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Coexpression cluster:C963: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.312007,0.479568,1.49249,1.12193,0.267236,0.439064,0.511871,0.492582,0.161941,0.285547,0.410439,0.553754,0.127813,1.25117,2.07751,0.782718,0.728104,0.218596,0.426514,0.216842,0.305279,0.0355541,1.9325,0.262652,0.347482,0.575764,0.112018,1.09816,0.270022,0.329945,1.01144,0.764231,0.190489,0.129565,0.23642,0.452714,1.22823,0.440165,0.213144,0.14756,0.235191,0.97787,0.0412835,0.264644,0.149259,0.333541,0.51292,0.4002,0.0372068,0.270138,0.589559,0.524278,0.546719,0.839846,0.99088,1.25719,0.752594,0.472204,0.100358,1.18788,0.804523,1.28186,0.488493,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.504216,0.0724994,0.988898,0.124338,0.114787,0.69735,0.684401,0.750836,0.341765,0.858505,2.80761,0.532172,0.166331,0.937974,0.0699734,12.9532,1.61674,0.614883,1.54397,1.17124,0.911274,0.78075,0.571859,0.267904,4.17125,0.423564,0.82268,0.619373,0.0858425,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.704291,0.846745,0.814459,0.812156,0.41935,1.12352,0.232218,1.01271,0.388709,0.664981,1.09481,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,2.79342,0.999117,0.430179,1.14186,1.99816,1.59626,1.10478,2.18551,0.819206,0.657732,1.17257,0.641461,1.83907,0.37143,0.565137,0.50389,0.0382049,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,0.183544,0.510589,0.333592
|tfbs_overrepresentation_for_novel_motifs=0.312007,0.479568,1.49249,1.12193,0.267236,0.439064,0.511871,0.492582,0.161941,0.285547,0.410439,0.553754,0.127813,1.25117,2.07751,0.782718,0.728104,0.218596,0.426514,0.216842,0.305279,0.0355541,1.9325,0.262652,0.347482,0.575764,0.112018,1.09816,0.270022,0.329945,1.01144,0.764231,0.190489,0.129565,0.23642,0.452714,1.22823,0.440165,0.213144,0.14756,0.235191,0.97787,0.0412835,0.264644,0.149259,0.333541,0.51292,0.4002,0.0372068,0.270138,0.589559,0.524278,0.546719,0.839846,0.99088,1.25719,0.752594,0.472204,0.100358,1.18788,0.804523,1.28186,0.488493,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.504216,0.0724994,0.988898,0.124338,0.114787,0.69735,0.684401,0.750836,0.341765,0.858505,2.80761,0.532172,0.166331,0.937974,0.0699734,12.9532,1.61674,0.614883,1.54397,1.17124,0.911274,0.78075,0.571859,0.267904,4.17125,0.423564,0.82268,0.619373,0.0858425,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.704291,0.846745,0.814459,0.812156,0.41935,1.12352,0.232218,1.01271,0.388709,0.664981,1.09481,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,2.79342,0.999117,0.430179,1.14186,1.99816,1.59626,1.10478,2.18551,0.819206,0.657732,1.17257,0.641461,1.83907,0.37143,0.565137,0.50389,0.0382049,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,0.183544,0.510589,0.333592
|tfbs_overrepresentation_jaspar=MA0003.1;0.0416606,MA0004.1;0.415381,MA0006.1;5.76038,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;0.367355,MA0017.1;0.815464,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;0.280275,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;0.514558,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;0.0764047,MA0050.1;1.04113,MA0051.1;0.510444,MA0052.1;1.86771,MA0055.1;2.32641,MA0056.1;0,MA0057.1;0.539841,MA0058.1;0.325084,MA0059.1;0.323879,MA0060.1;0.162248,MA0061.1;0.139804,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;0.109867,MA0069.1;0.856287,MA0070.1;0.845142,MA0071.1;0.47692,MA0072.1;0.840664,MA0073.1;0.0398695,MA0074.1;0.509711,MA0076.1;0.339975,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.324031,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;0.363555,MA0089.1;0,MA0090.1;0.353576,MA0091.1;0.417885,MA0092.1;0.381858,MA0093.1;0.26836,MA0095.1;0,MA0098.1;0,MA0100.1;0.528088,MA0101.1;0.271368,MA0103.1;0.257174,MA0105.1;0.0643619,MA0106.1;3.43646,MA0107.1;0.205358,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.366362,MA0113.1;0.57094,MA0114.1;0.200901,MA0115.1;1.11137,MA0116.1;0.208403,MA0117.1;0.908433,MA0119.1;0.308914,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;0.625452,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.129876,MA0140.1;0.474342,MA0141.1;0.322254,MA0142.1;2.74167,MA0143.1;0.571113,MA0144.1;0.1885,MA0145.1;0.046841,MA0146.1;0.0045741,MA0147.1;0.607251,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;0.135498,MA0035.2;0.473658,MA0039.2;0.0189957,MA0138.2;0.608783,MA0002.2;0.46405,MA0137.2;0.28622,MA0104.2;0.486672,MA0047.2;0.542971,MA0112.2;0.166662,MA0065.2;0.0483532,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.062786,MA0155.1;0.359913,MA0156.1;0.288314,MA0157.1;1.57029,MA0158.1;0,MA0159.1;0.212043,MA0160.1;0.453945,MA0161.1;0,MA0162.1;0.294626,MA0163.1;0.101664,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;0.379791,MA0102.2;1.41188,MA0258.1;1.01999,MA0259.1;2.57627,MA0442.1;0
}}
}}

