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Coexpression cluster:C2090: Difference between revisions

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{{Coexpression_clusters
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.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.0104945,0.0571822,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,1.42265,0.741427,1.32255,0.739643,0.821651,0.395818,0.392841,0.902371,0.706765,0.867962,0.341754,1.89595,0.532789,0.559384,1.05593,1.18793,0.356737,0.635753,0.581762,0.505745,1.73475,0.528529,0.632849,2.06579,0.316693,0.728867,0.537869,0.806311,0.682839,1.09415,0.433165,0.911389,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,1.31558,0.314427,2.53981,1.92371,2.79175,0.515703,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,1.92893,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,3.55571,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,4.58731,0.716653,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,1.32435,0.456994,0.354969,1.15558,0.939507,0.272395,2.04634,1.1057,1.14983,1.05974,2.24329,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,2.93345,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,2.52313,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,1.811,0.963351,2.1895,0.661255,0.437774,2.68745,0.175846,1.24902,0.383416,0.824835,1.65997,2.11789,1.28873,0.632914,1.4628,1.44595,2.75236,1.07918,0.604379,0.997702,1.96584,0.423521,0.820225,1.91266|tfbs_overrepresentation_jaspar=MA0003.1;0.233555,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.244769,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;2.48281,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;2.32784,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;2.70453,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;2.80362,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,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;0.0343867,MA0074.1;0.819248,MA0076.1;6.35561,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;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,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;0.602484,MA0142.1;1.00381,MA0143.1;2.05538,MA0144.1;1.92815,MA0145.1;1.70272,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;2.51225,MA0035.2;1.83323,MA0039.2;0.483275,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;2.35208,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;4.85059,MA0065.2;1.7213,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;2.36058,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;1.78721,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.00910927,MA0102.2;1.75932,MA0258.1;6.11668,MA0259.1;1.1888,MA0442.1;0}}
|full_id=C2090_epidermoid_pharyngeal_osteosarcoma_large_pagetoid_acute_mucinous
|id=C2090
}}

Latest revision as of 11:58, 17 September 2013


Full id: C2090_epidermoid_pharyngeal_osteosarcoma_large_pagetoid_acute_mucinous



Phase1 CAGE Peaks

Hg19::chr11:102962818..102962842,-p2@DCUN1D5
Hg19::chr11:102962853..102962864,-p3@DCUN1D5
Hg19::chr11:102962874..102962927,-p1@DCUN1D5
Hg19::chr11:102962929..102962940,-p4@DCUN1D5


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>

Cell Type
Ontology termp-valuen
animal cell2.24e-23679
eukaryotic cell2.24e-23679
epithelial cell5.36e-23253
embryonic cell1.27e-20250
native cell2.00e-12722
endo-epithelial cell2.30e-1042
squamous epithelial cell2.58e-1063
endodermal cell1.72e-0958
mesodermal cell2.56e-08121
Uber Anatomy
Ontology termp-valuen
unilaminar epithelium3.64e-07148
Disease
Ontology termp-valuen
disease of cellular proliferation1.76e-24239
cancer6.36e-24235
cell type cancer5.94e-14143
carcinoma2.94e-11106
organ system cancer1.07e-10137


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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.12.48281
MA0025.11.34373
MA0027.12.83281
MA0028.12.32784
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.12.70453
MA0046.11.19471
MA0048.10.25531
MA0050.12.80362
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
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
MA0073.10.0343867
MA0074.10.819248
MA0076.16.35561
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
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
MA0141.10.602484
MA0142.11.00381
MA0143.12.05538
MA0144.11.92815
MA0145.11.70272
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.21.83323
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.22.35208
MA0104.20.392359
MA0047.20.856092
MA0112.24.85059
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.11.78721
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.00910927
MA0102.21.75932
MA0258.16.11668
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
BATF#10538424.35780179230362.83869198020713e-069.77159366251986e-05
BCLAF1#9774421.65264761012184.54636978835329e-060.000141399140656888
CCNT2#90546.336201576962630.0006203100587215640.00511201469445447
CEBPB#105147.971147625824820.0002476385788090830.00267457347799812
E2F1#186944.907389214879320.001724022357361790.0106239775183212
E2F6#187645.017155731697390.00157802193473060.00994911155094048
ELF1#199744.258097958807540.003041525565781240.0160520434870194
ELK4#2005416.2356816584681.43847748454449e-050.000342841510744733
EP300#203346.77394172622320.0004748459821442640.00433462455459879
ETS1#211349.728760922202340.0001115955317418140.00154288135287044
FOSL2#2355416.93020060456171.2165416097647e-050.000303015476227559
GABPB1#255347.067683836182170.0004006876864423170.00389713366402953
GATA1#2623413.56030814380042.95627390049268e-050.00061296464144045
GATA2#2624412.7449317335543.78864877853583e-050.000719553900311882
GATA3#2625427.2365163572061.81561517799785e-066.743279999108e-05
GTF2B#2959431.94382993432429.59435337635006e-074.07990501739668e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000716316639912254
HEY1#2346244.040111043105710.00375304636917980.0185483820627849
HMGN3#932448.178547723350590.0002234570284440470.00247719229313957
IRF1#365947.63716375356390.0002938853996185490.00306900282479368
JUN#3725412.51282919233634.07770316866756e-050.00074154839148959
JUND#372746.994663941871030.000417684217818580.00390917842322383
MAX#414946.452555509007120.0005767613195645490.00484448893791233
MXI1#460149.96157162875930.0001015224754950450.00142092010429201
MYC#460945.22228187160940.001344309395272740.0088557038559915
NFKB1#479045.488063424193840.001102199566301980.00766446637625756
NFYA#4800418.42558069983058.67100748407158e-060.000234184471328925
NFYB#4801416.75979325353651.26678572070404e-050.00031093262957605
NR2C2#7182432.61461090524098.82887529809196e-073.81497272344819e-05
PAX5#507946.669565531177830.0005052774169483260.00443078657839347
REST#597849.650028716128020.0001152825614219170.00156811610215467
SETDB1#9869440.32002617801053.77887289069054e-071.8502658501211e-05
SIN3A#2594245.408884726815140.001168172384885160.00794081981938433
SP1#666745.69838137814090.0009482606065333980.00683002686108562
SRF#6722413.79717826216782.75840773062708e-050.000583404910852493
STAT3#6774410.51946499715428.16377768286615e-050.001228554434324
TAF1#687243.343046285745290.008005664898701650.032117068196347
TAF7#6879411.43306940492395.85061525419808e-050.000967129481692297
TBP#690843.706770687096390.005296377814784350.0243441775635183
TFAP2A#7020416.5186343730451.34240829060362e-050.000325894419949678
TFAP2C#7022410.80922860986027.32289634782688e-050.0011435346466368
THAP1#55145431.36914460285131.03171810326891e-064.30834094311483e-05
TRIM28#10155418.59052504526258.36730015875654e-060.000229724621787691
YY1#752844.911170749853860.00171871838055440.0106604839616772
ZEB1#6935416.88843201754391.22862303393937e-050.000303563191487092



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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