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Coexpression cluster:C2341: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2341_Smooth_Fibroblast_mesenchymal_Hepatic_Adipocyte_Pericytes_Preadipocyte
|full_id=C2341_Smooth_Fibroblast_mesenchymal_Hepatic_Adipocyte_Pericytes_Preadipocyte
|gostat_on_coexpression_clusters=GO:0044432!endoplasmic reticulum part!9.33494354018741e-06!29927;6184;811;5479$GO:0005783!endoplasmic reticulum!4.32238704894574e-05!29927;6184;811;5479$GO:0005788!endoplasmic reticulum lumen!0.00119892517736691!811;5479$GO:0048770!pigment granule!0.00121336223236269!6184;5479$GO:0042470!melanosome!0.00121336223236269!6184;5479$GO:0051082!unfolded protein binding!0.00450023955118235!811;5479$GO:0044446!intracellular organelle part!0.00450023955118235!29927;6184;811;5479$GO:0044422!organelle part!0.00450023955118235!29927;6184;811;5479$GO:0040020!regulation of meiosis!0.00450023955118235!811$GO:0044444!cytoplasmic part!0.00573535899024002!29927;6184;811;5479$GO:0006457!protein folding!0.00838247864021421!811;5479$GO:0016023!cytoplasmic membrane-bound vesicle!0.00838247864021421!6184;5479$GO:0031988!membrane-bound vesicle!0.00838247864021421!6184;5479$GO:0031410!cytoplasmic vesicle!0.0109134708244856!6184;5479$GO:0031982!vesicle!0.0109134708244856!6184;5479$GO:0005789!endoplasmic reticulum membrane!0.0112394684514031!29927;6184$GO:0042175!nuclear envelope-endoplasmic reticulum network!0.0112394684514031!29927;6184$GO:0030867!rough endoplasmic reticulum membrane!0.012370741454421!6184$GO:0006886!intracellular protein transport!0.0127422358547018!29927;811$GO:0030866!cortical actin cytoskeleton organization and biogenesis!0.0127422358547018!811$GO:0030865!cortical cytoskeleton organization and biogenesis!0.0127422358547018!811$GO:0006611!protein export from nucleus!0.0127422358547018!811$GO:0008250!oligosaccharyl transferase complex!0.0127422358547018!6184$GO:0018279!protein amino acid N-linked glycosylation via asparagine!0.0127422358547018!6184$GO:0018196!peptidyl-asparagine modification!0.0127422358547018!6184$GO:0005791!rough endoplasmic reticulum!0.0127422358547018!6184$GO:0004579!dolichyl-diphosphooligosaccharide-protein glycotransferase activity!0.0127422358547018!6184$GO:0004576!oligosaccharyl transferase activity!0.013009355382734!6184$GO:0005737!cytoplasm!0.0139458562098636!29927;6184;811;5479$GO:0022884!macromolecule transmembrane transporter activity!0.0169667838835292!29927$GO:0015450!P-P-bond-hydrolysis-driven protein transmembrane transporter activity!0.0169667838835292!29927$GO:0008320!protein transmembrane transporter activity!0.0176993602305049!29927$GO:0015031!protein transport!0.0196169772724579!29927;811$GO:0046907!intracellular transport!0.0202639729663448!29927;811$GO:0045184!establishment of protein localization!0.0202639729663448!29927;811$GO:0043231!intracellular membrane-bound organelle!0.0202639729663448!29927;6184;811;5479$GO:0043227!membrane-bound organelle!0.0202639729663448!29927;6184;811;5479$GO:0008104!protein localization!0.0202639729663448!29927;811$GO:0031974!membrane-enclosed lumen!0.0202639729663448!811;5479$GO:0043233!organelle lumen!0.0202639729663448!811;5479$GO:0005515!protein binding!0.02060231316098!29927;6184;811;5479$GO:0033036!macromolecule localization!0.02060231316098!29927;811$GO:0051168!nuclear export!0.02060231316098!811$GO:0012505!endomembrane system!0.02060231316098!29927;6184$GO:0009897!external side of plasma membrane!0.0224202744666166!811$GO:0051649!establishment of cellular localization!0.0224202744666166!29927;811$GO:0006487!protein amino acid N-linked glycosylation!0.022571110402564!6184$GO:0051641!cellular localization!0.022571110402564!29927;811$GO:0009306!protein secretion!0.0235002266741561!29927$GO:0051327!M phase of meiotic cell cycle!0.0267922280755042!811$GO:0065002!intracellular