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Coexpression cluster:C436: Difference between revisions

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|tf_chipseq_enrich=BHLHE40#8553;3:5.85284524525792:0.0140379903360432:0.0492678833492177
|tf_chipseq_enrich=BHLHE40#8553;3:5.85284524525792:0.0140379903360432:0.0492678833492177
|tfbs_overrepresentation=0.345042,0.370939,0.848059,0.312596,0.818862,0.00037806,0.286108,0.776842,0.225122,0.180986,0.319654,0.311905,0.79889,0.276126,0.349651,0.387308,0.113027,0.00879373,0.0659735,0.0590768,0.0791745,0.663925,0.480948,0.534399,0.277858,0.118654,0.108919,0.51767,0.695713,0.173887,0.258261,0.604798,0.130209,0.534229,0.410089,0.491667,0.942776,0.285884,0.25803,0.410956,0.5406,0.173908,0.111251,0.789681,0.259844,0.246489,0.257064,0.200139,0.229158,0.0184128,0.0101147,0.34757,0.108191,0.526841,0.817161,0.259426,0.217121,0.547069,0.4649,0.0557123,0.204685,0.710825,0.585794,0.000411246,0.349628,0.327796,0.426188,0.0125246,0.498439,0.16683,0.974051,0.415651,0.510774,0.622687,0.0559081,0.123985,0.540654,0.290028,0.25251,0.0542767,0.180687,0.316045,0.283201,0.0687914,0.740264,0.651323,0.399424,0.0103214,0.0325744,0.0892398,0.151431,0.322891,0.536306,0.310703,0.495555,0.608143,0.362701,0.721629,0.525843,0.703612,0.364853,0.450635,0.690572,0.25142,0.849819,0.274132,0.412331,0.389354,0.3352,0.0360169,0.786858,0.232931,0.352475,0.127857,0.558762,0.23144,0.0111795,0.360548,0.10935,0.488966,0.407545,0.843239,0.321927,0.497219,0.0515273,0.775221,0.517533,0.107977,0.491191,0.670858,0.37558,0.449173,0.36346,0.161981,0.643238,0.584005,0.401994,0.353661,0.227084,0.0299268,0.161914,0.648873,0.25562,0.727541,0.544202,0.423481,0.549655,0.147015,0.262525,0.0182203,0.00837225,0.695522,0.783057,0.186616,0.284398,0.616623,0.448829,0.0515528,0.334334,0.231273,0.862085,0.179642,0.613591,0.706553,0.231665,0.605609,0.268915,0.64814,0.270793,0.00929711,0.78097,0.31415,0.0547118,0.0688494,0.47202,0.515052,0.68629,0.200868,0.778419,0.242839,0.734507,0.003685,0.191882,0.609993,0.117686,0.253213,0.0210203,0.269752,0.484805,0.768111,0.580576,0.000249852,0.6342,0.591818,0.0142878,0.309034,0.464583,0.379177,0.415515,0.589595,0.511868,0.379745,0.21345,0.380785,0.675262,0.404589,0.0387945,0.717106,0.000506371,0.444224,0.302299,0.570429,0.0183881,0.600861,2.091e-06,0.414991,0.0509636,0.557713,0.0898538,0.565377,0.690727,0.0011965,0.14308,0.389414,0.00313155,0.27817,0.317804,0.498021,0.380024,0.3772,0.0649355,0.510915,0.279407,0.456742,0.538416,0.173362,0.30989,0.903723,0.158998,0.117532,0.0713646,0.962776,0.00885692,0.485762,0.612384,0.105321,0.478922,0.0641193,0.0298007,0.000466111,0.735009,0.208892,0.793062,0.546605,0.54684,0.385081,0.0579613,0.250346,0.424744,0.0198005,0.387416,0.434037,0.0501376,0.650382,0.236067,0.476994,0.477413,0.523109,0.618379,0.452279,0.712908,0.394242,0.391864,0.830692,0.500614,0.257237,0.0934619,0.802055,0.61747,0.000488928,0.0944163,1.15375e-05,0.00523585,0.881729,0.0050023,0.147601,0.902175,0.000857764,0.291115,0.00072709,0.0807584,0.370321,0.00218789,0.0369129,0.017236,1.2077e-09,0.037718,0.00593884,4.75096e-06,0.000710014,7.35886e-06,3.93524e-10,0.795983,0.0618783,0.45465,0.000135011,0.590705,0.037735,0.123332,0.000500772,2.72741e-05,7.09532e-07,0.406854,0.00094627,1.40415e-07,8.77121e-05,0.123429,0.00231,0.655589,0.106806,6.65096e-06,0.0144294,0.559034,0.00384761,2.51497e-07,0.563115,0.0460309,7.83532e-08,0.00136867,0.018621,8.44151e-05,0.00334835,3.96584e