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Coexpression cluster:C1962: Difference between revisions

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{{Coexpression_clusters
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phosphatase activity!0.0139516400949588!8611$GO:0008354!germ cell migration!0.0139516400949588!8611$GO:0046839!phospholipid dephosphorylation!0.028399509486818!8611$GO:0019216!regulation of lipid metabolic process!0.028399509486818!8611$GO:0030521!androgen receptor signaling pathway!0.028399509486818!8611$GO:0007205!protein kinase C activation!0.028399509486818!8611$GO:0030518!steroid hormone receptor signaling pathway!0.028399509486818!8611$GO:0030258!lipid modification!0.028399509486818!8611$GO:0030522!intracellular receptor-mediated signaling pathway!0.028399509486818!8611$GO:0032147!activation of protein kinase activity!0.0325231595799832!8611$GO:0007200!G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)!0.0371594678851849!8611$GO:0048015!phosphoinositide-mediated signaling!0.0454807681646362!8611$GO:0045860!positive regulation of protein kinase activity!0.0454807681646362!8611$GO:0033674!positive regulation of kinase activity!0.0454807681646362!8611$GO:0051347!positive regulation of transferase 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328,0.255358,0.0707105,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.0968383,0.312881,0.512825,0.244656,0.192188,0.0133669,0.174153,0.00489362,0.333309,0.249919,0.339517,0.303699,0.198326,0.394084,0.126349,0.0443031,0.0348179,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.000297378,0.392533,0.0919602,0.316002,0.330317,0.321404,0.225079,0.300542,0.379651,0.185715,0.345505,0.0814929,0.0407047,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.055329,0.461742,0.422872,0.0643015,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.0150105,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.0248943,0.316879,0.442567,0.430541,0.00605341,0.00227842,0.398887,0.389061,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.0494743,0.42392,0.425912,0.0840133,0.259046,0.00922992,0.151046,0.483953,0.00941969,0.321735,0.15463,0.13907,0.133591,0.0400826,0.250466,0.0986342,0.115686,0.408975,0.162633,0.0668707,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476|tfbs_overrepresentation_for_novel_motifs=0.508327,0.205703,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.345702,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.770467,0.645033,0.44943,1.35492,1.88178,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.94379,0.27659,1.0713,0.432883,0.413782,1.57519,1.00769,0.815792,0.415749,0.580638,0.132849,0.451846,0.824538,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,1.17039,1.64902,0.233662,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,1.36104,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,1.89992,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.780629,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,1.23742,0.631235,1.37132,0.412056,2.0547,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,1.46338,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,3.075,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,1.05945|tfbs_overrepresentation_jaspar=MA0003.1;1.04569,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;1.47524,MA0009.1;1.11255,MA0014.1;0.161847,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,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;0.569896,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,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;0.695094,MA0072.1;1.0812,MA0073.1;0.0469445,MA0074.1;0.730989,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;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;1.58771,MA0106.1;0.779931,MA0107.1;0.985964,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,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;0.868598,MA0146.1;1.35428,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;1.12758,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.839774,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.813062,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.469165,MA0163.1;0.680296,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.230892,MA0102.2;1.66336,MA0258.1;0.914277,MA0259.1;0.395396,MA0442.1;0}}
|full_id=C1962_Adipocyte_Synoviocyte_Mast_mature_tenocyte_Chondrocyte_leiomyoblastoma
|id=C1962
}}

Latest revision as of 11:55, 17 September 2013


Full id: C1962_Adipocyte_Synoviocyte_Mast_mature_tenocyte_Chondrocyte_leiomyoblastoma



Phase1 CAGE Peaks

Hg19::chr5:54721817..54721840,-p@chr5:54721817..54721840
-
Hg19::chr5:54771166..54771206,+p@chr5:54771166..54771206
+
Hg19::chr5:54830488..54830506,-p2@RNF138P1
Hg19::chr5:54830511..54830588,-p1@RNF138P1
Hg19::chr5:54830784..54830799,-p1@PPAP2A


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:0008195phosphatidate phosphatase activity0.0139516400949588
GO:0008354germ cell migration0.0139516400949588
GO:0046839phospholipid dephosphorylation0.028399509486818
GO:0019216regulation of lipid metabolic process0.028399509486818
GO:0030521androgen receptor signaling pathway0.028399509486818
GO:0007205protein kinase C activation0.028399509486818
GO:0030518steroid hormone receptor signaling pathway0.028399509486818
GO:0030258lipid modification0.028399509486818
GO:0030522intracellular receptor-mediated signaling pathway0.028399509486818
GO:0032147activation of protein kinase activity0.0325231595799832
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0371594678851849
GO:0048015phosphoinositide-mediated signaling0.0454807681646362
GO:0045860positive regulation of protein kinase activity0.0454807681646362
GO:0033674positive regulation of kinase activity0.0454807681646362
GO:0051347positive regulation of transferase activity0.0454807681646362



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
fat cell2.59e-1215
fibroblast8.47e-1076
Uber Anatomy
Ontology termp-valuen
adult organism3.16e-27114
multi-tissue structure3.81e-12342
neural tube1.48e-1056
neural rod1.48e-1056
future spinal cord1.48e-1056
neural keel1.48e-1056
multi-cellular organism2.24e-10656
structure with developmental contribution from neural crest2.70e-10132
anatomical cluster6.69e-10373
anatomical conduit1.34e-09240
regional part of nervous system2.45e-0953
regional part of brain2.45e-0953
central nervous system3.76e-0981
brain4.44e-0968
future brain4.44e-0968
primary circulatory organ1.79e-0827
organ system subdivision2.69e-08223
neural plate7.39e-0882
presumptive neural plate7.39e-0882
regional part of forebrain1.14e-0741
forebrain1.14e-0741
anterior neural tube1.14e-0741
future forebrain1.14e-0741
tube1.22e-07192
heart1.26e-0724
primitive heart tube1.26e-0724
primary heart field1.26e-0724
anterior lateral plate mesoderm1.26e-0724
heart tube1.26e-0724
heart primordium1.26e-0724
cardiac mesoderm1.26e-0724
cardiogenic plate1.26e-0724
heart rudiment1.26e-0724
nervous system1.88e-0789
mesenchyme2.78e-07160
entire embryonic mesenchyme2.78e-07160
epithelium6.40e-07306
adipose tissue7.92e-0714


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)
MA0003.11.04569
MA0004.10.626788
MA0006.10.452993
MA0007.11.47524
MA0009.11.11255
MA0014.10.161847
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
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
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0469445
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.11.58771
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
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
MA0145.10.868598
MA0146.11.35428
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.839774
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.230892
MA0102.21.66336
MA0258.10.914277
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
NR3C1#290838.983813998703820.002687995788940450.0147987133474513
TFAP2C#702236.485537165916130.006858951517940.0290664247345156



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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