protein transport across a membrane!0.0267922280755042!29927$GO:0007126!meiosis!0.0267922280755042!811$GO:0051321!meiotic cell cycle!0.0270462586568967!811$GO:0043229!intracellular organelle!0.0315541271581508!29927;6184;811;5479$GO:0043226!organelle!0.0315541271581508!29927;6184;811;5479$GO:0003755!peptidyl-prolyl cis-trans isomerase activity!0.0329087021205927!5479$GO:0016859!cis-trans isomerase activity!0.0329087021205927!5479$GO:0031090!organelle membrane!0.0331285673484481!29927;6184$GO:0006874!cellular calcium ion homeostasis!0.0389554397810922!811$GO:0055074!calcium ion homeostasis!0.0389554397810922!811$GO:0018193!peptidyl-amino acid modification!0.0393270725751541!6184$GO:0006875!cellular metal ion homeostasis!0.0393270725751541!811$GO:0055065!metal ion homeostasis!0.0393270725751541!811$GO:0044267!cellular protein metabolic process!0.0418384575583755!6184;811;5479$GO:0044260!cellular macromolecule metabolic process!0.0427315939816818!6184;811;5479$GO:0009986!cell surface!0.0448250058407225!811$GO:0019538!protein metabolic process!0.0448250058407225!6184;811;5479$GO:0006913!nucleocytoplasmic transport!0.0448250058407225!811$GO:0008565!protein transporter activity!0.0448250058407225!29927$GO:0051169!nuclear transport!0.0448250058407225!811$GO:0006486!protein amino acid glycosylation!0.0483741220471638!6184$GO:0043413!biopolymer glycosylation!0.0483741220471638!6184$GO:0030005!cellular di-, tri-valent inorganic cation homeostasis!0.0483741220471638!811$GO:0044424!intracellular part!0.0483741220471638!29927;6184;811;5479$GO:0009101!glycoprotein biosynthetic process!0.0483741220471638!6184$GO:0055066!di-, tri-valent inorganic cation homeostasis!0.0483741220471638!811
|gostat_on_coexpression_clusters=GO:0044432!endoplasmic reticulum part!9.33494354018741e-06!29927;6184;811;5479$GO:0005783!endoplasmic reticulum!4.32238704894574e-05!29927;6184;811;5479$GO:0005788!endoplasmic reticulum lumen!0.00119892517736691!811;5479$GO:0048770!pigment granule!0.00121336223236269!6184;5479$GO:0042470!melanosome!0.00121336223236269!6184;5479$GO:0051082!unfolded protein binding!0.00450023955118235!811;5479$GO:0044446!intracellular organelle part!0.00450023955118235!29927;6184;811;5479$GO:0044422!organelle part!0.00450023955118235!29927;6184;811;5479$GO:0040020!regulation of meiosis!0.00450023955118235!811$GO:0044444!cytoplasmic part!0.00573535899024002!29927;6184;811;5479$GO:0006457!protein folding!0.00838247864021421!811;5479$GO:0016023!cytoplasmic membrane-bound vesicle!0.00838247864021421!6184;5479$GO:0031988!membrane-bound vesicle!0.00838247864021421!6184;5479$GO:0031410!cytoplasmic vesicle!0.0109134708244856!6184;5479$GO:0031982!vesicle!0.0109134708244856!6184;5479$GO:0005789!endoplasmic reticulum membrane!0.0112394684514031!29927;6184$GO:0042175!nuclear envelope-endoplasmic reticulum network!0.0112394684514031!29927;6184$GO:0030867!rough endoplasmic reticulum membrane!0.012370741454421!6184$GO:0006886!intracellular protein transport!0.0127422358547018!29927;811$GO:0030866!cortical actin cytoskeleton organization and biogenesis!0.0127422358547018!811$GO:0030865!cortical cytoskeleton organization and biogenesis!0.0127422358547018!811$GO:0006611!protein export from nucleus!0.0127422358547018!811$GO:0008250!oligosaccharyl transferase complex!0.0127422358547018!6184$GO:0018279!protein amino acid N-linked glycosylation via asparagine!0.0127422358547018!6184$GO:0018196!peptidyl-asparagine modification!0.0127422358547018!6184$GO:0005791!rough endoplasmic reticulum!0.0127422358547018!6184$GO:0004579!dolichyl-diphosphooligosaccharide-protein glycotransferase activity!0.0127422358547018!6184$GO:0004576!oligosaccharyl transferase activity!0.013009355382734!6184$GO:0005737!cytoplasm!0.0139458562098636!29927;6184;811;5479$GO:0022884!macromolecule transmembrane transporter