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Coexpression cluster:C633: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!1.99e-16!365;UBERON:0003102!1.81e-15!95;UBERON:0000914!2.52e-15!83;UBERON:0002329!2.52e-15!83;UBERON:0003077!2.52e-15!83;UBERON:0003059!2.52e-15!83;UBERON:0007282!2.52e-15!83;UBERON:0009618!2.52e-15!83;UBERON:0007285!2.52e-15!83;UBERON:0002199!6.65e-14!45;UBERON:0002416!6.65e-14!45;UBERON:0002097!1.55e-12!40;UBERON:0004290!3.91e-12!70;UBERON:0000486!3.57e-10!82;UBERON:0001134!3.33e-08!61;UBERON:0002036!3.33e-08!61;UBERON:0003082!3.33e-08!61;UBERON:0002385!1.38e-07!63;UBERON:0001015!1.38e-07!63;UBERON:0000383!1.38e-07!63;UBERON:0005256!2.97e-07!143;UBERON:0002067!9.21e-07!9;UBERON:0004016!9.21e-07!9;UBERON:0010083!9.21e-07!9
|ontology_enrichment_uberon=UBERON:0000475!1.99e-16!365;UBERON:0003102!1.81e-15!95;UBERON:0000914!2.52e-15!83;UBERON:0002329!2.52e-15!83;UBERON:0003077!2.52e-15!83;UBERON:0003059!2.52e-15!83;UBERON:0007282!2.52e-15!83;UBERON:0009618!2.52e-15!83;UBERON:0007285!2.52e-15!83;UBERON:0002199!6.65e-14!45;UBERON:0002416!6.65e-14!45;UBERON:0002097!1.55e-12!40;UBERON:0004290!3.91e-12!70;UBERON:0000486!3.57e-10!82;UBERON:0001134!3.33e-08!61;UBERON:0002036!3.33e-08!61;UBERON:0003082!3.33e-08!61;UBERON:0002385!1.38e-07!63;UBERON:0001015!1.38e-07!63;UBERON:0000383!1.38e-07!63;UBERON:0005256!2.97e-07!143;UBERON:0002067!9.21e-07!9;UBERON:0004016!9.21e-07!9;UBERON:0010083!9.21e-07!9
|tf_chipseq_enrich=EP300#2033;9:4.35467682400063:3.27329906170514e-05:0.000651286112984231!GATA2#2624;9:8.19317040014185:1.56227145797145e-07:8.7533298711953e-06!RAD21#5885;9:6.65680750422193:9.27601497981902e-07:3.97855329970151e-05
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00123558,0.32162,0.380182,0.557129,0.459518,0.358174,0.235074,0.787759,0.966728,6.73231e-13,0.0663328,2.05411e-05,0.670561,0.687361,0.322854,0.307749,0.561179,0.632829,0.231656,0.315342,0.236502,0.180519,0.151296,0.168921,0.746322,0.00204024,1.33387e-16,0.208593,0.592326,0.884593,0.145253,0.864854,0.685519,0.171324,0.249488,0.920828,0.456489,2.12667e-05,0.419538,0.169955,0.126655,0.975758,0.517459,0.168817,0.34758,0.232128,0.516141,0.744761,3.69831e-07,9.11216e-06,3.42963e-08,0.903474,0.717178,0.793723,0.308916,0.586693,6.02855e-05,0.609958,0.851067,0.525647,0.509234,0.210808,0.506986,0.0711139,0.82251,0.793887,0.202394,0.372,0.936205,0.48593,0.313489,0.417019,0.473863,0.481952,0.995598,0.937933,0.219957,0.386498,0.213016,0.257581,0.306778,0.368009,0.000922837,0.149154,0.302107,0.780017,0.998129,0.0661707,0.681197,0.796833,0.447,0.631254,4.79505e-05,0.975381,0.241724,0.203517,0.902658,0.254032,0.593244,0.811464,0.291991,0.693556,0.799234,0.000710067,0.0039072,4.7507e-06,0.999988,0.999997,0.0242292,0.109579,0.414214,0.277745,0.415655,0.210578,0.375129,0.658666,0.052866,0.19593,0.420132,0.000425098,0.697766,0.54045,2.25876e-11,5.20337e-07,0.193367,0.227897,2.25778e-06,0.365739,0.221374,0.403936,0.689428,0.24021,0.712296,0.308426,0.793553,0.537664,0.63648,0.683095,0.000172148,0.842529,0.0606254,0.0478865,0.535687,0.0373926,1.3379e-19,0.527918,0.962287,0.0460647,0.294013,2.79244e-08,0.251684,0.516765,0.0420998,0.380058,0.544392,0.58155,0.633758,0.03279,0.701346,0.741186,0.00127019,0.446456,0.335602,0.290616,0.428988,0.427501,0.61865,0.0622763,0.371883,0.760919,0.151399,0.506747,0.387692,0.750933,0.399946,0.428759,0.113799,0.575907,0.358215,0.000352449,0.0112414,0.00329935,0.327109,7.27667e-08,0.54748,0.825205,0.9648,0.247428,0.734435,0.600262,0.318832,0.706597,0.912912