179
multilaminar epithelium1.79e-2082
splanchnic layer of lateral plate mesoderm3.35e-2084
cardiovascular system5.25e-19110
skeletal muscle tissue7.59e-1961
striated muscle tissue7.59e-1961
myotome7.59e-1961
vessel3.44e-1869
circulatory system3.89e-18113
muscle tissue1.02e-1763
musculature1.02e-1763
musculature of body1.02e-1763
blood vessel3.65e-1760
epithelial tube open at both ends3.65e-1760
blood vasculature3.65e-1760
vascular cord3.65e-1760
trunk mesenchyme6.55e-17143
epithelial tube6.95e-16118
lateral plate mesoderm9.08e-16216
artery1.74e-1542
arterial blood vessel1.74e-1542
arterial system1.74e-1542
musculoskeletal system8.07e-13167
mesoderm2.04e-12448
mesoderm-derived structure2.04e-12448
presumptive mesoderm2.04e-12448
systemic artery7.24e-1233
systemic arterial system7.24e-1233
unilaminar epithelium1.34e-11138
trunk3.95e-10216
multi-cellular organism1.72e-08659
parenchyma2.26e-0717
nephron epithelium3.30e-0716
nephron3.30e-0716
uriniferous tubule3.30e-0716
metanephric mesenchyme3.30e-0716
nephrogenic mesenchyme3.30e-0716
embryonic structure4.62e-07605
developing anatomical structure4.62e-07605
germ layer6.30e-07604
embryonic tissue6.30e-07604
presumptive structure6.30e-07604
epiblast (generic)6.30e-07604
excretory tube6.99e-0717
mesonephric epithelium6.99e-0717
mesonephric tubule6.99e-0717
nephric duct6.99e-0717
kidney epithelium6.99e-0717
renal duct6.99e-0717
mesonephric duct6.99e-0717
pronephric duct6.99e-0717
adipose tissue8.09e-0714


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
ATF3#467311.23158726300440.001593459971184230.0100409898594491
CCNT2#90544.224134384641760.007109805478875810.0296128005746086
EGR1#195854.156815912341780.001617966818864440.0101342711164318
ELF1#199764.258097958807540.0001677224776288830.00205282641990893
ELK4#200538.117840829234010.004056113134185760.019408796830442
ETS1#211358.107300768501956.29183579217211e-050.00102754188944279
GABPB1#255344.711789224121450.004730054311555960.0222894979129447
MXI1#460146.64104775250620.001288516958039140.00863911039228667
NFKB1#479043.658708949462560.01207927289015230.0438341619657615
POLR2A#543062.147453176558070.01019570676818780.0380269059053913
SIN3A#2594265.408884726815143.99207083571449e-050.000742789748817362
SP1#666743.79892091876060.01052246616798510.0389493476561472
SREBF1#6720215.66861648016280.006411283165809460.0278913651249208
TAF1#687263.343046285745290.0007162474284635620.00573211993726483
TAF7#687935.716534702461960.01092729379889660.0402140891878841
THAP1#55145315.68457230142570.0006023469800864850.00503187620006818
ZNF263#1012745.481227758007120.002675609380607230.0147468451159026



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.