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{{Coexpression_clusters
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0762523,0.128736,0.109171,0.04411,0.00229305,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.00157056,0.227491,0.29837,0.0352561,0.177664,0.28365,0.264413,0.131761,0.160658,0.0229018,0.19924,0.28689,0.236464,0.325148,0.115817,0.00206474,0.223831,0.11528,0.194982,0.190993,0.00472154,0.000393044,0.0032012,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.00694911,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=1.66899,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,1.55576,0.388328,1.86765,1.21459,0.534793,0.439574,0.599922,0.137917,3.61775,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.901413,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,2.14035,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,4.3166,1.45054,2.87582,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,1.55552,4.08917,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,3.13442,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,1.96632,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,2.29164,0.318511,6.63372,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,2.84192,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.265282|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;0.826076,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;0.658629,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;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;3.3282,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;1.15625,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;1.04561,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;11.3342,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;3.60951,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;1.5295,MA0106.1;0.986396,MA0107.1;1.36919,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;1.35563,MA0115.1;1.57693,MA0116.1;4.65896,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;0.531867,MA0145.1;0.273764,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;3.37171,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;0.264678,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;8.07038,MA0163.1;1.2663,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;12.3219,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0}}
|full_id=C3419_cerebellum_colon_medial_parietal_middle_occipital_testis
|id=C3419
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.47e-36!94;UBERON:0001016!1.47e-36!94;UBERON:0005743!2.64e-36!86;UBERON:0003075!1.08e-35!86;UBERON:0007284!1.08e-35!86;UBERON:0001017!3.25e-35!82;UBERON:0002346!9.15e-35!90;UBERON:0001049!1.10e-34!57;UBERON:0005068!1.10e-34!57;UBERON:0006241!1.10e-34!57;UBERON:0007135!1.10e-34!57;UBERON:0002616!1.43e-31!59;UBERON:0000119!8.15e-31!312;UBERON:0000483!2.08e-30!309;UBERON:0000955!7.97e-30!69;UBERON:0006238!7.97e-30!69;UBERON:0007023!2.03e-28!115;UBERON:0000475!4.00e-27!365;UBERON:0003056!2.32e-26!61;UBERON:0004121!4.94e-26!169;UBERON:0000033!5.74e-26!123;UBERON:0000924!7.13e-26!173;UBERON:0006601!7.13e-26!173;UBERON:0003080!1.90e-25!42;UBERON:0000153!4.35e-25!129;UBERON:0007811!4.35e-25!129;UBERON:0002780!7.24e-25!41;UBERON:0001890!7.24e-25!41;UBERON:0006240!7.24e-25!41;UBERON:0000025!9.36e-24!194;UBERON:0000481!2.73e-23!347;UBERON:0004111!1.18e-22!241;UBERON:0002020!5.75e-22!34;UBERON:0003528!5.75e-22!34;UBERON:0001893!6.94e-22!34;UBERON:0000477!1.11e-21!286;UBERON:0002791!3.22e-21!33;UBERON:0001869!1.54e-20!32;UBERON:0000956!4.65e-16!25;UBERON:0000203!4.65e-16!25;UBERON:0002619!8.91e-16!22;UBERON:0000468!9.61e-16!659;UBERON:0000922!3.17e-15!612;UBERON:0001950!1.58e-14!20;UBERON:0002050!2.62e-13!605;UBERON:0005423!2.62e-13!605;UBERON:0000467!5.04e-13!625;UBERON:0000923!5.98e-13!604;UBERON:0005291!5.98e-13!604;UBERON:0006598!5.98e-13!604;UBERON:0002532!5.98e-13!604;UBERON:0000480!8.46e-13!626;UBERON:0000064!6.67e-11!219;UBERON:0003076!3.02e-10!15;UBERON:0003057!3.02e-10!15;UBERON:0004732!5.83e-09!13;UBERON:0004733!2.48e-08!12;UBERON:0002028!2.48e-08!12;UBERON:0007277!2.48e-08!12;UBERON:0002308!2.21e-07!9;UBERON:0000125!2.21e-07!9;UBERON:0000062!2.85e-07!511;UBERON:0002420!3.16e-07!9;UBERON:0007245!3.16e-07!9;UBERON:0010009!3.16e-07!9;UBERON:0010011!3.16e-07!9;UBERON:0000454!3.16e-07!9;UBERON:0002298!8.73e-07!8
}}

