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Coexpression cluster:C685: Difference between revisions

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{{Coexpression_clusters
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lumen!0.000193512463740142!6150;79760;26517;51253;7329$GO:0043233!organelle lumen!0.000193512463740142!6150;79760;26517;51253;7329$GO:0000313!organellar ribosome!0.00299085559287461!6150;51253$GO:0005761!mitochondrial ribosome!0.00299085559287461!6150;51253$GO:0005739!mitochondrion!0.00299085559287461!6150;8192;26517;51253$GO:0030529!ribonucleoprotein complex!0.00411426777240149!6150;79760;51253;6142$GO:0044446!intracellular organelle part!0.00435327555541477!6150;79760;26517;51253;7329;6142$GO:0044422!organelle part!0.00435327555541477!6150;79760;26517;51253;7329;6142$GO:0043398!HLH domain binding!0.00526904509596138!7329$GO:0015934!large ribosomal subunit!0.00578115676195091!6150;6142$GO:0016604!nuclear body!0.00578115676195091!79760;7329$GO:0044429!mitochondrial part!0.00595076123775477!6150;26517;51253$GO:0043229!intracellular organelle!0.00840756935025863!6150;79760;8192;26517;51253;7329;6142;5425$GO:0043226!organelle!0.00840756935025863!6150;79760;8192;26517;51253;7329;6142;5425$GO:0008462!endopeptidase Clp activity!0.00948204782553061!8192$GO:0003735!structural constituent of ribosome!0.0100779420613185!6150;51253;6142$GO:0031980!mitochondrial lumen!0.0100779420613185!6150;51253$GO:0005759!mitochondrial matrix!0.0100779420613185!6150;51253$GO:0005840!ribosome!0.0109967187094474!6150;51253;6142$GO:0033279!ribosomal subunit!0.0123026770219084!6150;6142$GO:0042719!mitochondrial intermembrane space protein transporter complex!0.0123026770219084!26517$GO:0045039!protein import into mitochondrial inner membrane!0.0123026770219084!26517$GO:0032991!macromolecular complex!0.0123026770219084!6150;79760;26517;51253;6142$GO:0043231!intracellular membrane-bound organelle!0.0123026770219084!6150;79760;8192;26517;51253;7329;5425$GO:0043227!membrane-bound organelle!0.0123026770219084!6150;79760;8192;26517;51253;7329;5425$GO:0007007!inner mitochondrial membrane organization and biogenesis!0.0145791802178139!26517$GO:0000387!spliceosomal snRNP biogenesis!0.0157922524412481!79760$GO:0044424!intracellular part!0.0170194352354491!6150;79760;8192;26517;51253;7329;6142;5425$GO:0006412!translation!0.0197456222733237!6150;51253;6142$GO:0000795!synaptonemal complex!0.0197456222733237!7329$GO:0043681!protein import into mitochondrion!0.0197456222733237!26517$GO:0044444!cytoplasmic part!0.0197456222733237!6150;8192;26517;51253;6142$GO:0000315!organellar large ribosomal