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Coexpression cluster:C2050: Difference between revisions

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{{Coexpression_clusters
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specification!0.0100654842000056!648$GO:0048146!positive regulation of fibroblast proliferation!0.0100654842000056!648$GO:0048144!fibroblast proliferation!0.0100654842000056!648$GO:0048145!regulation of fibroblast proliferation!0.0100654842000056!648$GO:0035282!segmentation!0.0156537320258094!648$GO:0009880!embryonic pattern 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131,0.454761,0.0202528,0.0295677,0.0232851,0.0508933,0.261657,0.00938391,0.466529,0.545655,0.438176,0.349112,0.0124698,0.385425,0.0531591,0.461541,0.0135171,0.382854,0.232374,0.0285097,0.611661,0.00716065,0.475047,0.557967,0.0690544,0.282281,0.245336,0.2536,0.246827,0.000225418,0.0362483,0.387134,0.559969,0.358813,0.668972,0.574252,0.0317703,0.346636,0.125876,0.348802,0.137708,0.0574793,0.447581,0.42505,0.254628,0.131374,6.15661e-05,0.416962,0.264955,0.378333,0.387805,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.00789472,0.242783,0.0947248,0.336551,0.210656,0.000212417,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.0582227,0.0265924,0.325254,0.266651,0.00871319,0.231754,0.249415,0.283107,0.285648,0.0191181,0.0140903,0.0433305,0.25563,0.0316941,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.00399713,0.315656,0.284866,0.0887542,0.267811,0.0651578,0.147872,0.189388,0.0480552,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.113839,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.0136966,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,9.4893e-07,0.0181825,0.00314989,0.31749,0.000654477,0.00505104,0.313858,0.223773,0.25788,0.181895,0.00336176,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.028353,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.00363197,0.139723,0.0708274,0.0710478,0.196248,0.00545806,0.0539258,0.0709978,0.401939,6.45892e-05,0.271338,0.00288876,0.00571761,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.0805224,0.0109087,0.00277084,0.184359,0.000828779,0.000735605,0.257476,0.291176,0.0123861,0.322827,0.0286371,0.0105454,0.335984,0.171704,0.00010286,0.265058,0.256405,0.0109327,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.0345639,0.246177,0.35674,0.0737175,0.318525,0.213257,0.287217,0.122782,1.94338e-05,0.289049,0.266974,0.125746,0.112897,0.398354,0.00218951,0.205977,0.34423,0.0936726,0.00908363,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.0229223|tfbs_overrepresentation_for_novel_motifs=1.44014,1.03954,2.42852,0.741427,0.534346,0.739643,3.1911,0.395818,0.392841,0.151681,0.706765,0.867962,2.45508,0.809319,0.532789,0.559384,1.05593,1.18793,3.47223,0.635753,0.581762,0.169357,0.731221,0.528529,2.59358,0.892087,0.316693,2.89941,1.33003,0.806311,1.63433,1.09415,0.433165,0.344471,0.49475,4.07742,1.23038,1.75478,0.463978,3.56383,0.493145,1.59701,0.183156,0.53106,0.648765,1.49501,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,1.8276,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,5.56341,1.32819,6.51544,0.321165,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,4.5493,1.84544,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,5.0756,1.37313,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,1.70537,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,1.58937,1.95303,1.23342,11.944,1.24902,1.76758,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,2.50192,0.997702,0.843324,0.423521,0.820225,0.0401987|tfbs_overrepresentation_jaspar=MA0003.1;3.49532,MA0004.1;2.8475,MA0006.1;3.33615,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;1.34758,MA0017.1;1.41335,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;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;0.69331,MA0058.1;3.66086,MA0059.1;3.65449,MA0060.1;0.393285,MA0061.1;1.68681,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;1.52107,MA0069.1;2.67291,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;3.86888,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;2.13662,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;1.02755,MA0089.1;0,MA0090.1;1.54523,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;4.51906,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;5.38386,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;2.4958,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;2.92476,MA0147.1;5.25242,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;7.08088,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;0.577908,MA0150.1;0.633493,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;3.02177,MA0160.1;1.78721,MA0161.1;0,MA0162.1;5.86746,MA0163.1;1.37853,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;8.74376,MA0102.2;1.75932,MA0258.1;1.88931,MA0259.1;1.1888,MA0442.1;0}}
|full_id=C2050_chronic_acute_prostate_large_Mast_nonsmall_breast
|id=C2050
}}

