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Coexpression cluster:C1503: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.97464,1.82196,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,1.18908,0.650887,0.391663,0.415981,0.889639,0.336106,2.69471,0.127969,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,5.02822,0.574247,0.396295,1.04549,0.530785,0.92701,0.816912,0.225641,4.49706,0.134746,1.66498,0.585658,0.329602,0.248856,0.355745,1.2792,0.664116,0.390088,0.0393783,1.18176,0.66382,0.542147,0.630853,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,1.57403,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,3.49818,1.15727,0.218784,1.12235,0.562953,0.84426,0.913168,0.477584,1.25579,0.86037,0.684313,0.272514,1.10535,2.63849,1.29353,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,1.55741,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,1.35291,0.877269,1.56033,1.21459,2.62193,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,1.21803,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,1.96935,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,2.2605,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.639143,1.07915,1.32317,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,3.90135,1.48859
|tfbs_overrepresentation_jaspar=MA0003.1;0.00461978,MA0004.1;0.558729,MA0006.1;1.79433,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.0254709,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;2.6843,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;0.450439,MA0058.1;0.458909,MA0059.1;2.01959,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.578694,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00076337,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;2.28163,MA0078.1;0.763954,MA0081.1;1.15882,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;2.86388,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;1.29635,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,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;2.62599,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.347815,MA0146.1;0.718193,MA0147.1;1.57246,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.0313803,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;2.08061,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.0961854,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;2.38949,MA0160.1;0.600559,MA0161.1;0,MA0162.1;1.39622,MA0163.1;0.113377,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.62382,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:58, 22 January 2013


Full id: C1503_cerebellum_heart_small_left_hippocampus_skeletal_occipital



Phase1 CAGE Peaks

Hg19::chr2:229046330..229046346,-p4@SPHKAP
Hg19::chr2:229046362..229046373,-p6@SPHKAP
Hg19::chr2:229046385..229046408,-p1@SPHKAP
Hg19::chr2:229046419..229046438,-p2@SPHKAP
Hg19::chr2:229046447..229046465,-p3@SPHKAP
Hg19::chr2:229046721..229046736,-p7@SPHKAP


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 tube5.91e-6556
neural rod5.91e-6556
future spinal cord5.91e-6556
neural keel5.91e-6556
regional part of nervous system9.15e-6053
regional part of brain9.15e-6053
central nervous system1.79e-5981
neurectoderm3.25e-5986
nervous system4.11e-5789
adult organism7.12e-53114
neural plate6.83e-5282
presumptive neural plate6.83e-5282
regional part of forebrain2.54e-4941
forebrain2.54e-4941
anterior neural tube2.54e-4941
future forebrain2.54e-4941
brain2.22e-4868
future brain2.22e-4868
telencephalon8.45e-4734
brain grey matter1.23e-4634
gray matter1.23e-4634
cerebral hemisphere2.08e-4332
regional part of telencephalon6.85e-4332
ectoderm-derived structure4.68e-41171
ectoderm4.68e-41171
presumptive ectoderm4.68e-41171
ecto-epithelium8.64e-40104
regional part of cerebral cortex4.55e-3922
structure with developmental contribution from neural crest1.60e-36132
pre-chordal neural plate2.09e-3661
neocortex8.11e-3520
cerebral cortex8.23e-3425
pallium8.23e-3425
organ system subdivision1.33e-22223
tube1.30e-17192
posterior neural tube4.14e-1615
chordal neural plate4.14e-1615
basal ganglion1.55e-149
nuclear complex of neuraxis1.55e-149
aggregate regional part of brain1.55e-149
collection of basal ganglia1.55e-149
cerebral subcortex1.55e-149
neural nucleus4.40e-149
nucleus of brain4.40e-149
anatomical conduit1.34e-13240
anatomical cluster1.96e-13373
gyrus3.26e-136
segmental subdivision of nervous system4.82e-1313
organ part8.34e-13218
limbic system3.05e-125
temporal lobe1.15e-116
parietal lobe2.00e-115
segmental subdivision of hindbrain2.01e-1112
hindbrain2.01e-1112
presumptive hindbrain2.01e-1112
epithelium1.52e-10306
telencephalic nucleus1.94e-107
cell layer2.66e-10309
brainstem3.73e-096
multi-tissue structure4.45e-09342
regional part of metencephalon4.54e-099
metencephalon4.54e-099
future metencephalon4.54e-099
corpus striatum5.01e-094
striatum5.01e-094
ventral part of telencephalon5.01e-094
future corpus striatum5.01e-094
organ2.86e-08503
embryo3.25e-08592
germ layer3.57e-08560
germ layer / neural crest3.57e-08560
embryonic tissue3.57e-08560
presumptive structure3.57e-08560
germ layer / neural crest derived structure3.57e-08560
epiblast (generic)3.57e-08560
multi-cellular organism4.24e-08656
embryonic structure5.62e-08564
developing anatomical structure1.15e-07581
frontal cortex1.93e-073
occipital lobe2.04e-075
pons3.88e-073
caudate-putamen5.46e-073
dorsal striatum5.46e-073


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.11.79433
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
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
MA0051.12.6843
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.12.01959
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.12.28163
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.12.86388
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.11.29635
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
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
MA0139.12.62599
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.10.718193
MA0147.11.57246
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.0313803
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.22.08061
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.12.38949
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.62382
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
SUZ12#23512541.76315075921911.86145137032345e-081.33613827948598e-06



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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