subunit!0.0202899870466734!6150$GO:0005762!mitochondrial large ribosomal subunit!0.0202899870466734!6150$GO:0005744!mitochondrial inner membrane presequence translocase complex!0.0202899870466734!26517$GO:0016605!PML body!0.0210389911498501!7329$GO:0043232!intracellular non-membrane-bound organelle!0.0227072814930335!6150;51253;7329;6142$GO:0043228!non-membrane-bound organelle!0.0227072814930335!6150;51253;7329;6142$GO:0005737!cytoplasm!0.0235427243499324!6150;79760;8192;26517;51253;6142$GO:0007006!mitochondrial membrane organization and biogenesis!0.0236577228278529!26517$GO:0006626!protein targeting to mitochondrion!0.0253827994317314!26517$GO:0044451!nucleoplasm part!0.02547497433364!79760;7329$GO:0009059!macromolecule biosynthetic process!0.0276297379577305!6150;51253;6142$GO:0005758!mitochondrial intermembrane space!0.029801120846867!26517$GO:0043170!macromolecule metabolic process!0.029801120846867!6150;79760;8192;51253;7329;6142;5425$GO:0005654!nucleoplasm!0.0303935112857104!79760;7329$GO:0031970!organelle envelope lumen!0.0305183546678942!26517$GO:0000794!condensed nuclear chromosome!0.0305183546678942!7329$GO:0044267!cellular protein metabolic process!0.0307394584809551!6150;8192;51253;7329;6142$GO:0044260!cellular macromolecule metabolic process!0.0318604052842707!6150;8192;51253;7329;6142$GO:0005842!cytosolic large ribosomal subunit (sensu Eukaryota)!0.0356935228895277!6142$GO:0019538!protein metabolic process!0.0356935228895277!6150;8192;51253;7329;6142$GO:0044249!cellular biosynthetic process!0.0405523371864651!6150;51253;6142$GO:0006839!mitochondrial transport!0.0413585107437134!26517$GO:0003887!DNA-directed DNA polymerase activity!0.0413585107437134!5425$GO:0005622!intracellular!0.0413585107437134!6150;79760;8192;26517;51253;7329;6142;5425$GO:0008430!selenium binding!0.0413585107437134!280636$GO:0031981!nuclear lumen!0.0415450125925671!79760;7329$GO:0000793!condensed chromosome!0.0415450125925671!7329$GO:0007059!chromosome segregation!0.0463138328989554!7329$GO:0044237!cellular metabolic process!0.0482158782953958!6150;79760;8192;51253;7329;6142;5425$GO:0044454!nuclear chromosome part!0.0498887043556976!7329$GO:0065002!intracellular protein transport across a membrane!0.0498887043556976!26517$GO:0000398!nuclear mRNA splicing, via spliceosome!0.0498887043556976!79760$GO:0000375!RNA splicing, via transesterification reactions!0.0498887043556976!79760$GO:0000377!RNA splicing, via transesterification reactions with bulged adenosine as 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|full_id=C685_Alveolar_Mesenchymal_Renal_Smooth_Hepatic_Fibroblast_Keratocytes
|id=C685
}}

