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Coexpression cluster:C373: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;14:2.58770997320863:0.000278132429679436:0.00296165098116748!CTCFL#140690;6:4.0854774535809:0.00291795808612357:0.015766393737734!ESR1#2099;6:6.3659179233423:0.00029309653809919:0.00310831735809721!MAX#4149;15:3.33752871155541:6.20854210030502e-06:0.000183374979755021!RAD21#5885;12:4.28484161191296:7.02264511834706e-06:0.000202775237355557!RXRA#6256;5:3.46114088605746:0.0133687500993669:0.0472397784418657!SMC3#9126;7:3.63153551429414:0.0024278138891458:0.0136770297625815!ZEB1#6935;6:3.49415834845735:0.00627460375203944:0.0276830576740135
|tf_chipseq_enrich=CTCF#10664;14:2.58770997320863:0.000278132429679436:0.00296165098116748!CTCFL#140690;6:4.0854774535809:0.00291795808612357:0.015766393737734!ESR1#2099;6:6.3659179233423:0.00029309653809919:0.00310831735809721!MAX#4149;15:3.33752871155541:6.20854210030502e-06:0.000183374979755021!RAD21#5885;12:4.28484161191296:7.02264511834706e-06:0.000202775237355557!RXRA#6256;5:3.46114088605746:0.0133687500993669:0.0472397784418657!SMC3#9126;7:3.63153551429414:0.0024278138891458:0.0136770297625815!ZEB1#6935;6:3.49415834845735:0.00627460375203944:0.0276830576740135
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7,0.0962976,0.0281206,0.00137058,0.552381,0.62873,0.0288037,0.00985885,5.63248e-07,0.425981,3.02272e-07,2.64774e-11,0.760214,0.132529,0.140969,0.403971,0.0117992,0.193937,0.533214,0.508665,0.614023,0.420656,0.543758,0.428199,0.337932,0.288093,0.318376,0.540347,0.835486,0.88577,0.0855693,0.554391,2.76524e-07,0.277551,0.918535,0.220503,0.322452,0.448161,4.32442e-10,0.00193439,0.67184,0.675904,0.000239725,0.244611,0.000418391,0.000176821,0.3182,0.587136,0.421393,0.192102,0.314443,0.0915958,0.149713,0.742902,0.0110632,0.735705,0.961987,0.178821,0.277489,0.0512007,0.580362,0.555619,0.457081,0.0624726,0.261202,0.061321,0.593683,5.01675e-08,0.00206323,0.374018,0.618506,0.505138,0.161288,0.541196,0.103183,0.383859,0.395101,0.449247,0.68119,0.0946499,0.636524,0.391164,0.460416,0.176545,0.613467,0.77773,0.284366,0.525299,0.0408694,0.428183,0.991683,0.421914,0.00017144,0.0361683,0.873379,0.849595,0.00039819,0.436271,0.375843,0.212764,0.45506,0.555742,0.453867,0.00086412,0.231775,0.00018331,0.295481,0.142312,0.554977,0.974183,0.00917094,0.653967,0.424904,0.10116,0.490331,0.00570176,5.32188e-08,0.00327671,0.892102,0.532193,0.363464,0.311514,0.505588,0.105978,0.00622854,0.310229,0.747249,0.0740439,0.414769,0.690465,0.610585,0.839502,0.657599,0.0370251,0.0003105,0.0165607,0.53416,0.00015649,0.0235738,0.0202878,0.217188,0.645042,0.000181155,0.547781,0.0222814,0.213853,0.465098,0.87164,0.460351,0.0218615,0.487078,0.513825,0.606188,0.451501,0.0664549,0.21102,0.260713,0.224005,0.0104989,0.0602246,0.759911,0.109258,0.0244041,0.00671895,0.0359847,0.0544095,0.0997504,0.00676962,0.32117,0.864249,0.284677,0.618359,0.0317318,0.00763276,0.0611992,0.00391225,1.91068e-09,0.652833,0.322827,0.221396,0.0347583,0.0144018,0.970168,0.0339941,0.328977,0.00157624,0.861497,0.00682418,2.61591e-05,0.0252629,0.445019,0.0605424,0.566077,0.425024,0.921134,4.79568e-09,0.715573,0.299017,0.00253399,0.156529,0.349178,0.0137257,0.425173,0.0382155,0.68185,0.0339595,0.721756,0.0115314,0.657443,0.988521,0.621856,0.000941086,0.627203,0.122108,0.93016,0.1371,0.00822974,0.0474149,0.414167,0.794693,0.984,0.991638,0.205213,0.506502,0.921027,0.840573,0.999937,0.513323,0.917109,0.000403427,0.226909,0.0228504,0.627937,0.0219342,0.65653,0.0333756,0.0508388,0.823394,0.0201981,0.636933,0.583129,0.183813,0.0489183,0.984196,0.944282,0.821881,0.750616,0.913059,0.0103235,0.518323,0.863908,0.243787,0.475903,0.970832,0.0739876,0.904643,0.0412509,0.925577,0.596994,0.958623,0.185562,0.0890122,0.889026,0.636322,0.891902,0.670714,0.943066,0.621158,0.400888,0.84491,0.806152,0.770712,0.994097,0.623636,0.879077,0.611177,0.822638,0.719573,0.351134,0.833008,0.545521,0.495194,0.576131,0.829617,0.789978,0.22311,0.572478,0.554011,0.976707