-07,0.276328,0.0305968,1.07374e-06,0.0114717,9.24929e-09,0.297035,0.786399,0.154674,0.846921,0.000616102,0.915346,0.000302689,0.792903,3.74612e-05,0.534918,0.911356,1.17606e-07,4.65408e-05,0.00176845,8.88641e-05,0.0715925,0.250003,0.0017045,0.00284533,0.00219064,0.441175,0.0218768,0.0516042,0.314949,0.0776399,0.0239105,3.10149e-08,6.09279e-06,0.0236503,0.01843,0.00336239,0.00289794,0.0450716,0.298032,0.4488,0.0521025,0.414789,9.99243e-06,0.172052,9.28056e-07,0.108182,0.0132262,0.0503097,0.952036,0.00432081,0.24194,0.0104868,0.00475843,0.140156,0.00154767,0.503045,0.143604,0.0314755,0.000426513,0.00590321,2.05367e-06,2.73799e-08,0.962664,0.381636,0.337119,0.000258498,0.720188,0.000104994,6.00606e-06,0.00933057,0.0262861,0.362583,0.306239,0.312114,0.00064266,0.670437,0.189672,1.18668e-07,0.0193582,0.00136643,1.63579e-06,0.0656914,0.0243312,1.53025e-06,0.0469096,0.00222481,0.00496488,0.903171,0.854851,0.0153888,0.760841,0.0101153,0.00309658,0.52257,0.389576,0.829774,0.347828,0.81617,0.0360907,4.37805e-05,0.102829,0.41962,0.0151483,0.690252,5.03686e-07,0.117451,0.384898,0.00144182,0.0011911,0.147643,0.800299,0.511195,0.375501,0.820708,0.761397,0.00654467,1.1084e-09,0.000639801,0.0126579,1.85619e-05,2.50177e-07,0.0869606,0.000888881,0.425621,0.072376,0.805952,0.463449,0.365276,0.00761473,0.856048,0.520869,0.655143,0.462015,0.225039,0.597508,0.000396839,0.289141,0.0232549,0.645378,0.304832,0.0118764,0.701821,0.0141753,0.97483,0.129386,0.0631888,0.043122,0.977508,0.305745,0.759458,0.606632,0.571171,0.51454,0.501059,0.736884,0.580452,0.290992,0.0294438,0.636297,0.653628,0.836475,0.0859101,0.961612,0.325009,0.484917,0.410912,0.0206181,0.59523,0.0131824,0.0142751,0.811493,0.662804,0.798744,0.31516,0.00822839,0.565271,0.0893283,0.772851,0.463204,0.000118097,0.505008,0.535715,0.0831241,0.0464585,0.580208,0.235618,0.0363147,0.181889,0.113286,0.83841,0.208692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|tfbs_overrepresentation_for_novel_motifs=0.610853,4.11427,0.283006,0.165202,1.79318,0.164151,0.21518,3.00484,0.0978594,0.153481,0.446032,0.246281,0.0638208,0.207164,0.0634553,0.928857,0.386278,1.03518,1.27483,0.222044,0.0832107,0.681145,0.480786,0.061867,0.346469,2.06241,3.2421,0.157865,0.232674,0.242092,0.132203,1.07066,0.30708,3.02832,0.417757,0.6851,0.0488212,0.16489,0.157401,0.082891,0.185583,0.388602,0.777426,0.488521,1.02551,0.66769,0.617815,0.429484,1.21614,0.232836,0.273745,0.637443,1.28087,0.482679,1.50023,0.209199,0.512266,0.186863,4.08,0.18619,0.451758,0.217609,0.742416,0.363534,0.230363,0.33576,0.699678,1.04962,0.408258,0.893579,0.11533,0.10522,0.0215101,0.616804,0.0126142,1.07288,0.984849,0.349828,0.405538,0.103348,0.0167689,0.362659,0.230109,0.251709,0.570388,0.0119898,0.0475979,0.911538,0.293613,1.14619,0.786844,0.546282,0.43117,2.29069,0.496807,0.348406,0.0155039,0.467605,0.297172,1.8323,0.0408868,1.09109,0.462798,0.389311,0.326595,0.142545,0.376249,0.204779,0.106511,0.057369,0.0887009,0.460417,0.0805233,0.460536,0.741849,0.181704,0.0189649,0.131498,0.887846,0.14017,0.60929,0.291743,0.162396,0.670128,0.846043,0.350442,0.210743,0.435409,0.648109,0.350382,1.34916,0.826452,0.66129,1.23665,0.798972,0.215,0.128702,0.929703,0.759101,1.59408,1.19737,0.724259,1.14509,1.17354,0.327989,0.181235,0.84518,3.16865,0.3837,0.314918,0.41217,0.000779656,0.547236,0.706679,0.217268,0.922839,0.281215,0.058186,0.346552,0.0916077,0.723128,1.31504,0.404879,0.64194,0.340824,0.229543,0.029532,0.214247,1.33302
}}
}}

