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Coexpression cluster:C2524: Difference between revisions

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{{Coexpression_clusters
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3,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.000809519,0.000325197,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.00365225,0.13698,0.0874421,0.100355,0.167854,0.000543954,0.0583767,0.088258,0.00721029,0.0486914,0.175784,0.000282393,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.000132638,0.322827,0.000156623,0.359036,0.335984,0.0156657,0.208256,0.003871,0.0361085,0.00120337,0.000524161,0.40806,0.0120812,0.000371318,0.0457079,0.150674,0.251128,0.246177,0.0729297,0.00113802,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.00030277,0.125746,0.112897,0.398354,0.222091,5.6317e-09,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,1.42265,0.741427,0.534346,1.75218,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,1.37557,2.39977,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.911389,0.49475,0.0842336,3.15145,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.0946706,1.49501,0.822818,0.694903,0.173425,1.33034,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,1.28263,1.32819,0.336329,1.54953,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.353274,14.3026,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,1.88833,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,1.22649,0.12452,0.681522,0.988625,1.1313,1.31973,2.14757,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,1.58968,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.359498|tfbs_overrepresentation_jaspar=MA0003.1;0.0938548,MA0004.1;0.71247,MA0006.1;4.49931,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,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;1.30988,MA0050.1;0.69864,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;1.01899,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.841508,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;1.53734,MA0074.1;0.819248,MA0076.1;0.623864,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;1.54523,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;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.481,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.10559,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.577908,MA0150.1;3.7809,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.61785,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.06783,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;0.418966,MA0259.1;3.06353,MA0442.1;0}}
|full_id=C2524_Mast_neuroectodermal_teratocarcinoma_diffuse_chronic_acute_neuroblastoma
|id=C2524
}}

Latest revision as of 12:07, 17 September 2013


Full id: C2524_Mast_neuroectodermal_teratocarcinoma_diffuse_chronic_acute_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr1:150208291..150208309,-p6@ANP32E
Hg19::chr1:150208320..150208338,-p4@ANP32E
Hg19::chr1:150208343..150208360,-p5@ANP32E
Hg19::chr1:150208363..150208386,-p2@ANP32E


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><br>disease_data<br>

Disease
Ontology termp-valuen
hematologic cancer3.75e-2051
immune system cancer3.75e-2051
cancer2.26e-19235
disease of cellular proliferation6.69e-18239
leukemia4.83e-1739
myeloid leukemia4.07e-1331
organ system cancer5.34e-12137
lymphoma8.39e-0710


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.14.49931
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
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
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.53734
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.11.54523
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
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.13.7809
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.00910927
MA0102.21.75932
MA0258.10.418966
MA0259.13.06353
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
BCL3#602434.54710280373837.01262157705428e-073.15006961241278e-05
BCLAF1#9774421.65264761012184.54636978835329e-060.000141694513376852
BRCA1#672420.18423064322386.02116732184487e-060.000179464809910433
CHD2#1106410.34402283411698.73193255208051e-050.00129080580864365
E2F1#186944.907389214879320.001724022357361790.0106503709322435
E2F4#187439.501045236463330.001850751034728270.0109290165846424
ELF1#199744.258097958807540.003041525565781240.0160927042182799
EP300#203346.77394172622320.0004748459821442640.00434411698748816
FOS#235348.99795530889440.0001525147711168630.00194891596484449
FOXA1#3169411.08141974938556.62943068949433e-050.00107145018845574
GATA2#2624412.7449317335543.78864877853583e-050.00072178527869665
GTF2F1#2962412.73966087675773.79492332235515e-050.000718394049054649
HEY1#2346244.040111043105710.00375304636917980.0186126791277254
IRF1#365947.63716375356390.0002938853996185490.00307576883963941
IRF3#3661446.98195221148962.04940266214005e-071.10215017832773e-05
IRF4#3662421.91451268674414.33289161192893e-060.000136384227564269
MAX#414946.452555509007120.0005767613195645490.00485503147046038
MYC#460945.22228187160940.001344309395272740.00887866495496676
NFKB1#479045.488063424193840.001102199566301980.00768031895549855
NFYA#4800418.42558069983058.67100748407158e-060.00023436629157064
NFYB#4801416.75979325353651.26678572070404e-050.000311298432669669
NR3C1#2908414.9730233311731.98868032687801e-050.000443320778353922
NRF1#4899412.21027944771094.49717228915276e-050.000794049326638758
PAX5#507946.669565531177830.0005052774169483260.00443973314392278
PBX3#5090421.91451268674414.33289161192893e-060.000136425344304566
POU2F2#545249.106124057742520.000145395665174930.00188422606715529
REST#597849.650028716128020.0001152825614219170.0015705707581977
RFX5#5993412.04791082719514.74457429336527e-050.000826828958159145
SIN3A#2594245.408884726815140.001168172384885160.0079657061703461
SMARCB1#6598418.25271578115749.00423392720929e-060.000241497993611662
SP1#666745.69838137814090.0009482606065333980.0068441872484963
SP2#6668426.15353049384462.13562021071447e-067.74451524954198e-05
SPI1#668848.204323508522730.000220661881527680.00249520422746529
TAF1#687243.343046285745290.008005664898701650.0322334568162035
TAF7#6879411.43306940492395.85061525419808e-050.000969277294627527
TBP#690843.706770687096390.005296377814784350.0244301917939344
TCF12#6938410.63446490218647.8163066689251e-050.00120083443982917
TRIM28#10155418.59052504526258.36730015875654e-060.00023020876219188
USF1#739146.361499277207960.0006105011399140830.00508048833079577
WRNIP1#568974109.8199643493766.85077246696163e-095.35544779698358e-07
YY1#752844.911170749853860.00171871838055440.0106884142519186



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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