,0.0606965,0.909017,0.13237,0.107208,0.973494,0.00309858,0.978965,0.437346,0.96607,0.994506,0.71563,0.97127,0.00257125,0.890894,9.13594e-07,0.0589625,0.291769,0.26008,0.0652323,0.206253,0.16675,0.108781,0.555335,0.901875,0.939945,0.110899,0.073565,0.64009,9.23715e-05,0.000465253,0.441603,0.264497,0.072417,0.0139029,0.989491,0.348744,0.130272,0.601704,0.392901,0.469714,0.0541404,0.988758,0.686536,0.0652276,0.89622,0.198604,0.910503,0.306585,0.326739,0.981398,4.92953e-11,0.692571,0.998969,0.880038,0.338231,0.043614,0.784236,0.283966,2.13934e-08,0.831665,0.986409,0.946024,0.869418,0.371971,0.81923,0.955391,0.00116755,0.94954,0.928232,0.216854,0.628183,0.994048,0.00125521,0.353858,1.5446e-08,0.968137,0.754061,0.891682,0.846783,0.54342,0.819937,0.382989,0.0441927,0.869046,0.784726,0.866848,0.513974,0.3471,0.0954478,0.871186,0.821052,0.9088,0.89506,0.598458,0.620471,0.827292,0.00248517,0.989903,0.069764,0.894439,0.0324397,0.0450154,0.875075,0.910454,0.440383,0.000301335,0.972577,0.424313,0.630645,0.864516,0.363335,0.0672644,0.274076,0.0159043,0.0100374,0.852961,0.710086,6.04336e-06,0.214604,0.742989,0.895516,0.76025,0.698209,0.49025,0.0791381,0.184157,0.686556,0.0684663,0.0147333,0.509896,0.715445,0.533168,0.315775,0.483695,0.0158078,0.362804,0.012466,0.639649,0.129237,0.803555,0.128828,0.63368,0.670377,0.447678,0.2112,0.234335,0.222479,0.620243,0.722549,0.331692,0.870115,0.854198,0.814385,0.548322,0.793893,0.214215,0.365665,0.585646,0.588952,0.516042,0.000838621,0.946789,0.646123,0.410715,0.0778821,0.0630302,0.874218,0.30125,0.334328,0.445517,0.934837,0.27917,0.000415385,0.427186,0.880234,0.496272,0.806954,0.742877,0.163561,0.100506,0.544875,0.0126294,0.62679,0.887287,0.483215,0.958754,0.90736,0.563758,9.445e-05,0.664165,0.412918,0.413927,0.794821,0.543971,0.000789912,0.413698,0.173781,0.946775,0.899234,0.326011,0.118669,0.868889,0.55938,0.631478,0.473155,5.09242e-05,0.134568,0.656322,0.484904,0.179299,0.150358,0.672902,0.353439,0.488234,0.596475,0.303646,0.408715,0.647929,0.128147,0.633658,0.778992,0.771772,0.0791599,0.942617,0.884482,0.454923,0.66513,0.773355,0.849057,0.960231,0.796098,0.744821,0.504576,0.000521069,0.363279,0.837525,0.92632,0.00059391,0.695742,0.0343455,0.000236459,0.693951,0.877128,0.871115,0.397201,0.83124,0.765553,0.51875,0.914111,5.9654e-09,0.094394,0.707189,0.894776,0.254783,0.580421,0.711784,0.543326,0.812159,0.589921,0.509864,0.0890638,0.642801,0.0377206,0.845961,0.492364,0.904507,0.940217,0.0757001,0.986909
|tfbs_overrepresentation_for_novel_motifs=1.64233,1.85282,1.60143,0.115973,0.0369893,0.115097,0.930842,0.143186,0.139834,0.736998,1.11439,0.545475,1.10306,0.901904,0.0365764,0.382537,1.51899,0.0973406,0.218375,0.465955,0.422633,0.690486,0.357972,0.59814,1.33816,0.5812,0.955628,1.73302,1.86417,0.241089,0.62111,0.341173,0.368873,0.817618,0.275894,0.548149,0.111654,0.115713,0.0923384,0.66459,0.273433,2.02011,0.184982,0.948411,0.845136,0.224432,0.480607,0.0941929,0.0440903,0.149585,0.603841,0.498457,0.40926,1.04005,0.532737,0.466119,0.0392903,0.82781,0.398965,1.93493,0.373766,0.484178,0.140489,0.291591,0.511492,0.266103,0.611096,0.954146,0.33304,0.800453,0.261495,0.0558475,11.5337,0.530988,2.18934,0.295725,0.137448,0.278987,0.330507,0.234869,0.228404,1.44032,0.171482,0.0109843,0.486416,1.78829,0.046923,0.0506093,1.20635,1.04966,0.695939,1.17096,0.354445,0.0170841,1.84848,0.0876739,0.215305,0.388689,0.653388,1.57962,0.232609,0.349965,0.384158,0.846519,2.84126,0.321489,0.303327,0.149517,0.24191,4.6794,1.18654,0.381914,0.411216,0.340192,0.652077,0.267503,0.170573,0.0883435,0.264397,0.394953,0.523757,0.226179,0.113636,0.178598,0.753832,0.27955,0.154657,0.942299,0.561176,0.424823,0.463953,0.0902711,0.573914,1.00462,0.707783,0.0135319,0.086099,0.11017,1.60526,1.49486,1.10037,0.634967,0.919194,0.385822,0.259011,0.405791,0.24704,1.33792,0.576539,2.16705,0.72532,8.7099,0.464277,0.129488,0.160304,0.829202,0.216727,0.133083,0.242284,0.208636,0.633868,0.448609,0.329893,0.464668,0.270734,0.170987,0.582013,0.157687,0.504522
}}
}}

