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Coexpression cluster:C1891: Difference between revisions

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{{Coexpression_clusters
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0.100151,0.54408,0.018149,0.513592,0.0173299,0.00780578,0.000420384,0.36864,0.00811127,0.125335,0.453004,0.108097,0.557093,0.116707,0.382214,0.553161,0.639572,0.326875,0.339393,3.40276e-05,0.306231,0.298354,0.00428643,0.0202712,0.0243185,0.0206327,0.426239,0.0517097,0.289012,0.000254543,0.100067,0.00780261,0.41502,0.0487429,2.14686e-06,0.523749,0.499347,0.307426,0.00116449,0.196912,0.490527,0.132075,0.44799,0.236683,0.318338,0.0422834,0.126433,0.417412,0.318174,0.0555558,0.295666,0.393022,0.293641,0.116969,0.015383,0.255983,0.297663,0.256708,0.338258,0.322052,0.145568,0.0124905,0.0375572,0.38389,0.54721,0.388459,0.321362,0.000557936,0.280757,0.050816,7.35641e-05,0.343265,0.154685,0.462092,0.336254,0.308589,0.0473553,0.19697,0.000586569,0.0537285,0.15063,0.198077,0.281455,0.069449,0.104001,0.138495,0.208834,0.32256,0.082459,0.0667472,0.109684,0.322704,0.0952935,0.181288,0.0289693,0.352328,0.255358,0.0707105,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.00088495,0.244656,0.192188,0.158985,0.0161307,0.0972854,0.0630133,0.249919,0.339517,0.303699,0.198326,0.0905116,0.458518,0.282501,0.252005,0.390891,0.238377,0.334983,0.0210139,0.0461189,0.289389,0.117618,0.014271,0.396962,0.316002,6.19256e-05,0.0582923,0.000143779,0.050521,0.379651,0.185715,0.345505,0.375521,0.0407047,0.0544127,0.221943,0.306427,0.0778743,0.246925,0.208775,0.00168942,0.343014,0.270094,0.0424726,0.156279,0.313647,0.461742,0.10563,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.0311458,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.0478203,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.00103241,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.116796,0.430541,0.00605341,0.224871,0.398887,0.088016,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.000239765,0.0575641,0.309489,0.000297082,0.362154,0.480785,0.185476,0.0642384,0.344469,0.184651,0.0515336,0.297596,0.42392,0.425912,0.380826,0.259046,0.345068,0.151046,0.142558,0.347171,0.321735,0.15463,0.13907,0.470121,0.269432,0.00322239,0.0986342,0.115686,0.0981568,0.162633,0.342661,0.27567,0.248127,0.33299,0.0858973,0.319112,0.526476|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,1.25018,0.654974,0.454983,0.653236,0.733342,2.36918,0.321368,0.106358,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.501863,0.500405,0.770467,0.645033,0.44943,1.35492,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,1.68319,0.27659,0.417272,1.1597,3.81581,0.654459,0.388123,4.0746,0.415749,0.580638,0.414516,0.451846,0.824538,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,1.76707,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,1.64682,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,2.3794,0.330474,5.8101,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.914416,1.53439,1.20877,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,11.7937,0.381528,0.780629,1.06255,0.849074,3.3304,0.389604,1.01316,1.05685,0.967698,0.88799,1.49565,0.951411,0.717647,3.41206,0.437618,2.20213,1.05402,0.494368,1.52665,1.37132,0.412056,0.597842,1.45429,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,2.27985,12.7643,1.15522,1.51895,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,2.25941,0.522159,0.906429,0.754576,0.923751,0.731946,0.720819|tfbs_overrepresentation_jaspar=MA0003.1;0.136928,MA0004.1;0.626788,MA0006.1;2.00428,MA0007.1;2.50943,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;1.18667,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;2.41212,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;2.69304,MA0056.1;0,MA0057.1;0.554727,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;6.0382,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.692739,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;0.818263,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;2.02769,MA0103.1;0.442769,MA0105.1;4.69261,MA0106.1;4.40754,MA0107.1;4.65287,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;5.88637,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.777733,MA0035.2;0.691506,MA0039.2;0.801354,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.858845,MA0047.2;0.767096,MA0112.2;0.425004,MA0065.2;0.880827,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;1.91168,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;1.72541,MA0163.1;1.49262,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;3.15891,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;2.71109,MA0442.1;0}}
|full_id=C1891_Mesothelial_Placental_mesenchymal_Osteoblast_basal_leiomyoma_Olfactory
|id=C1891
}}

Latest revision as of 11:54, 17 September 2013


Full id: C1891_Mesothelial_Placental_mesenchymal_Osteoblast_basal_leiomyoma_Olfactory



Phase1 CAGE Peaks

Hg19::chr2:217498105..217498129,+p3@IGFBP2
Hg19::chr2:217498134..217498154,+p2@IGFBP2
Hg19::chr2:217498164..217498242,+p1@IGFBP2
Hg19::chr2:217526606..217526625,+p@chr2:217526606..217526625
+
Hg19::chr2:217526641..217526672,+p@chr2:217526641..217526672
+


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
ectodermal cell2.82e-1072
embryonic cell1.07e-09250
epithelial cell3.49e-08253
neurectodermal cell5.91e-0859
epithelial cell of nephron1.87e-0715
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.21e-13171
ectoderm1.21e-13171
presumptive ectoderm1.21e-13171
anatomical cluster1.07e-11373
head9.87e-1056
organism subdivision1.06e-09264
subdivision of head2.98e-0949
anterior region of body5.65e-0962
craniocervical region5.65e-0962
organ part1.15e-08218
multi-cellular organism1.51e-08656
ectodermal placode2.67e-0831
multi-tissue structure5.10e-08342
anterior segment of eyeball7.74e-0814
cell layer9.04e-08309
excretory tube1.24e-0716
kidney epithelium1.24e-0716
embryo1.72e-07592
nephron epithelium1.87e-0715
renal tubule1.87e-0715
nephron tubule1.87e-0715
nephron1.87e-0715
uriniferous tubule1.87e-0715
nephrogenic mesenchyme1.87e-0715
renal system1.89e-0748
urinary system structure2.03e-0747
epithelium3.42e-07306
sense organ4.82e-0724
sensory system4.82e-0724
entire sense organ system4.82e-0724
vasculature of organ4.99e-0711
eye5.29e-0721
visual system5.29e-0721
anatomical system6.91e-07624
face7.26e-0722


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)
MA0003.10.136928
MA0004.10.626788
MA0006.12.00428
MA0007.12.50943
MA0009.11.11255
MA0014.10.161847
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.11.18667
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
MA0048.12.41212
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.12.69304
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.16.0382
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
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
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.12.02769
MA0103.10.442769
MA0105.14.69261
MA0106.14.40754
MA0107.14.65287
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
MA0139.15.88637
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.425004
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.91168
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.11.49262
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.15891
MA0102.21.66336
MA0258.10.345771
MA0259.12.71109
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
MAFF#23764222.52614259597810.003041818451272880.0160487232751952
MAFK#7975210.8402932551320.01263683277337880.0456907799210285



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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