Latest revision as of 11:28, 17 September 2013


Full id: C685_Alveolar_Mesenchymal_Renal_Smooth_Hepatic_Fibroblast_Keratocytes



Phase1 CAGE Peaks

Hg19::chr11:1968548..1968589,+p1@MRPL23
Hg19::chr11:57508973..57509018,+p3@C11orf31
Hg19::chr16:1359622..1359697,+p1@UBE2I
Hg19::chr19:13885252..13885293,+p1@C19orf53
Hg19::chr19:17970677..17970686,+p2@RPL18A
Hg19::chr19:18043810..18043835,+p1@CCDC124
Hg19::chr19:2427539..2427591,-p1@TIMM13
Hg19::chr19:45582497..45582551,+p1@GEMIN7
Hg19::chr19:6361517..6361640,+p1@CLPP
Hg19::chr1:54665832..54665877,+p1@MRPL37
Hg19::chr3:49059510..49059579,+p1@NDUFAF3
Hg19::chr7:44163126..44163155,-p1@POLD2


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:0031974membrane-enclosed lumen0.000193512463740142
GO:0043233organelle lumen0.000193512463740142
GO:0000313organellar ribosome0.00299085559287461
GO:0005761mitochondrial ribosome0.00299085559287461
GO:0005739mitochondrion0.00299085559287461
GO:0030529ribonucleoprotein complex0.00411426777240149
GO:0044446intracellular organelle part0.00435327555541477
GO:0044422organelle part0.00435327555541477
GO:0043398HLH domain binding0.00526904509596138
GO:0015934large ribosomal subunit0.00578115676195091
GO:0016604nuclear body0.00578115676195091
GO:0044429mitochondrial part0.00595076123775477
GO:0043229intracellular organelle0.00840756935025863
GO:0043226organelle0.00840756935025863
GO:0008462endopeptidase Clp activity0.00948204782553061
GO:0003735structural constituent of ribosome0.0100779420613185
GO:0031980mitochondrial lumen0.0100779420613185
GO:0005759mitochondrial matrix0.0100779420613185
GO:0005840ribosome0.0109967187094474
GO:0033279ribosomal subunit0.0123026770219084
GO:0042719mitochondrial intermembrane space protein transporter complex0.0123026770219084
GO:0045039protein import into mitochondrial inner membrane0.0123026770219084
GO:0032991macromolecular complex0.0123026770219084
GO:0043231intracellular membrane-bound organelle0.0123026770219084
GO:0043227membrane-bound organelle0.0123026770219084
GO:0007007inner mitochondrial membrane organization and biogenesis0.0145791802178139
GO:0000387spliceosomal snRNP biogenesis0.0157922524412481
GO:0044424intracellular part0.0170194352354491
GO:0006412translation0.0197456222733237
GO:0000795synaptonemal complex0.0197456222733237
GO:0043681protein import into mitochondrion0.0197456222733237
GO:0044444cytoplasmic part0.0197456222733237
GO:0000315organellar large ribosomal subunit0.0202899870466734
GO:0005762mitochondrial large ribosomal subunit0.0202899870466734
GO:0005744mitochondrial inner membrane presequence translocase complex0.0202899870466734
GO:0016605PML body0.0210389911498501
GO:0043232intracellular non-membrane-bound organelle0.0227072814930335
GO:0043228non-membrane-bound organelle0.0227072814930335
GO:0005737cytoplasm0.0235427243499324
GO:0007006mitochondrial membrane organization and biogenesis0.0236577228278529
GO:0006626protein targeting to mitochondrion0.0253827994317314
GO:0044451nucleoplasm part0.02547497433364
GO:0009059macromolecule biosynthetic process0.0276297379577305
GO:0005758mitochondrial intermembrane space0.029801120846867
GO:0043170macromolecule metabolic process0.029801120846867
GO:0005654nucleoplasm0.0303935112857104
GO:0031970organelle envelope lumen0.0305183546678942
GO:0000794condensed nuclear chromosome0.0305183546678942
GO:0044267cellular protein metabolic process0.0307394584809551
GO:0044260cellular macromolecule metabolic process0.0318604052842707
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.0356935228895277
GO:0019538protein metabolic process0.0356935228895277
GO:0044249cellular biosynthetic process0.0405523371864651
GO:0006839mitochondrial transport0.0413585107437134
GO:0003887DNA-directed DNA polymerase activity0.0413585107437134
GO:0005622intracellular0.0413585107437134
GO:0008430selenium binding0.0413585107437134
GO:0031981nuclear lumen0.0415450125925671
GO:0000793condensed chromosome0.0415450125925671
GO:0007059chromosome segregation0.0463138328989554
GO:0044237cellular metabolic process0.0482158782953958
GO:0044454nuclear chromosome part0.0498887043556976
GO:0065002intracellular protein transport across a membrane0.0498887043556976
GO:0000398nuclear mRNA splicing, via spliceosome0.0498887043556976
GO:0000375RNA splicing, via transesterification reactions0.0498887043556976
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0498887043556976