activity!0.0169667838835292!29927$GO:0015450!P-P-bond-hydrolysis-driven protein transmembrane transporter activity!0.0169667838835292!29927$GO:0008320!protein transmembrane transporter activity!0.0176993602305049!29927$GO:0015031!protein transport!0.0196169772724579!29927;811$GO:0046907!intracellular transport!0.0202639729663448!29927;811$GO:0045184!establishment of protein localization!0.0202639729663448!29927;811$GO:0043231!intracellular membrane-bound organelle!0.0202639729663448!29927;6184;811;5479$GO:0043227!membrane-bound organelle!0.0202639729663448!29927;6184;811;5479$GO:0008104!protein localization!0.0202639729663448!29927;811$GO:0031974!membrane-enclosed lumen!0.0202639729663448!811;5479$GO:0043233!organelle lumen!0.0202639729663448!811;5479$GO:0005515!protein binding!0.02060231316098!29927;6184;811;5479$GO:0033036!macromolecule localization!0.02060231316098!29927;811$GO:0051168!nuclear export!0.02060231316098!811$GO:0012505!endomembrane system!0.02060231316098!29927;6184$GO:0009897!external side of plasma membrane!0.0224202744666166!811$GO:0051649!establishment of cellular localization!0.0224202744666166!29927;811$GO:0006487!protein amino acid N-linked glycosylation!0.022571110402564!6184$GO:0051641!cellular localization!0.022571110402564!29927;811$GO:0009306!protein secretion!0.0235002266741561!29927$GO:0051327!M phase of meiotic cell cycle!0.0267922280755042!811$GO:0065002!intracellular protein transport across a membrane!0.0267922280755042!29927$GO:0007126!meiosis!0.0267922280755042!811$GO:0051321!meiotic cell cycle!0.0270462586568967!811$GO:0043229!intracellular organelle!0.0315541271581508!29927;6184;811;5479$GO:0043226!organelle!0.0315541271581508!29927;6184;811;5479$GO:0003755!peptidyl-prolyl cis-trans isomerase activity!0.0329087021205927!5479$GO:0016859!cis-trans isomerase activity!0.0329087021205927!5479$GO:0031090!organelle membrane!0.0331285673484481!29927;6184$GO:0006874!cellular calcium ion homeostasis!0.0389554397810922!811$GO:0055074!calcium ion homeostasis!0.0389554397810922!811$GO:0018193!peptidyl-amino acid modification!0.0393270725751541!6184$GO:0006875!cellular metal ion homeostasis!0.0393270725751541!811$GO:0055065!metal ion homeostasis!0.0393270725751541!811$GO:0044267!cellular protein metabolic process!0.0418384575583755!6184;811;5479$GO:0044260!cellular macromolecule metabolic process!0.0427315939816818!6184;811;5479$GO:0009986!cell surface!0.0448250058407225!811$GO:0019538!protein metabolic process!0.0448250058407225!6184;811;5479$GO:0006913!nucleocytoplasmic transport!0.0448250058407225!811$GO:0008565!protein transporter activity!0.0448250058407225!29927$GO:0051169!nuclear transport!0.0448250058407225!811$GO:0006486!protein amino acid glycosylation!0.0483741220471638!6184$GO:0043413!biopolymer glycosylation!0.0483741220471638!6184$GO:0030005!cellular di-, tri-valent inorganic cation homeostasis!0.0483741220471638!811$GO:0044424!intracellular part!0.0483741220471638!29927;6184;811;5479$GO:0009101!glycoprotein biosynthetic process!0.0483741220471638!6184$GO:0055066!di-, tri-valent inorganic cation homeostasis!0.0483741220471638!811

Revision as of 15:03, 12 September 2012


Full id: C2341_Smooth_Fibroblast_mesenchymal_Hepatic_Adipocyte_Pericytes_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr15:64455164..64455227,-p1@PPIB
Hg19::chr19:13049413..13049432,+p1@CALR
Hg19::chr3:127771233..127771316,+p1@SEC61A1
Hg19::chr3:128369643..128369678,-p1@RPN1


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


p.valueFDRnGenesnPathwayName
7.83254338792028e-070.0004957999964553543167Protein processing in endoplasmic reticulum (KEGG):04141
0.0001767677946094820.02237880279756042156Phagosome (KEGG):04145
5.131046541619e-060.001623976230422413312Diabetes pathways (Reactome):REACT_15380
1.44809941098012e-050.002291617317876053441AR up reg. targets (Netpath):NetPath_2