Latest revision as of 11:57, 17 September 2013


Full id: C2050_chronic_acute_prostate_large_Mast_nonsmall_breast



Phase1 CAGE Peaks

Hg19::chr10:22605374..22605387,+p2@COMMD3
p4@BMI1
Hg19::chr10:22605396..22605408,+p3@COMMD3
p9@BMI1
Hg19::chr10:22605437..22605446,+p14@BMI1
p4@COMMD3
Hg19::chr10:22610271..22610284,+p7@BMI1


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:0007379segment specification0.0100654842000056
GO:0048146positive regulation of fibroblast proliferation0.0100654842000056
GO:0048144fibroblast proliferation0.0100654842000056
GO:0048145regulation of fibroblast proliferation0.0100654842000056
GO:0035282segmentation0.0156537320258094
GO:0009880embryonic pattern specification0.0156537320258094
GO:0003002regionalization0.0416538239019674



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><br>disease_data<br>

Disease
Ontology termp-valuen
myeloid leukemia1.69e-1131
leukemia4.13e-0939
hematologic cancer1.13e-0751
immune system cancer1.13e-0751
disease of cellular proliferation3.55e-07239


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)
MA0003.13.49532
MA0004.12.8475
MA0006.13.33615
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.11.41335
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.13.66086
MA0059.13.65449
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.11.52107
MA0069.12.67291
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.13.86888
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.12.13662
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.11.54523
MA0091.10.715356
MA0092.10.673508
MA0093.14.51906
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.15.38386
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
MA0141.12.4958
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.12.92476
MA0147.15.25242
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.27.08088
MA0047.20.856092
MA0112.21.05083
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.13.02177
MA0160.11.78721
MA0161.10
MA0162.15.86746
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.28.74376
MA0102.21.75932
MA0258.11.88931
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
ATF3#467316.84738089450660.0003409986823655640.00346300674713897
CCNT2#90546.336201576962630.0006203100587215640.00511040168989678
CTBP2#1488347.03775025449611.60047699357395e-050.00037013334085888
E2F1#186944.907389214879320.001724022357361790.0106214706807756
E2F4#187439.501045236463330.001850751034728270.0109228406032993
E2F6#187645.017155731697390.00157802193473060.00994731004595177
EGR1#195844.988179094810140.001615011500076050.0101206159880261
ELF1#199744.258097958807540.003041525565781240.0160487995030883
ETS1#211337.296570691651750.00400857377511390.0191953891104595
GABPB1#255335.300762877136630.01012678824234270.037834715505546
HMGN3#932448.178547723350590.0002234570284440470.00247692937737931
MAX#414934.839416631755340.01315737137836840.0465858463364211
NFE2#4778357.90319548872188.59734810665173e-060.00023352365121212
NFKB1#479045.488063424193840.001102199566301980.00766242564767439
NR2C2#7182324.46095817893070.0001125906063438030.00155478650481825
PAX5#507935.002174148383370.01196533174786410.0434659924318322
REST#597837.237521537096020.004104697304192610.0195668666645019
SIN3A#2594245.408884726815140.001168172384885160.00793875297403831
TAF1#687243.343046285745290.008005664898701650.0321059686796522
TBP#690843.706770687096390.005296377814784350.0243388217801849
USF1#739146.361499277207960.0006105011399140830.00506917860959508
USF2#7392412.99219738506963.50833029870167e-050.000680041774435975
ZBTB7A#5134135.513931980906920.009038352821081090.0342162001696712
ZNF263#1012748.221841637010680.0002187871180958320.00247991185444005



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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