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{{Coexpression_clusters
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255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.00482769,0.264413,0.131761,0.160658,9.86502e-05,0.19924,0.28689,0.236464,0.0597546,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.000158246,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,0.491742,0.221898,1.91835,0.985163,0.436625,0.925331,0.639839,1.60265,1.17594,0.575162,1.14835,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.85641,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,2.64886,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,0.901413,0.726632,0.939121,1.89324,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,1.81344,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,4.08917,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,3.495,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,4.14226,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,2.48899,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.99724,1.37083,2.09999,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,3.92523|tfbs_overrepresentation_jaspar=MA0003.1;0.708947,MA0004.1;1.93041,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.80735,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;1.58389,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,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;0.557638,MA0056.1;0,MA0057.1;4.3182,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,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;8.0808,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;2.03569,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;2.626,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,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;2.36034,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;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;2.15877,MA0138.2;1.04628,MA0002.2;1.20011,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;4.7367,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;3.52399,MA0163.1;1.84145,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;15.3859,MA0102.2;1.88331,MA0258.1;2.22591,MA0259.1;2.40872,MA0442.1;0}}
|full_id=C3272_endometrial_lung_lymphangiectasia_rhabdomyosarcoma_pineal_meningioma_spinal
|id=C3272
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.06e-35!115;UBERON:0003075!4.53e-26!86;UBERON:0007284!4.53e-26!86;UBERON:0002346!2.22e-25!90;UBERON:0001049!2.83e-23!57;UBERON:0005068!2.83e-23!57;UBERON:0006241!2.83e-23!57;UBERON:0007135!2.83e-23!57;UBERON:0005743!3.14e-20!86;UBERON:0002616!4.63e-20!59;UBERON:0000073!8.18e-20!94;UBERON:0001016!8.18e-20!94;UBERON:0001017!1.25e-18!82;UBERON:0000955!1.60e-18!69;UBERON:0006238!1.60e-18!69;UBERON:0003056!1.01e-16!61;UBERON:0000153!1.55e-15!129;UBERON:0007811!1.55e-15!129;UBERON:0000033!1.60e-15!123;UBERON:0003080!2.97e-15!42;UBERON:0002780!3.98e-15!41;UBERON:0001890!3.98e-15!41;UBERON:0006240!3.98e-15!41;UBERON:0000475!5.35e-15!365;UBERON:0004121!1.08e-14!169;UBERON:0000924!1.29e-14!173;UBERON:0006601!1.29e-14!173;UBERON:0001893!2.69e-11!34;UBERON:0002020!3.07e-11!34;UBERON:0003528!3.07e-11!34;UBERON:0002791!9.07e-11!33;UBERON:0001869!3.30e-10!32;UBERON:0004111!3.47e-10!241;UBERON:0000481!4.15e-10!347;UBERON:0000062!1.16e-09!511;UBERON:0003076!1.60e-09!15;UBERON:0003057!1.60e-09!15;UBERON:0000025!1.69e-09!194;UBERON:0000477!2.99e-09!286;UBERON:0000119!3.06e-09!312;UBERON:0000468!4.91e-09!659;UBERON:0000483!7.78e-09!309;UBERON:0004732!1.89e-08!13;UBERON:0002619!2.14e-08!22;UBERON:0000922!5.05e-08!612;UBERON:0004733!8.80e-08!12;UBERON:0002028!8.80e-08!12;UBERON:0007277!8.80e-08!12;UBERON:0001950!1.60e-07!20;UBERON:0000956!4.26e-07!25;UBERON:0000203!4.26e-07!25;UBERON:0000480!7.84e-07!626;UBERON:0002050!9.73e-07!605;UBERON:0005423!9.73e-07!605
}}

Latest revision as of 12:22, 17 September 2013


Full id: C3272_endometrial_lung_lymphangiectasia_rhabdomyosarcoma_pineal_meningioma_spinal



Phase1 CAGE Peaks

Hg19::chr12:26277994..26278001,-p6@BHLHE41
Hg19::chr12:26278008..26278024,-p4@BHLHE41
Hg19::chr12:26278030..26278039,-p7@BHLHE41


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.03e-37114
neural plate7.60e-2582
presumptive neural plate7.60e-2582
neural tube2.67e-2456
neural rod2.67e-2456
future spinal cord2.67e-2456
neural keel2.67e-2456
neurectoderm4.06e-2486
regional part of nervous system2.55e-2253
regional part of brain2.55e-2253
brain1.10e-1868
future brain1.10e-1868
central nervous system2.97e-1881
nervous system1.10e-1789
ecto-epithelium1.42e-17104
structure with developmental contribution from neural crest3.12e-17132
pre-chordal neural plate1.86e-1661
regional part of forebrain1.79e-1541
forebrain1.79e-1541
anterior neural tube1.79e-1541
future forebrain1.79e-1541
ectoderm-derived structure6.38e-13171
ectoderm6.38e-13171
presumptive ectoderm6.38e-13171
telencephalon2.17e-1134
brain grey matter2.58e-1134
gray matter2.58e-1134
organ3.15e-11503
posterior neural tube2.01e-1015
chordal neural plate2.01e-1015
cerebral hemisphere3.44e-1032
regional part of telencephalon3.67e-1032
segmental subdivision of nervous system3.56e-0913
segmental subdivision of hindbrain1.92e-0812
hindbrain1.92e-0812
presumptive hindbrain1.92e-0812
anatomical cluster2.07e-08373
organ system subdivision2.39e-08223
regional part of cerebral cortex2.39e-0822
anatomical conduit4.81e-08240
multi-tissue structure9.01e-08342
tube9.43e-08192
neocortex2.37e-0720
cerebral cortex4.49e-0725
pallium4.49e-0725
multi-cellular organism8.06e-07656


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)
MA0003.10.708947
MA0004.11.93041
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
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
MA0055.10.557638
MA0056.10
MA0057.14.3182
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
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
MA0073.18.0808
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.12.36034
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
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.24.7367
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
MA0162.13.52399
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.215.3859
MA0102.21.88331
MA0258.12.22591
MA0259.12.40872
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
JUND#372736.994663941871030.002921845042734990.0156305165403985
MAX#414936.452555509007120.003721913834265510.0185978163215566
SUZ12#23512350.11578091106297.93834897779404e-060.000221558853258106
TRIM28#10155318.59052504526250.0001555969297255280.00196593125376293
USF1#739136.361499277207960.00388404057290560.018967797315706



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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