8.74889515724365e-060.00184601687817841235{INS,35} (Static Module):NA



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:0044432endoplasmic reticulum part9.33494354018741e-06
GO:0005783endoplasmic reticulum4.32238704894574e-05
GO:0005788endoplasmic reticulum lumen0.00119892517736691
GO:0048770pigment granule0.00121336223236269
GO:0042470melanosome0.00121336223236269
GO:0051082unfolded protein binding0.00450023955118235
GO:0044446intracellular organelle part0.00450023955118235
GO:0044422organelle part0.00450023955118235
GO:0040020regulation of meiosis0.00450023955118235
GO:0044444cytoplasmic part0.00573535899024002
GO:0006457protein folding0.00838247864021421
GO:0016023cytoplasmic membrane-bound vesicle0.00838247864021421
GO:0031988membrane-bound vesicle0.00838247864021421
GO:0031410cytoplasmic vesicle0.0109134708244856
GO:0031982vesicle0.0109134708244856
GO:0005789endoplasmic reticulum membrane0.0112394684514031
GO:0042175nuclear envelope-endoplasmic reticulum network0.0112394684514031
GO:0030867rough endoplasmic reticulum membrane0.012370741454421
GO:0006886intracellular protein transport0.0127422358547018
GO:0030866cortical actin cytoskeleton organization and biogenesis0.0127422358547018
GO:0030865cortical cytoskeleton organization and biogenesis0.0127422358547018
GO:0006611protein export from nucleus0.0127422358547018
GO:0008250oligosaccharyl transferase complex0.0127422358547018
GO:0018279protein amino acid N-linked glycosylation via asparagine0.0127422358547018
GO:0018196peptidyl-asparagine modification0.0127422358547018
GO:0005791rough endoplasmic reticulum0.0127422358547018
GO:0004579dolichyl-diphosphooligosaccharide-protein glycotransferase activity0.0127422358547018
GO:0004576oligosaccharyl transferase activity0.013009355382734
GO:0005737cytoplasm0.0139458562098636
GO:0022884macromolecule transmembrane transporter activity0.0169667838835292
GO:0015450P-P-bond-hydrolysis-driven protein transmembrane transporter activity0.0169667838835292
GO:0008320protein transmembrane transporter activity0.0176993602305049
GO:0015031protein transport0.0196169772724579
GO:0046907intracellular transport0.0202639729663448
GO:0045184establishment of protein localization0.0202639729663448
GO:0043231intracellular membrane-bound organelle0.0202639729663448
GO:0043227membrane-bound organelle0.0202639729663448
GO:0008104protein localization0.0202639729663448
GO:0031974membrane-enclosed lumen0.0202639729663448
GO:0043233organelle lumen0.0202639729663448
GO:0005515protein binding0.02060231316098
GO:0033036macromolecule localization0.02060231316098
GO:0051168nuclear export0.02060231316098
GO:0012505endomembrane system0.02060231316098
GO:0009897external side of plasma membrane0.0224202744666166
GO:0051649establishment of cellular localization0.0224202744666166
GO:0006487protein amino acid N-linked glycosylation0.022571110402564
GO:0051641cellular localization0.022571110402564
GO:0009306protein secretion0.0235002266741561
GO:0051327M phase of meiotic cell cycle0.0267922280755042
GO:0065002intracellular protein transport across a membrane0.0267922280755042
GO:0007126meiosis0.0267922280755042
GO:0051321meiotic cell cycle0.0270462586568967
GO:0043229intracellular organelle0.0315541271581508
GO:0043226organelle0.0315541271581508
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.0329087021205927
GO:0016859cis-trans isomerase activity0.0329087021205927
GO:0031090organelle membrane0.0331285673484481
GO:0006874cellular calcium ion homeostasis0.0389554397810922
GO:0055074calcium ion homeostasis0.0389554397810922
GO:0018193peptidyl-amino acid modification0.0393270725751541
GO:0006875cellular metal ion homeostasis0.0393270725751541
GO:0055065metal ion homeostasis0.0393270725751541
GO:0044267cellular protein metabolic process0.0418384575583755
