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Coexpression cluster:C1556: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;3:37.6302002035969:3.95343056005017e-05:0.000737439425363601!SUZ12#23512;2:20.0463123644252:0.00382407565415475:0.0188717401712549
|tf_chipseq_enrich=CTBP2#1488;3:37.6302002035969:3.95343056005017e-05:0.000737439425363601!SUZ12#23512;2:20.0463123644252:0.00382407565415475:0.0188717401712549
|tfbs_overrepresentation=0.23317,0.0958562,3.63206e-07,0.078254,0.310241,0.43203,0.00255639,0.000328415,0.0539364,0.0424746,0.221396,0.0685476,0.294377,0.201017,0.235304,0.101024,0.223746,0.158251,0.0865245,0.173528,0.000465316,0.211047,0.13286,0.153106,0.0683222,0.332688,0.324018,0.146582,0.227906,0.150721,0.0568587,0.0178217,0.0298713,0.322378,0.108398,0.136785,0.00387794,0.070583,0.192426,0.108683,0.155571,0.0406818,0.222325,0.0459718,0.193292,0.0596699,0.0625547,0.28382,0.178503,0.193726,0.243359,0.0886583,0.114185,0.150136,0.308837,0.0632035,0.172598,0.061176,0.127101,0.169687,0.0485674,0.236408,0.174369,0.123348,0.0892839,0.0827236,0.515105,0.0980005,0.139298,0.262613,0.00136456,0.110232,0.143944,0.190944,0.012429,0.0283664,0.155593,0.0717582,0.0613084,0.0120583,0.154245,0.348799,0.0698251,0.183986,0.0206187,0.0015522,0.104918,0.323505,5.89584e-06,0.102375,0.138802,0.0812726,0.153861,0.0777027,0.0100263,0.184264,5.94573e-09,0.242703,0.0118178,0.413729,0.0939617,0.416542,0.225088,0.0610111,0.337778,0.0672793,0.109136,0.497282,0.228612,0.097251,0.285407,0.0560173,0.23661,0.0293017,0.162943,0.0556189,0.0336673,0.0926302,0.220791,0.13579,0.262107,0.0623132,0.222452,0.138843,0.164723,0.00447322,0.146529,0.0245339,0.136609,0.214614,0.00489616,0.121587,0.0935301,0.0376876,0.0216494,0.173595,0.00580006,0.0905147,0.0544577,0.0065834,0.037671,0.203496,0.316207,0.0331631,0.00464065,0.112838,0.159217,0.1364,0.0640569,0.193163,0.311509,0.227801,0.282656,0.0439093,0.070163,0.188135,0.121467,0.350865,0.0846706,0.0555742,0.349932,0.153706,0.186743,0.029797,0.0169705,0.0178954,0.065826,0.203135,0.0663482,0.0004689,0.281162,0.218835,0.0214914,0.0885874,0.129639,0.145577,0.22277,0.284267,0.27935,0.0586816,0.250461,0.195671,0.0452583,0.185103,0.11983,0.190123,0.286036,0.0660586,0.134265,0.272191,0.0157439,0.292239,0.196376,0.00981618,0.18064,0.00306112,0.126988,0.0984435,0.110187,0.00104685,0.144361,0.0986228,0.0508565,0.0989516,0.21691,0.393782,0.412989,0.0314403,0.319604,0.0432208,0.0752697,0.167805,0.193654,0.180992,0.464566,0.265567,0.0367027,0.162511,0.102771,0.165687,0.225173,0.044111,0.0331894,0.0033588,0.00751221,0.201982,0.220536,0.139142,0.0987108,0.09782,0.0543538,0.00945435,0.0687568,0.124225,0.1547,0.150448,0.0774663,0.00186541,0.257365,0.331711,0.285222,0.00620154,0.158559,0.134615,0.0185225,0.217494,0.132125,0.179065,0.00124634,0.187334,0.250769,0.00514033,0.0468257,0.157983,0.158078,0.251693,0.0157721,0.313249,0.113261,2.19895e-05,0.101058,0.274448,0.25718,0.204241,0.0568578,0.131428,0.131579,0.148683,0.188945,0.122666,0.419402,0.103245,0.013649,9.3097e-06,0.14011,0.0626022,0.2074,0.0169967,6.4516e-05,5.19608e-07,0.0907735,0.161661,3.09948e-10,2.23165e-07,0.0318717,0.0865603,0.0918284,0.0180957,0.183975,0.127393,0.675971,0.487888,0.0533299,0.0301802,0.0406603,0.00130812,0.410803,0.43779,0.579996,0.569955,0.0164342,0.0675907,0.00531909,0.173748,0.284119,0.234606,0.176507,0.488132,0.336705,0.237849,0.545464,0.277796,8.46335e-05,0.356237,0.00166895,0.181227,0.00229357,2.06945e-05,0.0134523,0.417358,0.000390703,0.665656,0.470142,0.344006,0.11323,5.1595e-06,0.107686,0.131857,0.000722513,0.437202,0.260795,0.0155792,0.227062,0.438692,1.76233e-05,0.000494275,0.541742,0.00362283,0.20757,0.285074,1.00528e-05,3.87879e-07,0.00928443,0.0173305,0.362164,0.289863,0.00599989,0.137929,0.0984273,0.000305132,0.113112,0.00151321,0.036478,0.379008,0.423719,0.288374,0.0362804,0.109234,0.11883,0.0463546,0.000179831,1.52684e-06,0.179485,4.35213e-06,0.117662,0.0450335,0.386101,0.0785559,0.337121,0.464864,0.00429812,0.0740433,0.121457,0.00984135,7.19158e-11,0.186962,4.33588e-07,0.115972,0.034252,0.0243803,0.111787,0.0294884,1.28025e-07,0.103509,1.24536e-06,0.0683965,0.350461,0.150002,0.307173,0.246694,0.000614025,0.231945,0.0256281,0.597346,0.0015704,8.63766e-06,0.493489,0.229501,0.230597,0.555864,0.544572,9.4251e-06,0.274083,0.0855214,0.241286,0.0764074,0.217887,0.393543,0.0248277,0.158849,0.732038,0.439833,0.427746,0.504398,0.125252,0.455709,0.0698698,0.113129,0.00864758,0.427794,0.398041,0.524026,0.347879,0.0119366,0.0627713,0.174576,0.0216775,8.91871e-12,0.319495,0.00889667,0.00225,0.0165193,0.407113,0.498776,1.97355e-10,0.423517,0.224914,0.268941,4.26663e-05,0.251608,0.365107,0.182645,0.356278,0.295455,0.144104,0.0972855,0.352039,8.64285e-06,0.0355006,0.0423027,0.512109,0.0944328,0.0570792,0.00191497,0.0270368,0.133028,0.113555,0.0910724,0.299839,0.126587,0.0940929,0.22877,0.343849,0.315824,7.12272e-05,8.34102e-06,0.29873,0.179502,0.0201883,0.0715061,0.122699,0.201779,0.0248508,0.171725,0.100099,0.102448,2.08218e-05,0.029672,0.123175,0.421335,0.561724,0.00298503,0.266371,0.183582,0.168118,0.145381,0.140277,0.251925,0.172066,0.0720324,0.00647589,0.19738,0.205854,0.32541,0.00589576,9.61279e-06,0.0818982,0.134306,0.108669,0.284804,0.178494,0.338195,0.00505862,0.00607558,0.0238916,0.294266,0.0790025,0.310539,0.000284269,0.203728,0.275452,0.288155,0.0389599,0.141761,0.153627,0.0186891,0.0668022,0.171961,0.415228,0.00800917,0.04102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}}
}}

