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Coexpression cluster:C1780: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!4.96e-23!83;UBERON:0002329!4.96e-23!83;UBERON:0003077!4.96e-23!83;UBERON:0003059!4.96e-23!83;UBERON:0007282!4.96e-23!83;UBERON:0009618!4.96e-23!83;UBERON:0007285!4.96e-23!83;UBERON:0000475!3.00e-21!365;UBERON:0004290!3.18e-21!70;UBERON:0002385!7.83e-20!63;UBERON:0001015!7.83e-20!63;UBERON:0000383!7.83e-20!63;UBERON:0001134!1.35e-19!61;UBERON:0002036!1.35e-19!61;UBERON:0003082!1.35e-19!61;UBERON:0000486!1.93e-19!82;UBERON:0005256!1.93e-17!143;UBERON:0004872!2.25e-17!84;UBERON:0002049!7.08e-17!79;UBERON:0007798!7.08e-17!79;UBERON:0001981!4.24e-15!60;UBERON:0007500!4.24e-15!60;UBERON:0004537!4.24e-15!60;UBERON:0006965!4.24e-15!60;UBERON:0000481!6.83e-15!347;UBERON:0000055!7.80e-15!69;UBERON:0002100!8.11e-15!216;UBERON:0000468!1.33e-14!659;UBERON:0001637!4.14e-14!42;UBERON:0003509!4.14e-14!42;UBERON:0004572!4.14e-14!42;UBERON:0000119!7.19e-14!312;UBERON:0000483!9.73e-14!309;UBERON:0003102!5.32e-13!95;UBERON:0000490!6.35e-13!138;UBERON:0001009!9.89e-13!113;UBERON:0004535!2.77e-12!110;UBERON:0000477!3.35e-12!286;UBERON:0003914!4.13e-12!118;UBERON:0004573!4.36e-12!33;UBERON:0004571!4.36e-12!33;UBERON:0000467!1.81e-11!625;UBERON:0003104!2.76e-11!238;UBERON:0009142!2.76e-11!238;UBERON:0000480!3.56e-11!626;UBERON:0004111!3.33e-10!241;UBERON:0002199!1.55e-08!45;UBERON:0002416!1.55e-08!45;UBERON:0007100!4.28e-08!27;UBERON:0000948!9.45e-08!24;UBERON:0005498!9.45e-08!24;UBERON:0004140!9.45e-08!24;UBERON:0009881!9.45e-08!24;UBERON:0004141!9.45e-08!24;UBERON:0003084!9.45e-08!24;UBERON:0007005!9.45e-08!24;UBERON:0004139!9.45e-08!24;UBERON:0004291!9.45e-08!24;UBERON:0002050!1.16e-07!605;UBERON:0005423!1.16e-07!605;UBERON:0000923!1.74e-07!604;UBERON:0005291!1.74e-07!604;UBERON:0006598!1.74e-07!604;UBERON:0002532!1.74e-07!604;UBERON:0001013!1.92e-07!14;UBERON:0000922!6.83e-07!612;UBERON:0000025!8.43e-07!194;UBERON:0002097!9.10e-07!40
|ontology_enrichment_uberon=UBERON:0000914!4.96e-23!83;UBERON:0002329!4.96e-23!83;UBERON:0003077!4.96e-23!83;UBERON:0003059!4.96e-23!83;UBERON:0007282!4.96e-23!83;UBERON:0009618!4.96e-23!83;UBERON:0007285!4.96e-23!83;UBERON:0000475!3.00e-21!365;UBERON:0004290!3.18e-21!70;UBERON:0002385!7.83e-20!63;UBERON:0001015!7.83e-20!63;UBERON:0000383!7.83e-20!63;UBERON:0001134!1.35e-19!61;UBERON:0002036!1.35e-19!61;UBERON:0003082!1.35e-19!61;UBERON:0000486!1.93e-19!82;UBERON:0005256!1.93e-17!143;UBERON:0004872!2.25e-17!84;UBERON:0002049!7.08e-17!79;UBERON:0007798!7.08e-17!79;UBERON:0001981!4.24e-15!60;UBERON:0007500!4.24e-15!60;UBERON:0004537!4.24e-15!60;UBERON:0006965!4.24e-15!60;UBERON:0000481!6.83e-15!347;UBERON:0000055!7.80e-15!69;UBERON:0002100!8.11e-15!216;UBERON:0000468!1.33e-14!659;UBERON:0001637!4.14e-14!42;UBERON:0003509!4.14e-14!42;UBERON:0004572!4.14e-14!42;UBERON:0000119!7.19e-14!312;UBERON:0000483!9.73e-14!309;UBERON:0003102!5.32e-13!95;UBERON:0000490!6.35e-13!138;UBERON:0001009!9.89e-13!113;UBERON:0004535!2.77e-12!110;UBERON:0000477!3.35e-12!286;UBERON:0003914!4.13e-12!118;UBERON:0004573!4.36e-12!33;UBERON:0004571!4.36e-12!33;UBERON:0000467!1.81e-11!625;UBERON:0003104!2.76e-11!238;UBERON:0009142!2.76e-11!238;UBERON:0000480!3.56e-11!626;UBERON:0004111!3.33e-10!241;UBERON:0002199!1.55e-08!45;UBERON:0002416!1.55e-08!45;UBERON:0007100!4.28e-08!27;UBERON:0000948!9.45e-08!24;UBERON:0005498!9.45e-08!24;UBERON:0004140!9.45e-08!24;UBERON:0009881!9.45e-08!24;UBERON:0004141!9.45e-08!24;UBERON:0003084!9.45e-08!24;UBERON:0007005!9.45e-08!24;UBERON:0004139!9.45e-08!24;UBERON:0004291!9.45e-08!24;UBERON:0002050!1.16e-07!605;UBERON:0005423!1.16e-07!605;UBERON:0000923!1.74e-07!604;UBERON:0005291!1.74e-07!604;UBERON:0006598!1.74e-07!604;UBERON:0002532!1.74e-07!604;UBERON:0001013!1.92e-07!14;UBERON:0000922!6.83e-07!612;UBERON:0000025!8.43e-07!194;UBERON:0002097!9.10e-07!40
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}}
}}

