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Coexpression cluster:C2480: Difference between revisions

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{{Coexpression_clusters
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presentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,1.02453,0.392841,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,2.06579,0.316693,1.72987,0.537869,0.806311,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,1.23038,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.648765,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,1.5667,0.402607,0.248021,1.32819,0.336329,0.321165,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.17995,0.6318,0.291738,2.1528,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,2.16273,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,2.21427,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,2.90135,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,1.23342,2.26519,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,1.91838,2.44891|tfbs_overrepresentation_jaspar=MA0003.1;0.720743,MA0004.1;0.71247,MA0006.1;1.31813,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;1.86845,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;1.35734,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;0.248209,MA0058.1;1.47358,MA0059.1;1.47051,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;1.93422,MA0074.1;0.819248,MA0076.1;1.51122,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;6.68216,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;1.32557,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;1.46638,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;1.75643,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;2.51225,MA0035.2;0.778873,MA0039.2;0.257871,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;1.37305,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;0.533581,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;0.539587,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.869502,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0}}
|full_id=C2480_Mesenchymal_liposarcoma_skeletal_Alveolar_heart_left_Osteoblast
|id=C2480
}}

Latest revision as of 12:06, 17 September 2013


Full id: C2480_Mesenchymal_liposarcoma_skeletal_Alveolar_heart_left_Osteoblast



Phase1 CAGE Peaks

Hg19::chr19:1605424..1605474,-p1@UQCR11
Hg19::chr19:5680503..5680541,-p1@C19orf70
Hg19::chr19:5680543..5680554,-p2@C19orf70
Hg19::chr2:110970096..110970134,-p1@LINC00116


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><br>

Uber Anatomy
Ontology termp-valuen
epithelial vesicle1.95e-2478
multilaminar epithelium1.73e-2183
somite3.79e-2171
presomitic mesoderm3.79e-2171
presumptive segmental plate3.79e-2171
dermomyotome3.79e-2171
trunk paraxial mesoderm3.79e-2171
dense mesenchyme tissue7.75e-2173
paraxial mesoderm9.91e-2172
presumptive paraxial mesoderm9.91e-2172
mesenchyme2.14e-20160
entire embryonic mesenchyme2.14e-20160
skeletal muscle tissue1.20e-1962
striated muscle tissue1.20e-1962
myotome1.20e-1962
muscle tissue1.10e-1864
musculature1.10e-1864
musculature of body1.10e-1864
trunk mesenchyme4.29e-18122
trunk1.81e-16199
unilaminar epithelium3.02e-16148
organism subdivision3.18e-16264
epithelial tube6.20e-14117
vasculature8.37e-1378
vascular system8.37e-1378
splanchnic layer of lateral plate mesoderm1.43e-1283
multi-tissue structure4.76e-12342
epithelium7.58e-12306
cell layer1.21e-11309
vessel1.42e-1168
epithelial tube open at both ends3.07e-1159
blood vessel3.07e-1159
blood vasculature3.07e-1159
vascular cord3.07e-1159
compound organ1.41e-1068
artery1.72e-0942
arterial blood vessel1.72e-0942
arterial system1.72e-0942
circulatory system4.60e-09112
cardiovascular system4.69e-08109
primary circulatory organ7.64e-0827
systemic artery4.58e-0733
systemic arterial system4.58e-0733


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)
MA0003.10.720743
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.11.47051
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.93422
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.16.68216
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.75643
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.869502
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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#9774210.82632380506090.01202203816432580.043653766909256
CCNT2#90534.752151182721970.01386206996689490.048722512124673
ELF1#199744.258097958807540.003041525565781240.0160894437808148
ESR1#2099215.38430164807720.006065572629693510.026839060283547
ETS1#211337.296570691651750.00400857377511390.019205075301579
FOXA1#316938.311064812039090.002740138182109850.0150366378521107
FOXA2#3170318.47284781449890.0002594484187437260.00278198494919671
GABPB1#255335.300762877136630.01012678824234270.0378590935438872
HEY1#2346244.040111043105710.00375304636917980.0186056111335629
MAX#414946.452555509007120.0005767613195645490.00485424896881311
MXI1#460137.471178721569470.003741314738550960.0186350233679666
MYC#460945.22228187160940.001344309395272740.00887754213929114
NANOG#79923214.62238924050630.006698757715363760.0284892925452977
NR2C2#7182324.46095817893070.0001125906063438030.00155581507487966
NRF1#489939.157709585783180.002061953791733420.0119618059242819
PAX5#507946.669565531177830.0005052774169483260.00443823954151944
SETDB1#9869220.16001308900520.00356908685407640.0180859709826728
SIN3A#2594245.408884726815140.001168172384885160.00796362635150267
SREBF1#6720223.50292472024410.002638454900768240.0145836248415631
SRF#6722413.79717826216782.75840773062708e-050.000584470166319661
TAF1#687243.343046285745290.008005664898701650.0322235185707597
TBP#690843.706770687096390.005296377814784350.0244226412909295
TCF7L2#693438.077632422353010.002978381685834620.0158638925380907
ZBTB7A#5134135.513931980906920.009038352821081090.0342435075919933



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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