Revision as of 14:12, 26 November 2012


Full id: C436_Sebocyte_Prostate_Keratinocyte_Urothelial_Small_Mammary_salivary



Phase1 CAGE Peaks

Hg19::chr16:68729719..68729736,+p@chr16:68729719..68729736
+
Hg19::chr17:38632848..38632877,-p@chr17:38632848..38632877
-
Hg19::chr17:38633713..38633724,-p@chr17:38633713..38633724
-
Hg19::chr17:38643526..38643552,-p@chr17:38643526..38643552
-
Hg19::chr17:38643557..38643572,-p@chr17:38643557..38643572
-
Hg19::chr17:38644869..38644880,-p6@TNS4
Hg19::chr17:38644941..38644954,-p3@TNS4
Hg19::chr17:38644978..38645006,-p2@TNS4
Hg19::chr17:38645025..38645036,-p5@TNS4
Hg19::chr17:38645088..38645099,-p20@TNS4
Hg19::chr17:38652289..38652317,-p4@TNS4
Hg19::chr17:38652332..38652344,-p18@TNS4
Hg19::chr17:38652393..38652403,-p16@TNS4
Hg19::chr17:38652451..38652464,-p8@TNS4
Hg19::chr17:73736444..73736457,+p@chr17:73736444..73736457
+
Hg19::chr17:73746889..73746902,+p@chr17:73746889..73746902
+
Hg19::chr17:73747066..73747079,+p@chr17:73747066..73747079
+
Hg19::chr17:73748563..73748616,+p@chr17:73748563..73748616
+
Hg19::chr17:73750773..73750793,+p@chr17:73750773..73750793
+
Hg19::chr17:73750800..73750821,+p@chr17:73750800..73750821
+
Hg19::chr17:73750858..73750868,+p@chr17:73750858..73750868
+
Hg19::chr17:73753525..73753536,+p@chr17:73753525..73753536
+
Hg19::chr5:93905715..93905716,+p2@uc003kkq.1


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>disease_data<br>

Cell Type
Ontology termp-valuen
endo-epithelial cell1.48e-4042
epithelial cell1.47e-33253
endodermal cell1.04e-3058
epithelial cell of alimentary canal3.68e-2420
respiratory epithelial cell6.19e-2013
general ecto-epithelial cell9.30e-1314
acinar cell2.16e-125
epithelial cell of tracheobronchial tree5.90e-129
epithelial cell of lower respiratory tract5.90e-129
transitional epithelial cell1.66e-104
urothelial cell1.66e-104
protein secreting cell3.12e-106
extraembryonic cell5.18e-0819
bronchial epithelial cell6.99e-083
acinar cell of salivary gland7.32e-083
duct epithelial cell8.57e-083
branched duct epithelial cell8.57e-083
tracheal epithelial cell8.57e-083
tracheoblast8.57e-083
gingival epithelial cell1.60e-073
chorionic membrane mesenchymal stem cell1.71e-073
stratified squamous epithelial cell6.89e-076
keratin accumulating cell6.89e-076
stratified epithelial cell6.89e-076
keratinizing barrier epithelial cell6.89e-076
epithelial fate stem cell6.89e-076
stratified epithelial stem cell6.89e-076
surface ectodermal cell6.89e-076
epidermal cell8.47e-079
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.03e-28160
endoderm2.03e-28160
presumptive endoderm2.03e-28160
respiratory system2.55e-2174
orifice1.41e-1836
digestive system5.64e-18145
digestive tract5.64e-18145
primitive gut5.64e-18145
subdivision of digestive tract7.02e-15118
extraembryonic membrane4.47e-1414
membranous layer4.47e-1414
oral opening9.47e-1422
respiratory tract1.73e-1354
foregut2.03e-1387
surface structure4.07e-1399
urothelium3.25e-125
mouth1.61e-1129
stomodeum1.61e-1129
chorion9.24e-117
mucosa1.13e-1020
transitional epithelium4.36e-106
segment of respiratory tract5.55e-1047
mouth mucosa1.08e-0913
respiratory primordium4.49e-0938
endoderm of foregut4.49e-0938
organ component layer5.70e-0966
mucosa of oral region1.13e-084
respiratory system mucosa1.13e-084
tracheobronchial tree1.88e-0815
lower respiratory tract1.88e-0815
epithelial bud1.89e-0837
head2.72e-0856
epithelial fold2.84e-0847
endo-epithelium6.09e-0882
lower respiratory tract epithelium6.99e-083
epithelium of bronchus6.99e-083
subdivision of head1.20e-0749
gingival epithelium1.60e-073
acellular anatomical structure1.71e-073
egg chorion1.71e-073
extraembryonic structure2.73e-0724
anterior region of body4.53e-0762
craniocervical region4.53e-0762
urinary system structure6.92e-0747
Disease
Ontology termp-valuen
carcinoma1.58e-12106
squamous cell carcinoma3.46e-0814
cell type cancer3.23e-07143


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
BHLHE40#855335.852845245257920.01403799033604320.0492678833492177



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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