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Coexpression cluster:C3129: Difference between revisions

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{{Coexpression_clusters
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1,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.0404514,0.101021,0.222548,0.175934,0.157274,0.00199458,0.252796,0.205954,0.0107847|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,2.77894,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,1.10051,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,2.58159,0.960908,0.498519,1.39759,2.95969,0.303648,2.64731,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,4.86269,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,2.3415,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.96295|tfbs_overrepresentation_jaspar=MA0003.1;1.0927,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;3.14798,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;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;6.72372,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0185922,MA0074.1;0.935474,MA0076.1;0.734647,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;2.19699,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;2.3269,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;3.02012,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;3.4624,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;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;2.26598,MA0145.1;1.37817,MA0146.1;0.107247,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.15986,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;2.70092,MA0104.2;2.13189,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;1.51687,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;0.455568,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.00160703,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3129_Melanocyte_melanoma_occipital_brain_parietal_aorta_Fibroblast
|id=C3129
}}

Latest revision as of 12:19, 17 September 2013


Full id: C3129_Melanocyte_melanoma_occipital_brain_parietal_aorta_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:19734342..19734353,+p@chr11:19734342..19734353
+
Hg19::chr11:19734369..19734391,+p1@NAV2
Hg19::chr11:19734399..19734410,+p4@NAV2


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
mesodermal cell1.01e-13121
fibroblast2.15e-1076
endothelial cell of vascular tree5.42e-0924
endothelial cell1.04e-0836
lining cell1.18e-0858
barrier cell1.18e-0858
meso-epithelial cell3.72e-0845
non-terminally differentiated cell1.35e-07106
embryonic cell8.04e-07250
Uber Anatomy
Ontology termp-valuen
anatomical cluster5.61e-32373
anatomical conduit1.90e-28240
tube3.45e-26192
cell layer1.60e-25309
epithelium1.35e-24306
structure with developmental contribution from neural crest6.04e-23132
neural plate8.11e-2282
presumptive neural plate8.11e-2282
neural tube3.37e-2056
neural rod3.37e-2056
future spinal cord3.37e-2056
neural keel3.37e-2056
multi-tissue structure9.00e-20342
neurectoderm5.10e-1986
regional part of nervous system7.10e-1953
regional part of brain7.10e-1953
central nervous system8.57e-1981
nervous system1.80e-1889
ectoderm-derived structure8.86e-17171
ectoderm8.86e-17171
presumptive ectoderm8.86e-17171
brain1.36e-1668
future brain1.36e-1668
ecto-epithelium9.43e-16104
vasculature1.79e-1578
vascular system1.79e-1578
pre-chordal neural plate3.21e-1561
multi-cellular organism5.05e-15656
anatomical system8.37e-15624
anatomical group1.61e-14625
regional part of forebrain2.34e-1441
forebrain2.34e-1441
anterior neural tube2.34e-1441
future forebrain2.34e-1441
brain grey matter1.16e-1334
gray matter1.16e-1334
vessel1.41e-1368
telencephalon1.60e-1334
cerebral hemisphere2.68e-1332
organ part2.79e-13218
epithelial tube5.86e-13117
regional part of telencephalon8.07e-1332
splanchnic layer of lateral plate mesoderm1.39e-1283
epithelial tube open at both ends1.02e-1159
blood vessel1.02e-1159
blood vasculature1.02e-1159
vascular cord1.02e-1159
developing anatomical structure1.93e-11581
cerebral cortex1.85e-1025
pallium1.85e-1025
germ layer2.09e-10560
germ layer / neural crest2.09e-10560
embryonic tissue2.09e-10560
presumptive structure2.09e-10560
germ layer / neural crest derived structure2.09e-10560
epiblast (generic)2.09e-10560
embryo2.66e-10592
circulatory system3.78e-10112
embryonic structure6.11e-10564
adult organism6.23e-10114
cardiovascular system6.64e-10109
regional part of cerebral cortex3.11e-0922
neocortex4.06e-0920
organ system subdivision9.91e-09223
artery1.29e-0842
arterial blood vessel1.29e-0842
arterial system1.29e-0842
systemic artery5.88e-0833
systemic arterial system5.88e-0833
simple squamous epithelium1.19e-0722
posterior neural tube3.79e-0715
chordal neural plate3.79e-0715
epithelial vesicle5.06e-0778


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.14798
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.16.72372
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
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
MA0100.12.19699
MA0101.10.646932
MA0103.10.628063
MA0105.12.3269
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.13.02012
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.13.4624
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.12.26598
MA0145.11.37817
MA0146.10.107247
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.22.70092
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CCNT2#90536.336201576962630.003930750035764890.018918138386417
E2F1#186934.907389214879320.008460985347239390.0323671971239271
E2F4#1874312.66806031528440.0004917987006298980.00435537729967659
E2F6#187635.017155731697390.00791769806886330.0320472994850992
FOS#235338.99795530889440.001372499272417130.00894939448785494
IRF1#365937.63716375356390.002244692747297240.0127631460058241
MXI1#460139.96157162875930.001011470541259020.00718227983808478
NFYA#4800318.42558069983050.0001598135507814160.00199055067740732
NFYB#4801316.75979325353650.0002123649923296180.00244992681253872
PBX3#5090321.91451268674419.49854535978121e-050.00136060702075187
SP1#666735.69838137814090.005403962701712170.0245469928933593
SUZ12#23512350.11578091106297.93834897779404e-060.000221263204935103
TCF7L2#6934310.77017656313730.0008003181298398380.00611757484903337
USF1#739136.361499277207960.00388404057290560.0189562742835501
YY1#752834.911170749853860.008441455341808260.032799477452402



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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