GO:0044260cellular macromolecule metabolic process0.0427315939816818
GO:0009986cell surface0.0448250058407225
GO:0019538protein metabolic process0.0448250058407225
GO:0006913nucleocytoplasmic transport0.0448250058407225
GO:0008565protein transporter activity0.0448250058407225
GO:0051169nuclear transport0.0448250058407225
GO:0006486protein amino acid glycosylation0.0483741220471638
GO:0043413biopolymer glycosylation0.0483741220471638
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0483741220471638
GO:0044424intracellular part0.0483741220471638
GO:0009101glycoprotein biosynthetic process0.0483741220471638
GO:0055066di-, tri-valent inorganic cation homeostasis0.0483741220471638



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
trunk mesenchyme1.20e-21143
epithelial tube8.57e-21118
unilaminar epithelium5.58e-17138
somite5.69e-1783
paraxial mesoderm5.69e-1783
presomitic mesoderm5.69e-1783
presumptive segmental plate5.69e-1783
trunk paraxial mesoderm5.69e-1783
presumptive paraxial mesoderm5.69e-1783
vasculature9.64e-1779
vascular system9.64e-1779
multilaminar epithelium9.65e-1782
trunk1.24e-16216
dermomyotome5.37e-1670
artery1.29e-1542
arterial blood vessel1.29e-1542
arterial system1.29e-1542
vessel3.33e-1569
splanchnic layer of lateral plate mesoderm1.80e-1484
blood vessel3.24e-1460
epithelial tube open at both ends3.24e-1460
blood vasculature3.24e-1460
vascular cord3.24e-1460
skeletal muscle tissue4.40e-1461
striated muscle tissue4.40e-1461
myotome4.40e-1461
systemic artery9.73e-1333
systemic arterial system9.73e-1333
muscle tissue1.02e-1263
musculature1.02e-1263
musculature of body1.02e-1263
mesenchyme4.06e-12238
entire embryonic mesenchyme4.06e-12238
mesoderm5.06e-12448
mesoderm-derived structure5.06e-12448
presumptive mesoderm5.06e-12448
cardiovascular system1.83e-11110
circulatory system1.61e-10113
subdivision of trunk2.23e-08113
integument1.51e-0745
integumental system1.51e-0745
abdominal segment of trunk2.38e-0761
abdomen2.38e-0761
surface structure9.03e-0795
Disease
Ontology termp-valuen
ovarian cancer8.35e-0714


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
ATF3#467211.23158726300440.01119559039922220.0411261041013107
BRCA1#672210.09211532161190.0137713969900260.0484674281462957
CCNT2#90534.752151182721970.01386206996689490.048712675816707
E2F1#186944.907389214879320.001724022357361790.0106396721019032
E2F4#1874412.66806031528443.88145892637771e-050.000725959328101651
ELF1#199744.258097958807540.003041525565781240.0160756016480074
ETS1#211349.728760922202340.0001115955317418140.00154390326395328
GABPB1#255335.300762877136630.01012678824234270.0378496094636235
HEY1#2346244.040111043105710.00375304636917980.0185800345919022
HMGN3#932436.133910792512940.006640696683324720.0282895954033998
IRF1#365935.727872815172930.008097114790333330.0320020651499573
MAX#414934.839416631755340.01315737137836840.0466095485172449
MXI1#460137.471178721569470.003741314738550960.018630580745698
NFKB1#479045.488063424193840.001102199566301980.00767366312279263
NFYA#4800313.81918552487290.0006132411806734510.00508626871572066
NFYB#4801312.56984494015230.000811456397697350.0061864146812989
PAX5#507935.002174148383370.01196533174786410.0434841423347197
POU2F2#545249.106124057742520.000145395665174930.00188259085980715
SIN3A#2594245.408884726815140.001168172384885160.00795324352705481
SIX5#147912312.81503651659420.0007664471136930380.0060144992190989
SP2#6668213.07676524692230.008330036536614940.0328047015779611
TAF1#687243.343046285745290.008005664898701650.0321776337883121
TAF7#687938.574802053692940.00250055433515240.0140292986413635
TBP#690843.706770687096390.005296377814784350.024384958675642
USF1#739134.771124457905970.01370465887188020.0482927615871615
ZNF143#7702310.12565741417090.001534861610688180.00976304353241143



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.