Revision as of 14:10, 26 November 2012


Full id: C373_epidermoid_Prostate_cord_squamous_testicular_pharyngeal_testis



Phase1 CAGE Peaks

Hg19::chr10:134260508..134260546,+p@chr10:134260508..134260546
+
Hg19::chr11:69867159..69867175,-p3@ENST00000528507
Hg19::chr14:94405820..94405831,-p@chr14:94405820..94405831
-
Hg19::chr14:94405844..94405870,-p@chr14:94405844..94405870
-
Hg19::chr14:94405954..94405968,-p@chr14:94405954..94405968
-
Hg19::chr14:94405974..94405997,-p@chr14:94405974..94405997
-
Hg19::chr14:94406004..94406024,-p@chr14:94406004..94406024
-
Hg19::chr15:48442084..48442096,-p9@MYEF2
Hg19::chr17:34838949..34838959,-p@chr17:34838949..34838959
-
Hg19::chr17:39755734..39755747,-p@chr17:39755734..39755747
-
Hg19::chr17:39755914..39755961,-p@chr17:39755914..39755961
-
Hg19::chr20:43726566..43726571,+p@chr20:43726566..43726571
+
Hg19::chr20:43726572..43726588,+p@chr20:43726572..43726588
+
Hg19::chr20:43726947..43726954,-p@chr20:43726947..43726954
-
Hg19::chr20:43727145..43727152,-p@chr20:43727145..43727152
-
Hg19::chr20:43727168..43727209,-p@chr20:43727168..43727209
-
Hg19::chr20:43727212..43727217,-p@chr20:43727212..43727217
-
Hg19::chr20:57036925..57036961,-p9@APCDD1L
Hg19::chr2:99438974..99439027,-p5@C2orf55
Hg19::chr3:55205086..55205090,-p@chr3:55205086..55205090
-
Hg19::chr5:1882170..1882182,-p3@IRX4
Hg19::chr5:1882184..1882203,-p4@IRX4
Hg19::chr5:40984132..40984133,+p@chr5:40984132..40984133
+
Hg19::chr6:129597668..129597672,+p@chr6:129597668..129597672
+
Hg19::chr7:106101158..106101197,-p@chr7:106101158..106101197
-
Hg19::chr7:150871938..150871949,-p3@GBX1
Hg19::chr7:54900686..54900691,-p@chr7:54900686..54900691
-
Hg19::chrX:15683092..15683103,-p4@TMEM27
Hg19::chrX:15683147..15683159,-p3@TMEM27


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:0008241peptidyl-dipeptidase activity0.0314118382538923
GO:0004246peptidyl-dipeptidase A activity0.0314118382538923



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
epithelial cell of cervix1.55e-982
Uber Anatomy
Ontology termp-valuen
uterine epithelium1.55e-982
cervix epithelium1.55e-982
uterine cervix4.27e-346
neck of organ4.27e-346
uterus6.74e-1121
embryonic uterus1.80e-1022
internal female genitalia1.80e-1022
internal genitalia2.15e-0925
female reproductive organ8.21e-0737
female reproductive system8.21e-0737
Disease
Ontology termp-valuen
cervical cancer1.48e-405
squamous cell carcinoma1.43e-1514
female reproductive organ cancer8.32e-0927
reproductive organ cancer2.67e-0829


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)

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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
CTCF#10664142.587709973208630.0002781324296794360.00296165098116748
CTCFL#14069064.08547745358090.002917958086123570.015766393737734
ESR1#209966.36591792334230.000293096538099190.00310831735809721
MAX#4149153.337528711555416.20854210030502e-060.000183374979755021
RAD21#5885124.284841611912967.02264511834706e-060.000202775237355557
RXRA#625653.461140886057460.01336875009936690.0472397784418657
SMC3#912673.631535514294140.00242781388914580.0136770297625815
ZEB1#693563.494158348457350.006274603752039440.0276830576740135



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.