Revision as of 14:58, 26 November 2012


Full id: C1556_epididymis_seminal_Renal_ductus_kidney_rhabdomyosarcoma_renal



Phase1 CAGE Peaks

Hg19::chr10:102505147..102505162,+p9@PAX2
Hg19::chr10:102505297..102505302,+p11@PAX2
Hg19::chr10:102505493..102505546,+p2@PAX2
Hg19::chr10:102505946..102505949,+p14@PAX2
Hg19::chr10:102505954..102505973,+p3@PAX2


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><br>

Uber Anatomy
Ontology termp-valuen
kidney5.34e-4726
kidney mesenchyme5.34e-4726
upper urinary tract5.34e-4726
kidney rudiment5.34e-4726
kidney field5.34e-4726
cavitated compound organ5.86e-4431
nephron tubule epithelium2.65e-3110
excretory tube4.58e-3016
kidney epithelium4.58e-3016
urinary system structure1.68e-2747
renal system7.61e-2748
nephron epithelium6.77e-2615
renal tubule6.77e-2615
nephron tubule6.77e-2615
nephron6.77e-2615
uriniferous tubule6.77e-2615
nephrogenic mesenchyme6.77e-2615
abdomen element1.83e-2354
abdominal segment element1.83e-2354
abdominal segment of trunk1.00e-2060
abdomen1.00e-2060
cortex2.84e-2015
cortex of kidney7.09e-2012
renal parenchyma7.09e-2012
compound organ6.82e-1868
male genital duct1.01e-163
internal male genitalia1.01e-163
parenchyma1.03e-1515
posterior neural tube5.82e-1515
chordal neural plate5.82e-1515
mesonephros1.87e-149
pronephros1.87e-149
nephrogenic cord1.87e-149
pronephric mesoderm1.87e-149
rostral part of nephrogenic cord1.87e-149
presumptive pronephric mesoderm1.87e-149
segmental subdivision of hindbrain6.12e-1412
hindbrain6.12e-1412
presumptive hindbrain6.12e-1412
brainstem4.53e-136
segmental subdivision of nervous system7.97e-1313
duct of male reproductive system1.16e-124
trunk region element3.21e-12101
urogenital ridge8.97e-1211
abdomen connective tissue1.72e-112
abdominal segment connective tissue1.72e-112
trunk connective tissue1.72e-112
interstitial tissue1.72e-112
extraglomerular mesangium1.72e-112
kidney interstitium1.72e-112
juxtaglomerular apparatus1.72e-112
mesangium1.72e-112
intraembryonic coelom9.12e-1112
mesonephric epithelium1.10e-108
mesonephric tubule1.10e-108
nephric duct1.10e-108
renal duct1.10e-108
mesonephric duct1.10e-108
pronephric duct1.10e-108
locus ceruleus1.42e-102
brainstem nucleus1.42e-102
hindbrain nucleus1.42e-102
adult organism9.07e-10114
duct2.05e-0919
subdivision of trunk2.49e-09112
regional part of metencephalon9.82e-099
metencephalon9.82e-099
future metencephalon9.82e-099
intermediate mesoderm5.38e-0828
male reproductive organ1.17e-0711
renal cortex tubule1.26e-073
region of nephron tubule1.26e-073
proximal tubule1.26e-073
medulla oblongata2.13e-073
myelencephalon2.13e-073
future myelencephalon2.13e-073
pons2.50e-073
primitive nephron3.26e-077
renal glomerulus3.26e-077
renal corpuscle3.26e-077
glomerular capsule3.26e-077
metanephric mesenchyme3.26e-077
glomerular tuft3.26e-077


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)

{{{tfbs_overrepresentation_jaspar}}}



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
CTBP2#1488337.63020020359693.95343056005017e-050.000737439425363601
SUZ12#23512220.04631236442520.003824075654154750.0188717401712549



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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