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Coexpression cluster:C895: Difference between revisions

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{{Coexpression_clusters
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87061,0.51292,0.4002,0.147122,0.270138,0.589559,0.524278,0.929597,1.9587,0.99088,0.503626,0.273964,1.18995,0.67562,1.18788,0.804523,0.5152,0.488493,0.700946,2.2681,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,1.37801,0.988898,0.784625,0.367887,0.105027,1.63758,0.750836,0.341765,0.141333,0.699894,0.532172,0.498312,0.937974,0.358653,0.0591186,0.320664,1.4924,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,0.207949,0.136404,0.82268,0.619373,1.0179,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.917554,1.30109,0.315525,0.814459,0.300169,0.41935,1.12352,1.22295,1.39526,1.00897,0.664981,0.577715,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,0.307751,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.971016,1.07409,1.3062,1.39433,0.912334,1.47041,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,1.31632,0.183544,0.510589,0.51231|tfbs_overrepresentation_jaspar=MA0003.1;1.0633,MA0004.1;0.415381,MA0006.1;2.07537,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;1.50001,MA0017.1;0.815464,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;7.00862,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;0.514558,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;0.948258,MA0050.1;0.403421,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;0.693769,MA0056.1;0,MA0057.1;0.539841,MA0058.1;0.325084,MA0059.1;0.323879,MA0060.1;0.9464,MA0061.1;0.432181,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;0.354973,MA0069.1;0.856287,MA0070.1;0.845142,MA0071.1;0.47692,MA0072.1;0.840664,MA0073.1;0.0176541,MA0074.1;2.19307,MA0076.1;5.43197,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.865814,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;1.92658,MA0089.1;0,MA0090.1;0.353576,MA0091.1;0.417885,MA0092.1;0.381858,MA0093.1;0.26836,MA0095.1;0,MA0098.1;0,MA0100.1;0.528088,MA0101.1;0.746654,MA0103.1;0.257174,MA0105.1;0.854766,MA0106.1;1.366,MA0107.1;0.592696,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.959847,MA0113.1;0.57094,MA0114.1;1.10197,MA0115.1;1.11137,MA0116.1;0.599942,MA0117.1;0.908433,MA0119.1;0.83188,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;1.51455,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.129876,MA0140.1;0.474342,MA0141.1;0.861836,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;1.0529,MA0145.1;0.706237,MA0146.1;1.3662,MA0147.1;0.607251,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;8.77016,MA0035.2;0.473658,MA0039.2;1.17223,MA0138.2;0.608783,MA0002.2;0.152495,MA0137.2;0.780538,MA0104.2;0.943754,MA0047.2;0.542971,MA0112.2;0.674448,MA0065.2;0.408099,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.062786,MA0155.1;0.359913,MA0156.1;1.43134,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.212043,MA0160.1;0.453945,MA0161.1;0,MA0162.1;1.85802,MA0163.1;0.101664,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;3.20763,MA0102.2;1.41188,MA0258.1;0.532421,MA0259.1;0.624802,MA0442.1;0}}
|full_id=C895_Mesenchymal_Renal_Alveolar_Fibroblast_Pericytes_Trabecular_Osteoblast
|id=C895
}}

Latest revision as of 11:33, 17 September 2013


Full id: C895_Mesenchymal_Renal_Alveolar_Fibroblast_Pericytes_Trabecular_Osteoblast



Phase1 CAGE Peaks

Hg19::chr12:53693466..53693537,+p1@C12orf10
Hg19::chr16:2933231..2933309,+p1@FLYWCH2
Hg19::chr17:42092313..42092389,-p1@TMEM101
Hg19::chr19:17530838..17530885,+p1@FAM125A
Hg19::chr19:17530888..17530938,+p2@FAM125A
Hg19::chr19:49314305..49314316,-p2@BCAT2
Hg19::chr19:7985198..7985257,+p1@SNAPC2
Hg19::chr3:49055991..49056026,-p1@DALRD3
Hg19::chr9:131133622..131133661,+p1@URM1