Revision as of 12:10, 5 September 2012


Full id: C1780_Mesenchymal_tenocyte_Osteoblast_Smooth_mature_Synoviocyte_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr17:40575190..40575206,-p4@PTRF
Hg19::chr17:40575209..40575222,-p2@PTRF
Hg19::chr17:40575228..40575241,-p3@PTRF
Hg19::chr17:46115174..46115183,-p2@COPZ2
Hg19::chr19:13106214..13106382,+p1@NFIX


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:0042134rRNA primary transcript binding0.00629911987840746
GO:0003716RNA polymerase I transcription termination factor activity0.00629911987840746
GO:0006361transcription initiation from RNA polymerase I promoter0.00629911987840746
GO:0003715transcription termination factor activity0.00944812353844312
GO:0006353transcription termination0.0132262048248837
GO:0006360transcription from RNA polymerase I promoter0.0144102097285995
GO:0005801cis-Golgi network0.0144102097285995
GO:0030126COPI vesicle coat0.0144102097285995
GO:0030663COPI coated vesicle membrane0.0144102097285995
GO:0065003macromolecular complex assembly0.0144102097285995
GO:0030137COPI-coated vesicle0.0144102097285995
GO:0022607cellular component assembly0.0144102097285995
GO:0005783endoplasmic reticulum0.0144102097285995
GO:0016599caveolar membrane0.0144102097285995
GO:0043624cellular protein complex disassembly0.0144102097285995
GO:0043241protein complex disassembly0.0144102097285995
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0144102097285995
GO:0032984macromolecular complex disassembly0.0144102097285995
GO:0005901caveola0.0144102097285995
GO:0019843rRNA binding0.0169906068743104
GO:0022411cellular component disassembly0.0209212139325074
GO:0030120vesicle coat0.0209212139325074
GO:0030662coated vesicle membrane0.0209212139325074
GO:0005798Golgi-associated vesicle0.0271114120113892
GO:0006352transcription initiation0.0343031653617995
GO:0030659cytoplasmic vesicle membrane0.0364124261128975
GO:0044433cytoplasmic vesicle part0.0364124261128975
GO:0012506vesicle membrane0.0364124261128975
GO:0030117membrane coat0.0364124261128975
GO:0048475coated membrane0.0364124261128975
GO:0030135coated vesicle0.0446140550686479
GO:0005792microsome0.0476089978154376
GO:0042598vesicular fraction0.0481512019910992