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>

Cell Type
Ontology termp-valuen
animal cell7.69e-29679
eukaryotic cell7.69e-29679
embryonic cell4.86e-27250
mesodermal cell1.23e-22121
somatic cell1.15e-17588
contractile cell1.78e-1759
non-terminally differentiated cell3.14e-17106
native cell9.66e-17722
muscle cell3.73e-1555
electrically responsive cell4.54e-1561
electrically active cell4.54e-1561
muscle precursor cell8.22e-1558
myoblast8.22e-1558
multi-potent skeletal muscle stem cell8.22e-1558
epithelial cell2.61e-14253
smooth muscle cell6.60e-1343
smooth muscle myoblast6.60e-1343
vascular associated smooth muscle cell3.07e-1032
meso-epithelial cell2.07e-0845
epithelial cell of nephron4.16e-0815
lining cell5.37e-0858
barrier cell5.37e-0858
endothelial cell8.55e-0836
ectodermal cell2.59e-0772
kidney cortical cell3.37e-0712
renal cortical epithelial cell3.37e-0712
kidney cell4.13e-0717
kidney epithelial cell4.13e-0717
blood vessel endothelial cell4.37e-0718
embryonic blood vessel endothelial progenitor cell4.37e-0718
Uber Anatomy
Ontology termp-valuen
epithelial vesicle1.97e-2178
somite8.46e-1871
presomitic mesoderm8.46e-1871
presumptive segmental plate8.46e-1871
dermomyotome8.46e-1871
trunk paraxial mesoderm8.46e-1871
multilaminar epithelium1.92e-1783
unilaminar epithelium4.05e-17148
paraxial mesoderm4.32e-1772
presumptive paraxial mesoderm4.32e-1772
dense mesenchyme tissue5.15e-1773
mesenchyme1.69e-14160
entire embryonic mesenchyme1.69e-14160
skeletal muscle tissue2.50e-1462
striated muscle tissue2.50e-1462
myotome2.50e-1462
vasculature7.72e-1478
vascular system7.72e-1478
epithelial tube7.98e-14117
trunk mesenchyme7.17e-13122
muscle tissue7.18e-1364
musculature7.18e-1364
musculature of body7.18e-1364
vessel1.55e-1268
trunk1.96e-12199
splanchnic layer of lateral plate mesoderm2.73e-1283
epithelial tube open at both ends3.92e-1259
blood vessel3.92e-1259
blood vasculature3.92e-1259
vascular cord3.92e-1259
organism subdivision2.84e-11264
artery4.76e-1142
arterial blood vessel4.76e-1142
arterial system4.76e-1142
cell layer7.03e-09309
epithelium2.32e-08306
circulatory system2.81e-08112
cardiovascular system3.05e-08109
parenchyma3.59e-0815
nephron epithelium4.16e-0815
renal tubule4.16e-0815
nephron tubule4.16e-0815
nephron4.16e-0815
uriniferous tubule4.16e-0815
nephrogenic mesenchyme4.16e-0815
systemic artery1.36e-0733
systemic arterial system1.36e-0733
cortex of kidney3.37e-0712
renal parenchyma3.37e-0712
blood vessel endothelium4.37e-0718
endothelium4.37e-0718
cardiovascular system endothelium4.37e-0718
excretory tube4.55e-0716
kidney epithelium4.55e-0716


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)
MA0003.12.56508
MA0004.11.55339
MA0006.10.552945
MA0007.10.305951
MA0009.10.756202
MA0014.13.50505
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.12.45278
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.10.357781
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.107116
MA0056.10
MA0057.10.3421
MA0058.11.94628
MA0059.12.71991
MA0060.11.13897
MA0061.10.605357
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.142258
MA0074.10.40963
MA0076.12.81657
MA0077.10.719193
MA0078.10.502027
MA0081.10.67392
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.11.76419
MA0089.10
MA0090.10.734839
MA0091.10.324543
MA0092.10.291716
MA0093.13.15425
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.10.535462
MA0105.10.890241
MA0106.11.14663
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.418165
MA0115.10.992167
MA0116.10.140463
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.567946
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.39221
MA0145.10.232227
MA0146.11.65937
MA0147.12.69996
MA0148.10.344198
MA0149.10.367947
MA0062.23.32063
MA0035.20.376007
MA0039.20.991464
MA0138.20.503176
MA0002.20.0954816
MA0137.20.595725
MA0104.23.65997
MA0047.20.440861
MA0112.20.216805
MA0065.20.452385
MA0150.10.723395
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.126936
MA0155.10.392911
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.867657
MA0160.10.357736
MA0161.10
MA0162.10.894383
MA0163.10.936674
MA0164.10.478818
MA0080.20.191221
MA0018.21.14938
MA0099.20.382887
MA0079.20.990475
MA0102.21.28978
MA0258.10.117513
MA0259.12.76095
MA0442.10