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:0009098leucine biosynthetic process0.00653479335923701
GO:0006549isoleucine metabolic process0.00653479335923701
GO:0006550isoleucine catabolic process0.00653479335923701
GO:0009082branched chain family amino acid biosynthetic process0.00980074736638496
GO:0006551leucine metabolic process0.00980074736638496
GO:0009301snRNA transcription0.00980074736638496
GO:0006420arginyl-tRNA aminoacylation0.0130647783764645
GO:0004814arginine-tRNA ligase activity0.0130647783764645
GO:0004084branched-chain-amino-acid transaminase activity0.0130647783764645
GO:0009083branched chain family amino acid catabolic process0.017633557274085
GO:0006520amino acid metabolic process0.0261103347061558
GO:0009081branched chain family amino acid metabolic process0.0261103347061558
GO:0007595lactation0.0295901655496141
GO:0006519amino acid and derivative metabolic process0.0295901655496141
GO:0006383transcription from RNA polymerase III promoter0.0346414888684331
GO:0009308amine metabolic process0.0346414888684331
GO:0006807nitrogen compound metabolic process0.036932758980158
GO:0019752carboxylic acid metabolic process0.0449410093543494
GO:0006082organic acid metabolic process0.0449410093543494
GO:0008483transaminase activity0.0449410093543494



