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Coexpression cluster:C2865: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,1.92131,0.395818,0.392841,1.44778,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,1.18793,0.356737,0.635753,0.581762,0.975621,0.731221,0.528529,2.59358,2.06579,0.316693,0.728867,0.537869,0.806311,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,1.31558,1.59529,1.49501,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,1.03936,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,1.69485,1.02594,0.844168,0.399165,1.27559,0.716653,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,1.15724,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,0.575476,1.70537,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,4.72148,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,2.16698,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,1.811,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,1.96584,0.423521,0.820225,0.156682
|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;0.532262,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;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.791759,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;0.00636811,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;0.640115,MA0091.1;2.85665,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;3.36866,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;2.00595,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;0.912459,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;1.92815,MA0145.1;1.08195,MA0146.1;0.8309,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.257871,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;1.37305,MA0104.2;0.392359,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;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;1.1691,MA0160.1;0.756582,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;0.0626799,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:58, 22 January 2013


Full id: C2865_cervix_uterus_lung_rectum_rectal_Prostate_stomach



Phase1 CAGE Peaks

Hg19::chr6:56407223..56407227,-p1@BC038763
Hg19::chr6:56407600..56407638,-p11@DST
Hg19::chr6:56407645..56407662,-p25@DST
Hg19::chr6:56407665..56407745,-p7@DST


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:0045104intermediate filament cytoskeleton organization and biogenesis0.00772695160720593
GO:0045103intermediate filament-based process0.00772695160720593
GO:0005200structural constituent of cytoskeleton0.0260140704109266
GO:0007050cell cycle arrest0.0260140704109266
GO:0045786negative regulation of progression through cell cycle0.0463617096432356



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.06e-18114
anatomical cluster3.11e-15373
organ system subdivision2.67e-13223
multi-cellular organism8.50e-11656
subdivision of digestive tract1.44e-09118
multi-tissue structure1.63e-09342
organ3.17e-09503
digestive system3.76e-09145
digestive tract3.76e-09145
primitive gut3.76e-09145
anatomical group3.48e-08625
anatomical conduit4.02e-08240
anatomical system4.84e-08624
endoderm-derived structure9.11e-08160
endoderm9.11e-08160
presumptive endoderm9.11e-08160


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
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
MA0073.10.00636811
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
MA0090.10.640115
MA0091.12.85665
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.13.36866
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.12.00595
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
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.92815
MA0145.11.08195
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BHLHE40#8553333.65386016023314.35025573591721e-050.00077545034784683
CCNT2#90546.336201576962630.0006203100587215640.00513470414700971
CEBPB#105147.971147625824820.0002476385788090830.00268624070754485
CTCF#1066445.360256373075030.001211145381643620.00819718829067969
E2F1#186944.907389214879320.001724022357361790.0106775289675922
E2F4#187439.501045236463330.001850751034728270.0109321071950673
ELF1#199744.258097958807540.003041525565781240.0161237444071177
EP300#203335.08045629466740.01144298405398240.0419198783406596
FOS#235348.99795530889440.0001525147711168630.00195393647947425
FOXA1#3169411.08141974938556.62943068949433e-050.00107327718459169
FOXA2#3170318.47284781449890.0002594484187437260.00278227060326276
GATA1#2623413.56030814380042.95627390049268e-050.000615040418114651
GTF2F1#296239.554745657568240.001820362319304780.0109049455240262
HDAC2#3066413.41562023662633.0859005065161e-050.000628487447347962
HEY1#2346244.040111043105710.00375304636917980.0186569760460169
HMGN3#932448.178547723350590.0002234570284440470.00248589993541413
IRF1#365935.727872815172930.008097114790333330.0320202412566309
JUN#372539.384621894252250.001918994502030470.0112898753265863
JUNB#3726322.95797449486590.0001359772504018780.00177983808180496
JUND#372735.245997956403270.01043432751748420.0387177834007864
MAX#414946.452555509007120.0005767613195645490.00486365566847008
MYC#460945.22228187160940.001344309395272740.00889666871129139
NANOG#79923321.93358386075950.0001557535816382770.00196600777286923
PAX5#507935.002174148383370.01196533174786410.0435250350881257
RAD21#5885410.35503389545638.6948481184721e-050.00129892896959678
REST#597849.650028716128020.0001152825614219170.00157529706036158
SIN3A#2594245.408884726815140.001168172384885160.00797977341258557
SMARCB1#6598418.25271578115749.00423392720929e-060.000242119770114266
SMC3#9126311.28369963369960.001115802366868050.00766011196958738
TAF1#687243.343046285745290.008005664898701650.0323256770290161
TBP#690843.706770687096390.005296377814784350.0244983569953613
TCF12#6938410.63446490218647.8163066689251e-050.00120260349469044
TCF7L2#693438.077632422353010.002978381685834620.0158727971060306
TFAP2C#7022410.80922860986027.32289634782688e-050.00114851474946793
TRIM28#10155418.59052504526258.36730015875654e-060.000230938811120606
USF1#739134.771124457905970.01370465887188020.0483400610598228
USF2#739239.74414803880220.001718341848410070.0107269518413688
YY1#752844.911170749853860.00171871838055440.0107056258690715
ZNF263#1012748.221841637010680.0002187871180958320.00249862305377918



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2865&oldid=2571376"