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#46759.359656052503650.0001062669261519880.00148117062596923
BCLAF1#9774610.82632380506097.02962092283241e-060.000202864487305801
BHLHE40#8553311.21795338674440.002092471767150690.0121193244725738
BRCA1#67258.410096101343240.0001760319087753190.00214048160677442
CCNT2#905126.336201576962632.3835512786724e-102.44054619601242e-08
CHD2#110686.896015222744572.63477013316703e-069.24018663323811e-05
CTCF#1066462.680128186537510.01385375074811150.0487277093719736
E2F1#186983.271592809919550.000663878513766830.00542695742793472
E2F4#187444.222686771761480.01146510237446740.0419405893830824
E2F6#187683.344770487798260.0005669246133432460.00483378559008533
EGR1#195883.325452729873420.0005908801842285490.00494597543966061
ELF1#1997113.903256462240241.12752972864617e-064.63432024124665e-05
ELK4#200545.411893886156010.004768663331909550.0224107649606849
ESR1#209937.692150824038620.006055325582880180.0268608625785943
ETS1#2113129.728760922202341.38661421527458e-121.92064458924485e-10
GABPB1#2553105.889736530151811.60938692426694e-078.91685734660555e-06
GATA1#262355.650128393250180.001110393113343090.00771219966512199
GTF2F1#296255.308192031982350.001473564228069450.00942711022452345
HEY1#23462124.040111043105715.2821272507085e-083.35763900144093e-06
HMGN3#932485.452365148900391.56099565068508e-050.000365699472323686
IRF1#365985.091442502375932.6084996882713e-050.000563219141913099
IRF3#3661311.74548805287240.001835389598021640.0108628728452784
IRF4#366259.131046952810050.0001194522965794710.00162124475665541
JUND#372774.08022063275810.0004970206459471620.0043941707645878
MAX#414984.301703672671419.11628330297238e-050.0013293710023445
MEF2A#420546.247743636548020.002834712427412020.0153722691316519
MXI1#460164.980785814379650.000552377387836090.0047162967632614
MYC#4609114.787091715641951.25420998476009e-077.18532290720566e-06
NANOG#79923512.18532436708863.02153395836246e-050.000620948416130297
NFKB1#479094.116047568145382.84752237283376e-050.000599944299165595
NRF1#489955.087616436546210.001784141756987680.0109460130974585
PAX5#507995.002174148383375.4522949797447e-060.000165292376020191
POLR2A#5430122.147453176558070.0001039292038462010.00145246381914805
POU2F2#545286.070749371828356.94099287930325e-060.000200528452371107
RDBP#7936225.60640066500420.002675327429872020.0147476259605407
REST#597854.020845298386680.005055691111689180.0235477556086922
RFX5#599377.027947982530471.47424002832586e-050.000349768637706326
RXRA#625646.691539046377760.002204954724098080.0127038818574546
SIN3A#25942104.507403939012612.12990021740309e-067.75338615564175e-05
SIX5#147912811.3911435703065.49078835696466e-083.46496945748056e-06
SMARCB1#659846.084238593719140.003122319756373760.0164096192147705
SMC3#912645.014977614977610.006261783977021150.0276288321409426
SP1#6667104.748651148450751.29045571010307e-065.15190764172227e-05
SP2#6668613.07676524692232.36047960027179e-068.379542113283e-05
SRF#672266.89858913108399.12062420494223e-050.0013298183321792
TAF1#6872123.343046285745295.12776278934579e-072.39721762737907e-05
TAF7#687987.622046269949281.22550270089133e-064.94552846129788e-05
TBP#6908123.706770687096391.48467551517722e-078.36343183007517e-06
TCF12#693865.317232451093210.0003865425927634440.00378245309150392
THAP1#55145513.07047691785472.15728753020685e-050.000475126428442162
USF1#739184.240999518138640.0001012169499783790.00142408689731805
USF2#739266.49609869253480.0001276632672591170.00169760936710911
YY1#7528124.911170749853865.07192667060765e-094.07780561625552e-07
ZBTB33#1000937.916181257495290.005590521092772240.025278972698101
ZBTB7A#5134184.901272871917263.46590017012669e-050.000679893215379154
ZEB1#693557.03684667397660.0004049017717332030.00389495589371317
ZNF143#77021213.50087655222792.71467069397623e-144.52903342824574e-12



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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