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{{Coexpression_clusters
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,0.0537285,0.15063,0.198077,0.281455,0.348739,2.27604e-05,0.138495,0.208834,0.32256,0.082459,0.342366,0.109684,0.322704,0.403482,0.181288,0.230841,0.352328,0.255358,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.512825,0.244656,0.192188,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.0905116,0.458518,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.392533,0.396962,0.316002,0.330317,0.321404,0.225079,0.300542,0.379651,0.185715,0.345505,0.375521,0.271405,0.311201,0.221943,0.306427,0.0778743,0.246925,0.208775,0.0886961,0.343014,0.270094,0.276922,0.156279,0.313647,0.461742,0.10563,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.0735747,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.508546,0.224871,0.092937,0.389061,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.470121,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.342661,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,1.16078,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.501863,0.500405,1.83059,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,1.1597,1.87167,0.654459,0.388123,2.25858,0.415749,1.42042,0.414516,0.451846,1.74542,0.533483,0.734485,0.609718,0.124583,1.16046,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,1.22844,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,1.30959,0.675933,0.917983,0.987729,0.543014,0.293154,2.1521,0.755403,1.57121,1.18161,0.914416,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,1.23742,1.52665,1.37132,0.412056,1.00558,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,1.60094,0.79475,1.15522,2.31232,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,2.92355|tfbs_overrepresentation_jaspar=MA0003.1;2.72292,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;2.48957,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;2.29497,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;4.04387,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.554727,MA0058.1;1.29981,MA0059.1;1.29682,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;1.65981,MA0072.1;1.0812,MA0073.1;0.0140295,MA0074.1;4.19986,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.818263,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;1.15584,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;2.93136,MA0105.1;1.58771,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;1.40074,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;1.82062,MA0147.1;1.00307,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;1.41923,MA0035.2;0.691506,MA0039.2;1.50246,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;1.54865,MA0047.2;0.767096,MA0112.2;4.17482,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.98952,MA0155.1;0.130813,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;2.88007,MA0163.1;0.382496,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.823998,MA0102.2;1.66336,MA0258.1;1.63655,MA0259.1;0.395396,MA0442.1;0}}
|full_id=C1727_colon_small_stomach_papillotubular_breast_duodenum_prostate
|gostat_on_coexpression_clusters=GO:0005923!tight junction!0.0279220393075104!153562$GO:0043296!apical junction complex!0.0279220393075104!153562$GO:0016327!apicolateral plasma membrane!0.0279220393075104!153562$GO:0050954!sensory perception of mechanical stimulus!0.0279220393075104!153562$GO:0007605!sensory perception of sound!0.0279220393075104!153562$GO:0005911!intercellular junction!0.0304772232795939!153562
|id=C1727
}}

Latest revision as of 11:50, 17 September 2013


Full id: C1727_colon_small_stomach_papillotubular_breast_duodenum_prostate



Phase1 CAGE Peaks

Hg19::chr14:61747949..61747974,-p2@TMEM30B
Hg19::chr14:61747978..61747991,-p7@TMEM30B
Hg19::chr14:61748025..61748074,-p1@TMEM30B
Hg19::chr15:41136563..41136613,-p@chr15:41136563..41136613
-
Hg19::chr5:68711211..68711238,+p4@MARVELD2


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:0005923tight junction0.0279220393075104
GO:0043296apical junction complex0.0279220393075104
GO:0016327apicolateral plasma membrane0.0279220393075104
GO:0050954sensory perception of mechanical stimulus0.0279220393075104
GO:0007605sensory perception of sound0.0279220393075104
GO:0005911intercellular junction0.0304772232795939



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 cell1.62e-1942
epithelial cell9.69e-19253
endodermal cell1.52e-1358
respiratory epithelial cell9.82e-1013
epithelial cell of alimentary canal1.32e-0920
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.82e-26160
endoderm5.82e-26160
presumptive endoderm5.82e-26160
digestive system8.75e-21145
digestive tract8.75e-21145
primitive gut8.75e-21145
subdivision of digestive tract7.88e-19118
endo-epithelium2.67e-1382
respiratory system1.20e-1274
epithelial bud4.98e-1137
foregut7.44e-1187
anatomical space3.04e-1095
immaterial anatomical entity1.08e-09117
orifice1.64e-0936
respiratory tract1.98e-0954
epithelial fold2.24e-0947
thoracic cavity element2.44e-0934
thoracic cavity2.44e-0934
thoracic segment organ7.25e-0935
renal system8.50e-0848
gastrointestinal system9.38e-0825
reproductive structure1.00e-0759
reproductive system1.00e-0759
thoracic segment of trunk1.46e-0752
trunk region element1.51e-07101
urinary system structure2.02e-0747
lung2.57e-0722
respiratory tube2.57e-0722
respiration organ2.57e-0722
pair of lungs2.57e-0722
lung primordium2.57e-0722
lung bud2.57e-0722
respiratory system epithelium3.94e-0728
male organism6.97e-0722
male reproductive system6.97e-0722
oral opening8.97e-0722
Disease
Ontology termp-valuen
carcinoma1.38e-12106
squamous cell carcinoma5.62e-1214
adenocarcinoma1.69e-0725
cell type cancer4.12e-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)
MA0003.12.72292
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.12.48957
MA0017.10.496101
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.14.04387
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.11.29981
MA0059.11.29682
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.11.65981
MA0072.11.0812
MA0073.10.0140295
MA0074.14.19986
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.12.93136
MA0105.11.58771
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.11.82062
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.21.41923
MA0035.20.691506
MA0039.21.50246
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.24.17482
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.12.88007
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.823998
MA0102.21.66336
MA0258.11.63655
MA0259.10.395396
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
E2F1#186954.907389214879320.0003512818099256460.00352595107610039
MYC#460944.177825497287520.005691969036823440.0256765529646166
ZEB1#6935310.13305921052630.001895556924357070.0111601595142301



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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