,0.989048,0.157609,0.916225,0.48095,0.187268,0.487947,0.920115,0.883605,0.526182,0.912972,7.96796e-09,0.881259,0.00665124,0.0678872,0.000367255,0.303552,0.641807,7.18167e-06,0.876715,0.912043,0.654813,0.982634,0.991907,0.0184755,0.997463,0.00265393,0.956056,0.628402,0.757166,0.00911265,0.999941,0.99993,0.0015139,0.967007,0.167555,0.89771,0.790513,0.962345,0.9764,0.997747,0.00590343,0.0105726,0.553764,0.794926,0.981484,0.806063,0.852336,0.947613,0.751904,0.146268,0.143239,0.999097,0.20354,0.99796,0.29282,0.00997094,0.998483,0.992011,0.218996,0.999442,0.887261,0.999235,0.951586,0.999214,0.99836,0.998991,0.654004,0.648031,2.00285e-06,0.0884384,0.749305,0.925001,0.00458886,0.000123258,0.0462869,0.159636,0.916061,0.376091,9.35594e-05,0.335456,0.566109,0.70572,0.0228939,0.789986,0.978865,0.0337009,0.0685992,0.0209193,0.999146,0.988567,0.913685,0.852178,7.79294e-17,0.993135,1.43227e-07,0.987697,0.00907502,0.968273,0.99948,0.874013,0.690156,0.0146078,0.000288154,0.944923,0.945974,0.982438,0.656826,0.533057,0.50228,0.994611,0.573511,0.642527,0.333901,0.830598,0.809277,4.71671e-07,0.848819,0.887251,0.968588,0.444149,0.880311,0.971865,0.672236,0.878277,0.715288,0.654138,0.774723,0.889111,0.93678,0.59884,0.0187156,0.94962,0.818025,0.000381534,0.885439,0.81897,0.815347,0.959092,0.897747,0.421994,0.00266881,0.895185,0.942576,0.636311,2.93533e-05,0.963849,0.640746,1.05519e-06,0.029085,0.986404,0.0952395,0.943481,1.00324e-07,0.0177247,0.949646,0.907496,0.018094,0.361718,7.77629e-12,0.661121,0.951843,0.344173,0.000188295,0.274743,0.152973,0.0291418,0.0128603,0.0270015,6.09527e-05,0.000116445,0.658026,5.0377e-06,0.315097,0.0672554,0.657795,0.147894,8.31298e-09,0.752893,0.0173987,0.00543616,0.00361853,0.201283,1.03164e-06,0.56424,0.111127,0.0248878,0.356279,0.373564,0.208482,0.0489015,0.00208118,2.40648e-07,0.000904591,0.000602172,0.602579,4.77173e-12,0.112992,0.6919,0.857865,4.20152e-08,0.00119911,0.0210955,4.13306e-11,0.458936,0.64592,0.14327,0.366902,0.461022,0.603657,5.7001e-10,0.450416,0.341247,0.0289962,0.000141145,0.00045644,0.000219719,0.277689,0.664123,0.000132939,0.000288877,0.520437,0.343234,0.56202,0.702807,0.577896,0.167392,0.27322,0.22134,0.195528,4.26718e-07,0.650305,0.866489,1.21111e-08,2.37588e-07,0.384185,6.19642e-09,0.249171,0.678642,2.1495e-06,0.686951,1.25462e-06,0.46149,0.754102,0.820512,0.605271,0.19589,0.750457,0.177778,0.680896,7.53987e-15,7.46207e-07,0.000472143,0.295569,3.33113e-10,3.69531e-08,1.86572e-08,6.97363e-15,0.662315,0.51031,8.39551e-10,0.737348,0.437434,0.332632,0.379663,0.587939,0.28037,0.156735,0.64103,0.367371,0.547991,2.23342e-09,9.95476e-05,3.72448e-11,0.000308107,0.596617,0.378621,1.48694e-05,0.0983976,0.785434,0.682887,0.329999,0.65125,0.0984235,0.00233893,0.227361,1.55868e-05,0.315496,0.176359,0.227215,0.536931,0.757328,0.303866,0.621034,0.129686,0.0768086,0.326761,2.50634e-09,0.266095,0.454858,0.265087,1.22633e-06,7.32494e-11,0.000582739,0.474347,0.416949,0.189841,0.276311,0.0101275,0.160298,0.147723,1.62389e-05,0.805312,0.793321,0.00105972,0.509942,0.759521,1.4544e-05,0.279669,0.339005,0.0070415,0.744466,0.598612,7.88422e-07,2.75669e-06,7.67714e-12,0.558381,0.292861,7.25402e-12,0.00565932,0.716075,0.840422,0.436971,0.0294217,0.00139372,0.435373,0.0825511,1.0294e-06,1.19596e-09,0.0725914,0.000486854,2.91135e-06,0.0324846,0.367768,0.117266,3.57189e-05,0.662776,0.375214,0.342479,0.009824,4.06286e-06,0.00936056,0.771635,0.291242,0.00408014,0.00171377,0.691105,0.594658,1.77789e-07,3.09375e-06,1.74366e-06,2.03605e-06,2.16459e-06
}}
}}