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>

Uber Anatomy
Ontology termp-valuen
somite4.96e-2383
paraxial mesoderm4.96e-2383
presomitic mesoderm4.96e-2383
presumptive segmental plate4.96e-2383
trunk paraxial mesoderm4.96e-2383
presumptive paraxial mesoderm4.96e-2383
organism subdivision3.00e-21365
dermomyotome3.18e-2170
muscle tissue7.83e-2063
musculature7.83e-2063
musculature of body7.83e-2063
skeletal muscle tissue1.35e-1961
striated muscle tissue1.35e-1961
myotome1.35e-1961
multilaminar epithelium1.93e-1982
trunk mesenchyme1.93e-17143
splanchnic layer of lateral plate mesoderm2.25e-1784
vasculature7.08e-1779
vascular system7.08e-1779
blood vessel4.24e-1560
epithelial tube open at both ends4.24e-1560
blood vasculature4.24e-1560
vascular cord4.24e-1560
multi-tissue structure6.83e-15347
vessel7.80e-1569
trunk8.11e-15216
multi-cellular organism1.33e-14659
artery4.14e-1442
arterial blood vessel4.14e-1442
arterial system4.14e-1442
cell layer7.19e-14312
epithelium9.73e-14309
surface structure5.32e-1395
unilaminar epithelium6.35e-13138
circulatory system9.89e-13113
cardiovascular system2.77e-12110
anatomical cluster3.35e-12286
epithelial tube4.13e-12118
systemic artery4.36e-1233
systemic arterial system4.36e-1233
anatomical system1.81e-11625
mesenchyme2.76e-11238
entire embryonic mesenchyme2.76e-11238
anatomical group3.56e-11626
anatomical conduit3.33e-10241
integument1.55e-0845
integumental system1.55e-0845
primary circulatory organ4.28e-0827
heart9.45e-0824
primitive heart tube9.45e-0824
primary heart field9.45e-0824
anterior lateral plate mesoderm9.45e-0824
heart tube9.45e-0824
heart primordium9.45e-0824
cardiac mesoderm9.45e-0824
cardiogenic plate9.45e-0824
heart rudiment9.45e-0824
embryonic structure1.16e-07605
developing anatomical structure1.16e-07605
germ layer1.74e-07604
embryonic tissue1.74e-07604
presumptive structure1.74e-07604
epiblast (generic)1.74e-07604
adipose tissue1.92e-0714
embryo6.83e-07612
tube8.43e-07194
skin of body9.10e-0740


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

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

TF#promotersEnrichmentp-valueq-value
CCNT2#90545.068961261570110.002709998091280770.0148962889818564
CTBP2#1488337.63020020359693.95343056005017e-050.000737702937754297
E2F6#187644.013724585357910.006632118233933880.0282957553917162
ETS1#211335.83725655332140.009253279045631430.0349727937700105
FOS#235335.398773185336640.01153895317278740.0421900549787406
GTF2B#2959319.16629796059450.0002924229654472410.00310243418207481
NANOG#79923317.54686708860760.0003794200090681830.00376103325048139
NFYA#4800311.05534841989830.001470892907644430.0094117500540054
NFYB#4801310.05587595212190.001938165606725460.0113872681031053
REST#597835.790017229676810.009468788694433940.0356994629240095
SMC3#912639.02695970695970.002650964449467550.0146380499174126
TAF7#687936.859841642954350.005843286407019040.0262457848384079



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.

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