Revision as of 19:35, 22 January 2013


Full id: C963_mesodermal_hippocampus_amygdala_medulla_thalamus_brain_corpus



Phase1 CAGE Peaks

Hg19::chr9:87284248..87284254,+p27@NTRK2
Hg19::chr9:87284266..87284277,+p12@NTRK2
Hg19::chr9:87284438..87284450,+p16@NTRK2
Hg19::chr9:87284467..87284474,+p24@NTRK2
Hg19::chr9:87284530..87284552,+p6@NTRK2
Hg19::chr9:87284556..87284567,+p9@NTRK2
Hg19::chr9:87285257..87285270,+p19@NTRK2
Hg19::chr9:87285459..87285471,+p28@NTRK2
Hg19::chr9:87285630..87285643,+p15@NTRK2


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 organism2.01e-73114
neural tube1.90e-7156
neural rod1.90e-7156
future spinal cord1.90e-7156
neural keel1.90e-7156
regional part of nervous system2.03e-6653
regional part of brain2.03e-6653
neural plate3.27e-6082
presumptive neural plate3.27e-6082
neurectoderm1.44e-5686
brain7.11e-5568
future brain7.11e-5568
central nervous system8.07e-5581
regional part of forebrain1.45e-5041
forebrain1.45e-5041
anterior neural tube1.45e-5041
future forebrain1.45e-5041
nervous system1.14e-4789
ecto-epithelium4.52e-47104
telencephalon1.05e-4534
brain grey matter2.11e-4534
gray matter2.11e-4534
cerebral hemisphere1.92e-4232
regional part of telencephalon3.60e-4232
pre-chordal neural plate6.85e-4261
structure with developmental contribution from neural crest9.45e-41132
regional part of cerebral cortex6.30e-3622
neocortex1.74e-3220
ectoderm-derived structure3.70e-32171
ectoderm3.70e-32171
presumptive ectoderm3.70e-32171
cerebral cortex6.62e-3125
pallium6.62e-3125
organ system subdivision4.70e-29223
posterior neural tube3.92e-2115
chordal neural plate3.92e-2115
anatomical cluster2.15e-19373
multi-tissue structure5.50e-17342
tube1.52e-16192
segmental subdivision of hindbrain1.97e-1612
hindbrain1.97e-1612
presumptive hindbrain1.97e-1612
basal ganglion2.46e-169
nuclear complex of neuraxis2.46e-169
aggregate regional part of brain2.46e-169
collection of basal ganglia2.46e-169
cerebral subcortex2.46e-169
neural nucleus5.29e-169
nucleus of brain5.29e-169
organ part8.00e-16218
anatomical conduit5.93e-15240
segmental subdivision of nervous system6.08e-1513
telencephalic nucleus7.50e-137
epithelium2.47e-12306
cell layer4.98e-12309
gyrus7.85e-126
brainstem1.81e-116
regional part of metencephalon2.00e-119
metencephalon2.00e-119
future metencephalon2.00e-119
organ5.15e-11503
limbic system2.15e-105
temporal lobe9.29e-106
occipital lobe1.30e-095
parietal lobe1.37e-095
embryo9.06e-09592
corpus striatum1.64e-084
striatum1.64e-084
ventral part of telencephalon1.64e-084
future corpus striatum1.64e-084
embryonic structure5.43e-08564
developing anatomical structure5.95e-08581
germ layer9.06e-08560
germ layer / neural crest9.06e-08560
embryonic tissue9.06e-08560
presumptive structure9.06e-08560
germ layer / neural crest derived structure9.06e-08560
epiblast (generic)9.06e-08560
regional part of diencephalon1.25e-074
multi-cellular organism3.75e-07656
cerebellum6.08e-076
rhombic lip6.08e-076
medulla oblongata8.04e-073
myelencephalon8.04e-073
future myelencephalon8.04e-073
frontal cortex9.00e-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)
MA0003.10.0416606
MA0004.10.415381
MA0006.15.76038
MA0007.10.397529
MA0009.10.870971
MA0014.10.367355
MA0017.10.815464
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.11.04113
MA0051.10.510444
MA0052.11.86771
MA0055.12.32641
MA0056.10
MA0057.10.539841
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.0398695
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.0643619
MA0106.13.43646
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.12.74167
MA0143.10.571113
MA0144.10.1885
MA0145.10.046841
MA0146.10.0045741
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.0189957
MA0138.20.608783
MA0002.20.46405
MA0137.20.28622
MA0104.20.486672
MA0047.20.542971
MA0112.20.166662
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.359913
MA0156.10.288314
MA0157.11.57029
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.294626
MA0163.10.101664
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.379791
MA0102.21.41188
MA0258.11.01999
MA0259.12.57627
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
MYC#460963.48152124773960.002423669811459260.0136573676183767
SUZ12#23512950.11578091106294.96674080237076e-169.62377444635992e-14
ZNF263#1012765.481227758007120.0001955116010530990.00235215252878523



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C963&oldid=2569474"