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Coexpression cluster:C1377: Difference between revisions

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{{Coexpression_clusters
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0771,0.613566,0.445744,0.371991,0.117376,0.326635,0.0698709,0.39301,0.396235,0.566617,0.171264,0.0877354,0.357781,0.338712,0.231439,0.359148,0.0641227,0.177916,0.232711,0.327419,0.402268,0.139798,0.163801,0.245045,0.080461,0.433875,0.0910933,0.130132,0.373481,0.462042,0.213394,0.270174,0.406219,0.298,0.40549,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.465261,0.362561,0.578088,0.285875,0.225945,0.18761,0.20516,0.115576,0.086142,0.291842,0.392097,0.352327,0.232997,0.451856,0.521039,0.328594,0.294205,0.448388,0.278746,0.387086,0.232479,0.334662,0.336321,0.139427,0.450171,0.454978,0.366035,0.0845395,0.372037,0.263608,0.3488,0.43615,0.218495,0.398705,0.431643,0.316114,0.360691,0.0371914,0.35537,0.423126,0.288449,0.244977,0.447896,0.395958,0.0557026,0.322324,0.184473,0.363414,0.170988,0.482957,0.388728,0.157712,0.3633,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.537494,0.0238,0.378002,0.340219,0.100112,0.343186,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.0155687,0.0721407,0.251724,0.36701,0.504058,0.491191,0.573638,0.263371,0.457065,0.446399,0.360168,0.0951629,0.0352084,0.442751,0.323763,0.486842,0.458912,0.246162,0.295506,0.369944,0.358783,0.491474,0.102439,0.544575,0.21822,0.388558,0.397562,0.21727,0.351946,0.0680717,0.484083,0.144065,0.437432,0.302171,0.398223,0.178399,0.547908,0.400541,0.372405,0.182559,0.164471,0.533328,0.313891,0.292462,0.132855,0.137165,0.467981,0.191837,0.395568,0.320916,0.289812,0.384881,0.116282,0.369492,0.226443|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.555913,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,1.23744,0.127969,0.436569,2.10217,0.576478,0.387783,0.483957,1.73319,0.202389,0.574247,0.396295,1.04549,0.530785,0.92701,0.302275,0.225641,0.35719,0.316592,0.93226,0.585658,0.878269,0.69481,0.355745,0.513952,0.323162,0.390088,0.992846,0.468392,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.882224,1.15727,0.624519,0.206105,0.562953,0.84426,0.913168,1.20149,0.676305,0.86037,0.684313,0.272514,1.10535,1.10459,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,1.35291,2.03545,0.647343,0.483695,0.982236,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.460936,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,1.56093,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.826087,0.424432,0.308967,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,1.58953,1.90555|tfbs_overrepresentation_jaspar=MA0003.1;2.58181,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.262822,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.465994,MA0056.1;0,MA0057.1;0.450439,MA0058.1;1.16137,MA0059.1;1.15845,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.0569999,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.660742,MA0089.1;0,MA0090.1;0.490736,MA0091.1;1.37996,MA0092.1;0.522012,MA0093.1;1.02138,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.419295,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;1.25994,MA0113.1;0.725375,MA0114.1;1.52717,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;1.19942,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.707171,MA0146.1;1.8938,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.35955,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.680553,MA0065.2;2.35074,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;1.3291,MA0155.1;0.0961854,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;1.39622,MA0163.1;1.18186,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.35176,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0}}
|full_id=C1377_skeletal_cerebellum_corpus_thalamus_heart_occipital_parietal
|id=C1377
}}

Latest revision as of 11:43, 17 September 2013


Full id: C1377_skeletal_cerebellum_corpus_thalamus_heart_occipital_parietal



Phase1 CAGE Peaks

Hg19::chr13:114144998..114145038,-p1@DCUN1D2
Hg19::chr14:77564569..77564685,+p1@KIAA1737
Hg19::chr17:42925242..42925265,+p1@HIGD1B
Hg19::chr19:17579587..17579618,+p3@SLC27A1
Hg19::chr1:202317815..202317854,+p1@PPP1R12B
Hg19::chr7:56160666..56160678,-p2@PHKG1


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:0005964phosphorylase kinase complex0.0348414601404088
GO:0004689phosphorylase kinase activity0.0348414601404088
GO:0009250glucan biosynthetic process0.0365625377286801
GO:0005978glycogen biosynthetic process0.0365625377286801
GO:0004683calmodulin-dependent protein kinase activity0.0365625377286801
GO:0006937regulation of muscle contraction0.0417359612450667
GO:0033692cellular polysaccharide biosynthetic process0.0417359612450667
GO:0000271polysaccharide biosynthetic process0.0417359612450667
GO:0005977glycogen metabolic process0.0417359612450667
GO:0006073glucan metabolic process0.0417359612450667
GO:0006112energy reserve metabolic process0.0434615205705794



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 organism7.08e-56114
neural tube3.55e-3456
neural rod3.55e-3456
future spinal cord3.55e-3456
neural keel3.55e-3456
central nervous system7.80e-3381
regional part of nervous system2.95e-3253
regional part of brain2.95e-3253
nervous system1.10e-3189
brain1.13e-3068
future brain1.13e-3068
regional part of forebrain8.75e-2741
forebrain8.75e-2741
anterior neural tube8.75e-2741
future forebrain8.75e-2741
telencephalon9.06e-2334
brain grey matter9.26e-2334
gray matter9.26e-2334
neural plate5.41e-2282
presumptive neural plate5.41e-2282
regional part of telencephalon2.35e-2132
cerebral hemisphere2.47e-2132
neurectoderm6.65e-2186
organ system subdivision6.41e-18223
ectoderm-derived structure5.34e-17171
ectoderm5.34e-17171
presumptive ectoderm5.34e-17171
cerebral cortex1.32e-1625
pallium1.32e-1625
pre-chordal neural plate3.32e-1661
regional part of cerebral cortex4.56e-1622
ecto-epithelium2.35e-15104
neocortex1.11e-1420
structure with developmental contribution from neural crest2.13e-11132
posterior neural tube1.58e-0815
chordal neural plate1.58e-0815
neural nucleus1.26e-079
nucleus of brain1.26e-079
basal ganglion1.52e-079
nuclear complex of neuraxis1.52e-079
aggregate regional part of brain1.52e-079
collection of basal ganglia1.52e-079
cerebral subcortex1.52e-079
segmental subdivision of nervous system3.08e-0713
segmental subdivision of hindbrain9.11e-0712
hindbrain9.11e-0712
presumptive hindbrain9.11e-0712


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)
MA0003.12.58181
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.262822
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.450439
MA0058.11.16137
MA0059.11.15845
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0569999
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.10.725375
MA0114.11.52717
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.19942
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.11.8938
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.680553
MA0065.22.35074
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.3291
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.11.18186
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.35176
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
BCLAF1#9774310.82632380506090.001772351046991060.0108883865292176
NRF1#489936.105139723855450.009090162079396740.0344036034575146
SIX5#14791238.54335767772950.003504759488012430.0177971301681592
SMARCB1#659839.126357890578710.002900247150367020.0156763747095115
ZNF143#770236.750438276113950.006850259204468580.0290378367178949



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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