Latest revision as of 12:25, 17 September 2013


Full id: C3419_cerebellum_colon_medial_parietal_middle_occipital_testis



Phase1 CAGE Peaks

Hg19::chr14:27067411..27067418,-p13@NOVA1
Hg19::chr14:27067428..27067485,-p2@NOVA1
Hg19::chr14:27067502..27067512,-p@chr14:27067502..27067512
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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
neural tube1.47e-3656
neural rod1.47e-3656
future spinal cord1.47e-3656
neural keel1.47e-3656
neural plate4.47e-3682
presumptive neural plate4.47e-3682
neurectoderm3.33e-3586
nervous system1.83e-3489
regional part of nervous system4.50e-3453
regional part of brain4.50e-3453
central nervous system1.05e-3381
structure with developmental contribution from neural crest1.17e-31132
adult organism4.84e-29114
brain5.89e-2868
future brain5.89e-2868
ecto-epithelium9.79e-27104
pre-chordal neural plate1.32e-2661
regional part of forebrain7.29e-2641
forebrain7.29e-2641
anterior neural tube7.29e-2641
future forebrain7.29e-2641
brain grey matter5.62e-2434
gray matter5.62e-2434
telencephalon6.69e-2434
ectoderm-derived structure5.14e-23171
ectoderm5.14e-23171
presumptive ectoderm5.14e-23171
cell layer1.99e-22309
regional part of telencephalon2.39e-2232
cerebral hemisphere2.72e-2232
epithelium1.08e-21306
anatomical cluster3.60e-21373
organ system subdivision6.69e-21223
multi-tissue structure3.01e-18342
regional part of cerebral cortex2.09e-1722
cerebral cortex3.48e-1725
pallium3.48e-1725
tube6.05e-17192
neocortex6.90e-1620
anatomical conduit2.91e-15240
posterior neural tube1.04e-1115
chordal neural plate1.04e-1115
embryo2.00e-11592
multi-cellular organism1.25e-10656
germ layer2.27e-10560
germ layer / neural crest2.27e-10560
embryonic tissue2.27e-10560
presumptive structure2.27e-10560
germ layer / neural crest derived structure2.27e-10560
epiblast (generic)2.27e-10560
embryonic structure2.99e-10564
segmental subdivision of nervous system3.73e-1013
organ part1.54e-09218
developing anatomical structure1.96e-09581
segmental subdivision of hindbrain2.33e-0912
hindbrain2.33e-0912
presumptive hindbrain2.33e-0912
anatomical system3.39e-09624
anatomical group4.65e-09625
neural nucleus2.75e-089
nucleus of brain2.75e-089
basal ganglion5.97e-089
nuclear complex of neuraxis5.97e-089
aggregate regional part of brain5.97e-089
collection of basal ganglia5.97e-089
cerebral subcortex5.97e-089
regional part of metencephalon4.31e-079
metencephalon4.31e-079
future metencephalon4.31e-079


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)
MA0003.10.178364
MA0004.10.826076
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
MA0028.10.658629
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.13.3282
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.111.3342
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
MA0100.13.60951
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.14.65896
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
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
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
MA0162.18.07038
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.212.3219
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
CTCF#1066435.360256373075030.0064925092527670.0278823625087271
NANOG#79923329.24477848101273.99627955670032e-050.000736097778875177
NFYB#4801316.75979325353650.0002123649923296180.00245236482020267
NRF1#4899312.21027944771090.0005492172401020010.00470200010976415
SP1#666735.69838137814090.005403962701712170.0245919154947328



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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