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
embryonic cell5.25e-24250
mesodermal cell7.26e-20121
non-terminally differentiated cell9.86e-19106
contractile cell1.53e-1659
animal cell1.90e-16679
eukaryotic cell1.90e-16679
electrically responsive cell4.09e-1561
electrically active cell4.09e-1561
muscle cell2.97e-1455
muscle precursor cell5.79e-1458
myoblast5.79e-1458
multi-potent skeletal muscle stem cell5.79e-1458
somatic cell2.65e-12588
smooth muscle cell3.44e-1243
smooth muscle myoblast3.44e-1243
epithelial cell1.15e-10253
native cell3.39e-09722
vascular associated smooth muscle cell5.26e-0932
ectodermal cell1.65e-0872
meso-epithelial cell4.47e-0845
fibroblast4.94e-0876
epithelial cell of nephron7.13e-0815
kidney cell1.54e-0717
kidney epithelial cell1.54e-0717
neurectodermal cell2.01e-0759
endothelial cell2.38e-0736
lining cell7.32e-0758
barrier cell7.32e-0758
Uber Anatomy
Ontology termp-valuen
epithelial vesicle1.39e-1778
multilaminar epithelium1.38e-1483
somite2.14e-1471
presomitic mesoderm2.14e-1471
presumptive segmental plate2.14e-1471
dermomyotome2.14e-1471
trunk paraxial mesoderm2.14e-1471
dense mesenchyme tissue4.56e-1473
paraxial mesoderm7.92e-1472
presumptive paraxial mesoderm7.92e-1472
vasculature1.31e-1378
vascular system1.31e-1378
unilaminar epithelium1.62e-13148
organism subdivision1.85e-12264
skeletal muscle tissue3.18e-1262
striated muscle tissue3.18e-1262
myotome3.18e-1262
mesenchyme7.02e-12160
entire embryonic mesenchyme7.02e-12160
muscle tissue3.89e-1164
musculature3.89e-1164
musculature of body3.89e-1164
splanchnic layer of lateral plate mesoderm3.99e-1183
trunk4.21e-11199
vessel5.16e-1168
epithelial tube1.06e-10117
epithelial tube open at both ends3.16e-1059
blood vessel3.16e-1059
blood vasculature3.16e-1059
vascular cord3.16e-1059
cell layer6.98e-10309
artery8.30e-1042
arterial blood vessel8.30e-1042
arterial system8.30e-1042
epithelium1.81e-09306
trunk mesenchyme4.08e-09122
anatomical cluster3.47e-08373
multi-tissue structure4.77e-08342
cardiovascular system5.62e-08109
nephron epithelium7.13e-0815
renal tubule7.13e-0815
nephron tubule7.13e-0815
nephron7.13e-0815
uriniferous tubule7.13e-0815
nephrogenic mesenchyme7.13e-0815
parenchyma2.27e-0715
circulatory system2.65e-07112
excretory tube4.60e-0716
kidney epithelium4.60e-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)
MA0003.11.0633
MA0004.10.415381
MA0006.12.07537
MA0007.10.397529
MA0009.10.870971
MA0014.11.50001
MA0017.10.815464
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.17.00862
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.948258
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.693769
MA0056.10
MA0057.10.539841
MA0058.10.325084
MA0059.10.323879
MA0060.10.9464
MA0061.10.432181
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.354973
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.0176541
MA0074.12.19307
MA0076.15.43197
MA0077.10.832987
MA0078.10.607575
MA0081.10.865814
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.11.92658
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.746654
MA0103.10.257174
MA0105.10.854766
MA0106.11.366
MA0107.10.592696
MA0108.20.707575
MA0109.10
MA0111.10.959847
MA0113.10.57094
MA0114.11.10197
MA0115.11.11137
MA0116.10.599942
MA0117.10.908433
MA0119.10.83188
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.11.51455
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.861836
MA0142.10.679161
MA0143.10.571113
MA0144.11.0529
MA0145.10.706237
MA0146.11.3662
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.28.77016
MA0035.20.473658
MA0039.21.17223
MA0138.20.608783
MA0002.20.152495
MA0137.20.780538
MA0104.20.943754
MA0047.20.542971
MA0112.20.674448
MA0065.20.408099
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.359913
MA0156.11.43134
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.11.85802
MA0163.10.101664
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.23.20763
MA0102.21.41188
MA0258.10.532421
MA0259.10.624802
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
BCLAF1#9774614.43509840674797.2101191630514e-073.21527598321915e-05
CCNT2#90564.224134384641760.000840335063808250.0063381059961775
CHD2#110655.746679352287140.0007610423709220.00597612813358817
E2F1#186973.816858278239470.0003547577053237570.00355264550640597
E2F6#187673.902232235764630.0003067423599492730.00316216220814749
EGR1#195873.8796948515190.0003186557858542290.00326243423378393
ELF1#199794.258097958807542.17161853202127e-067.8234449074084e-05
ELK4#200559.019823143593359.04446507305493e-050.00132018852238265
ETS1#211388.647787486402081.01768374293787e-075.96441483887138e-06
FOS#235343.999091248397510.01211384991200480.0439291101027732
FOSL2#235535.643400201520560.01321558041905920.0467586558501971
GABPB1#255375.497087428141693.13640621886058e-050.000632849940285124
HEY1#2346294.040111043105713.4850025352467e-060.000115950997062323
HMGN3#932476.361092673717131.17234969197953e-050.000298050217820474
IRF1#365986.788590003167916.86477102732501e-073.09831383458426e-05
MAX#414964.301703672671410.0007597563851723660.00596782469246516
MXI1#460166.64104775250626.5621720999513e-050.0010635423524935
MYC#460963.48152124773960.002423669811459260.0136566307763147
NFYB#480135.586597751178820.01358500277111940.0479487700038166
NRF1#489968.140186298473942.03653511272495e-050.00045157896101461
POLR2A#543092.147453176558070.001029412892608020.0072859076369673
POLR3A#11128275.36269113149850.0003081865015822640.00317235265511039
REST#597844.288901651612450.009457025945962830.035662839240672
RFX5#599368.03194055146342.20018388626684e-050.000482538859508236
SIN3A#2594284.807897534946791.02597602607548e-050.000267946762158783
SIX5#147912611.3911435703062.88946640975924e-069.93000929150529e-05
SP1#666753.16576743230050.01119721686091820.0411190622973782
SRF#672257.665099034537670.0001964447812163450.00236147519629994
STAT3#677444.6753177765130.006946825355778890.0293815856045111
TAF1#687282.971596698440260.0004233749951234810.00395889167478747
TBP#690872.883043867741630.002187802002126050.0126161919993397
TCF7L2#693455.983431423965190.0006305154397321440.0051842546063758
THAP1#55145413.94184204571170.0001142867648675440.00156435064692023
TRIM28#1015536.196841681754170.0102278065029780.0380813505655799
USF1#739153.534166265115530.00692296754081810.0293091656327983
YY1#752884.365485110981212.17675027117712e-050.000479109845250721
ZBTB7A#5134175.718151683903472.40589727322203e-050.000524242656620145
ZEB1#693547.505969785575050.001215903324635610.00818272616287248
ZNF143#770257.500486973459950.0002177465175801830.00249164331648479



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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