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Coexpression cluster:C1419: Difference between revisions

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{{Coexpression_clusters
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1;0,MA0159.1;0.875329,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.62636,MA0163.1;0.113377,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;1.69036,MA0099.2;0.629739,MA0079.2;0.0607789,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0}}
|full_id=C1419_Mesenchymal_Alveolar_Renal_Bronchial_Keratocytes_Trabecular_Pericytes
|id=C1419
}}

Latest revision as of 11:44, 17 September 2013


Full id: C1419_Mesenchymal_Alveolar_Renal_Bronchial_Keratocytes_Trabecular_Pericytes



Phase1 CAGE Peaks

Hg19::chr16:2255447..2255492,+p1@MLST8
Hg19::chr16:28857613..28857627,-p3@TUFM
Hg19::chr16:28857630..28857675,-p1@TUFM
Hg19::chr16:28857677..28857690,-p2@TUFM
Hg19::chr19:19249255..19249307,-p1@TMEM161A
Hg19::chr9:138392519..138392558,+p1@MRPS2


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

No GOStat results

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
trunk2.63e-12199
unilaminar epithelium3.15e-12148
epithelial tube8.05e-12117
cell layer1.70e-11309
mesenchyme2.70e-11160
entire embryonic mesenchyme2.70e-11160
epithelial vesicle2.97e-1178
epithelium4.11e-11306
organism subdivision7.39e-11264
subdivision of trunk4.69e-09112
multi-tissue structure8.62e-09342
anatomical cluster1.14e-08373
somite1.46e-0871
presomitic mesoderm1.46e-0871
presumptive segmental plate1.46e-0871
dermomyotome1.46e-0871
trunk paraxial mesoderm1.46e-0871
multilaminar epithelium1.94e-0883
dense mesenchyme tissue3.42e-0873
paraxial mesoderm3.57e-0872
presumptive paraxial mesoderm3.57e-0872
trunk mesenchyme3.83e-08122
trunk region element4.59e-08101
nephron epithelium7.29e-0815
renal tubule7.29e-0815
nephron tubule7.29e-0815
nephron7.29e-0815
uriniferous tubule7.29e-0815
nephrogenic mesenchyme7.29e-0815
parenchyma3.00e-0715
cortex of kidney6.81e-0712
renal parenchyma6.81e-0712
excretory tube7.52e-0716
kidney epithelium7.52e-0716
vasculature7.90e-0778
vascular system7.90e-0778
vessel8.45e-0768
Disease
Ontology termp-valuen
disease of cellular proliferation2.63e-13239
cancer3.53e-13235
hematologic cancer1.44e-0851
immune system cancer1.44e-0851
organ system cancer1.20e-07137
leukemia5.96e-0739


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)
MA0003.11.73878
MA0004.10.558729
MA0006.10.391183
MA0007.11.33289
MA0009.11.03681
MA0014.10.491287
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.12.77054
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.12.69832
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.11.35477
MA0061.11.93637
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.51617
MA0074.10.660398
MA0076.12.07987
MA0077.10.997832
MA0078.11.80244
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.11.94389
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.86787
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.718193
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.22.67639
MA0035.20.621793
MA0039.20.569061
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.21.12726
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.11.52275
MA0153.11.13732
MA0154.10.819655
MA0155.11.09123
MA0156.11.88357
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.21.69036
MA0099.20.629739
MA0079.20.0607789
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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#467414.97544968400585.47577390976406e-050.000927329903294712
BCLAF1#9774414.43509840674796.32554335174458e-050.00103240103471301
BRCA1#672310.09211532161190.002171044253359580.0125264731659368
CCNT2#90555.280167980802190.0005100943974832530.00446777497305883
CTCF#1066443.573504248716680.01316635007238510.046603417447632
E2F4#187436.334030157642220.008197175368374340.0323607937364448
EGR1#195854.156815912341780.001617966818864440.0101330556845397
ELF1#199764.258097958807540.0001677224776288830.00205258587310557
ELK4#2005410.8237877723120.0001950599973010460.00234969677717693
EP300#203355.644951438519330.0003688138931814860.00367018143782575
ETS1#211346.485840614801560.001410474068463220.0091701009235701
FOSL2#235538.465100302280850.003598315634615090.0182234742781285
GABPB1#255355.889736530151810.0003000175973670210.00309864891726803
GATA1#262336.780154071900220.006765763983348560.0287520192324601
GTF2F1#296248.493107251171770.0005001017319378380.00441132810657567
HEY1#2346264.040111043105710.0002298968555807510.00253192003585342
HMGN3#932456.815456436125490.0001472107253583660.00189996798636955
IRF1#365956.364303127969920.000205667514205090.00244004424810467
JUND#372744.663109294580680.004917643408260230.0229898728699772
MAX#414944.301703672671410.006644923910676370.0282983692834419
MEF2A#420539.371615454822030.002687399947103910.0148024557288954
MYC#460965.22228187160944.92821127172503e-050.000853986157304946
NFKB1#479054.57338618682820.00102196259371130.00724545185829978
NR3C1#290849.982015554115360.0002673219180401920.00286024319211143
PAX5#507966.669565531177831.13557256338955e-050.000289899933873969
PBX3#5090414.60967512449616.03404227507469e-050.000991175434360689
POLR2A#543062.147453176558070.01019570676818780.0380241900858008
POU2F2#545257.588436714785448.70203885493171e-050.00129058823625421
RAD21#588546.903355930304220.00111085151625360.00771281887421953
RFX5#599348.03194055146340.0006204615428381410.00511044030540005
SIN3A#2594254.507403939012610.001096110061208640.00766037464417618
SIX5#147912514.23892946288253.91539088341565e-060.000127548193534949
SMC3#9126410.02995522995520.0002623881821065520.00281004505240219
SP1#666765.69838137814092.91961319085282e-050.000609599124429184
SP2#6668521.79460874487054.74083619440168e-072.23837337842277e-05
SRF#672249.19811884144520.0003672404582485860.00365800917682633
STAT1#6772310.35329374859960.002016680459920930.0117206505594704
TAF1#687263.343046285745290.0007162474284635620.00573168072801364
TAF7#687947.622046269949280.000759279015141480.00596676757429353
TBP#690863.706770687096390.000385416472907960.00377780488165504
TCF7L2#693447.180117708758230.0009553297120679730.0068752535693679
TFAP2A#702038.259317186522480.003860738477055590.0190445714058761
TFAP2C#702247.206152406573480.0009421413689212550.00681887057718413
THAP1#55145420.91276306856751.46974095435158e-050.000349177150890637
USF1#739144.240999518138640.007005367750829420.0296028162059022
YY1#752854.092642291544880.001743365462849530.0107260881045386
ZBTB7A#5134156.126591089896580.0002476072821414750.00268925300952304
ZEB1#693538.444216008771930.003623843810733590.0183376434783277
ZNF143#7702613.50087655222791.64963374888971e-079.1156666190631e-06



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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