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Coexpression cluster:C3963: Difference between revisions

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{{Coexpression_clusters
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39,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.0268373,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,1.99148,0.641468,0.853988,2.1595,0.494933,0.491742,1.18351,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,2.0644,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.87308,1.02656,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.22068,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,1.67826,1.26794,1.63757,0.830777,1.58942,0.594137,0.553386,1.86486,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,3.23473,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,0.265282|tfbs_overrepresentation_jaspar=MA0003.1;1.54338,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;3.13838,MA0009.1;1.3275,MA0014.1;4.7105,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;2.16573,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;2.13518,MA0061.1;1.15625,MA0063.1;0,MA0066.1;2.1667,MA0067.1;1.65513,MA0068.1;11.1165,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;32.5673,MA0074.1;0.935474,MA0076.1;1.74184,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;1.5295,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;2.91906,MA0140.1;0.894983,MA0141.1;1.6959,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.752137,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;6.2923,MA0138.2;1.04628,MA0002.2;3.08747,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;1.39232,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;7.47293,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;22.9787,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0}}
|full_id=C3963_Mesenchymal_Smooth_Fibroblast_Alveolar_Keratocytes_Hair_Renal
|id=C3963
}}

Latest revision as of 12:36, 17 September 2013


Full id: C3963_Mesenchymal_Smooth_Fibroblast_Alveolar_Keratocytes_Hair_Renal



Phase1 CAGE Peaks

Hg19::chr1:27320176..27320200,+p1@TRNP1
Hg19::chr1:27320224..27320235,+p3@TRNP1
Hg19::chr1:27320382..27320395,+p2@TRNP1


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
cell layer8.04e-29309
epithelium1.02e-27306
multi-cellular organism3.67e-24656
multi-tissue structure3.59e-22342
anatomical system1.35e-21624
anatomical group3.23e-21625
mesenchyme1.23e-18160
entire embryonic mesenchyme1.23e-18160
organism subdivision2.39e-18264
trunk mesenchyme5.07e-16122
epithelial vesicle8.24e-1678
trunk1.60e-15199
surface structure4.82e-1599
anatomical cluster6.20e-15373
anatomical conduit2.66e-14240
embryo3.98e-14592
developing anatomical structure5.40e-14581
dense mesenchyme tissue4.66e-1373
organ part4.67e-13218
paraxial mesoderm5.11e-1372
presumptive paraxial mesoderm5.11e-1372
unilaminar epithelium7.11e-13148
somite7.69e-1371
presomitic mesoderm7.69e-1371
presumptive segmental plate7.69e-1371
dermomyotome7.69e-1371
trunk paraxial mesoderm7.69e-1371
integument2.23e-1246
integumental system2.23e-1246
multilaminar epithelium4.22e-1283
organ4.54e-12503
tube7.48e-12192
embryonic structure3.12e-11564
skin of body4.55e-1141
germ layer6.02e-11560
germ layer / neural crest6.02e-11560
embryonic tissue6.02e-11560
presumptive structure6.02e-11560
germ layer / neural crest derived structure6.02e-11560
epiblast (generic)6.02e-11560
epithelial tube1.62e-10117
skeletal muscle tissue1.70e-0962
striated muscle tissue1.70e-0962
myotome1.70e-0962
muscle tissue2.96e-0964
musculature2.96e-0964
musculature of body2.96e-0964
nephron epithelium3.74e-0915
renal tubule3.74e-0915
nephron tubule3.74e-0915
nephron3.74e-0915
uriniferous tubule3.74e-0915
nephrogenic mesenchyme3.74e-0915
structure with developmental contribution from neural crest4.51e-09132
renal system1.18e-0848
urinary system structure1.49e-0847
excretory tube1.69e-0816
kidney epithelium1.69e-0816
vasculature5.49e-0878
vascular system5.49e-0878
ecto-epithelium8.51e-08104
cortex of kidney9.17e-0812
renal parenchyma9.17e-0812
splanchnic layer of lateral plate mesoderm1.79e-0783
parenchyma2.87e-0715
ectoderm-derived structure3.88e-07171
ectoderm3.88e-07171
presumptive ectoderm3.88e-07171
cortex4.39e-0715
nephron tubule epithelium5.25e-0710


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.13.13838
MA0009.11.3275
MA0014.14.7105
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.12.16573
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
MA0061.11.15625
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.111.1165
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.132.5673
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.12.91906
MA0140.10.894983
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.26.2923
MA0138.21.04628
MA0002.23.08747
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.17.47293
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.222.9787
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
CTCFL#140690319.74647435897440.0001298372005551160.00171907548032148
EP300#203336.77394172622320.003216880500103790.0167615137971632
FOSL2#2355316.93020060456170.0002060162053171620.00243202514605166
FOXA1#3169311.08141974938550.000734755275698670.0058173835371612
GABPB1#255337.067683836182170.002832212825417420.0154235830260596
HDAC2#3066313.41562023662630.0004140761399857210.00391470064125724
HMGN3#932438.178547723350590.001827766942164210.0108800314432994
HNF4A#3172323.13229036295378.07584663437677e-050.00122877818567552
HNF4G#3174328.75342252644684.20470658818262e-050.000757129916143457
IRF1#365937.63716375356390.002244692747297240.0128189777906265
JUND#372736.994663941871030.002921845042734990.0156907946533422
NR3C1#2908314.9730233311730.0002978331194675480.00309168006799238
PBX3#5090321.91451268674419.49854535978121e-050.00136735848219185
SIN3A#2594235.408884726815140.006318961977991520.027707870938763
SP1#666735.69838137814090.005403962701712170.0246768598051732
SP2#6668326.15353049384465.58768218891694e-050.000940789843830882



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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