Revision as of 12:56, 5 September 2012


Full id: C633_Olfactory_Fibroblast_Preadipocyte_Hair_tenocyte_mesenchymal_basal



Phase1 CAGE Peaks

Hg19::chr1:215178636..215178662,+p5@KCNK2
Hg19::chr1:215178669..215178685,+p13@KCNK2
Hg19::chr1:215178693..215178706,+p28@KCNK2
Hg19::chr1:215178726..215178743,+p24@KCNK2
Hg19::chr1:215178832..215178850,+p16@KCNK2
Hg19::chr1:215178858..215178873,+p17@KCNK2
Hg19::chr1:215178875..215178906,+p2@KCNK2
Hg19::chr1:215178908..215178935,+p3@KCNK2
Hg19::chr1:215178944..215178967,+p11@KCNK2
Hg19::chr1:215179028..215179060,+p9@KCNK2
Hg19::chr1:215179111..215179149,+p4@KCNK2
Hg19::chr1:215179154..215179167,+p12@KCNK2
Hg19::chr1:215179188..215179201,+p21@KCNK2
Hg19::chr1:215202322..215202325,+p@chr1:215202322..215202325
+


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell3.29e-23180
fibroblast1.60e-2175
skin fibroblast1.87e-1423
preadipocyte3.09e-1012
muscle precursor cell2.22e-0857
myoblast2.22e-0857
multi-potent skeletal muscle stem cell2.22e-0857
multi fate stem cell3.92e-08430
somatic stem cell1.78e-07436
muscle cell3.88e-0754
contractile cell8.53e-0759
Uber Anatomy
Ontology termp-valuen
organism subdivision1.99e-16365
surface structure1.81e-1595
somite2.52e-1583
paraxial mesoderm2.52e-1583
presomitic mesoderm2.52e-1583
presumptive segmental plate2.52e-1583
trunk paraxial mesoderm2.52e-1583
presumptive paraxial mesoderm2.52e-1583
integument6.65e-1445
integumental system6.65e-1445
skin of body1.55e-1240
dermomyotome3.91e-1270
multilaminar epithelium3.57e-1082
skeletal muscle tissue3.33e-0861
striated muscle tissue3.33e-0861
myotome3.33e-0861
muscle tissue1.38e-0763
musculature1.38e-0763
musculature of body1.38e-0763
trunk mesenchyme2.97e-07143
dermis9.21e-079
dermatome9.21e-079
future dermis9.21e-079


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
EP300#203394.354676824000633.27329906170514e-050.000651286112984231
GATA2#262498.193170400141851.56227145797145e-078.7533298711953e-06
RAD21#588596.656807504221939.27601497981902e-073.97855329970151e-05



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.