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Coexpression cluster:C3284: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.843849,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,1.10051,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.22068,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,1.39614,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,2.82894,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
|tfbs_overrepresentation_jaspar=MA0003.1;1.0927,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.24048,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;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;1.23283,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;0.211629,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;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;2.59836,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,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;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.62945,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.760954,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;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.311277,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:16, 22 January 2013


Full id: C3284_Neurons_Neural_brain_duodenum_occipital_temporal_parietal



Phase1 CAGE Peaks

Hg19::chr12:49582837..49582875,-p1@TUBA1A
Hg19::chr16:89989741..89989759,+p1@TUBB3
Hg19::chr5:43233373..43233374,-p1@ENST00000501221


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

p.valueFDRnGenesnPathwayName
2.96743344876993e-050.006261284576904552156Phagosome (KEGG):04145
9.83008350895251e-060.00311122143058347290Gap junction (KEGG):04540
4.05721049695343e-060.00256821424457152258Pathogenic Escherichia coli infection (KEGG):05130
0.0001071614097380440.01695829309104552296Metabolism of proteins (Reactome):REACT_17015
0.000146494016037910.01854614243039942346{CDC2,351} (Static Module):NA



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:0051258protein polymerization0.000564821943157806
GO:0007018microtubule-based movement0.000772748234088321
GO:0030705cytoskeleton-dependent intracellular transport0.000772748234088321
GO:0003924GTPase activity0.000999902247954942
GO:0005874microtubule0.000999902247954942
GO:0007017microtubule-based process0.000999902247954942
GO:0015630microtubule cytoskeleton0.00231158995183011
GO:0007010cytoskeleton organization and biogenesis0.00323121690947206
GO:0005525GTP binding0.00323121690947206
GO:0032561guanyl ribonucleotide binding0.00323121690947206
GO:0019001guanyl nucleotide binding0.00323121690947206
GO:0046907intracellular transport0.0039276904959845
GO:0044430cytoskeletal part0.0039276904959845
GO:0017111nucleoside-triphosphatase activity0.00398252561133767
GO:0016462pyrophosphatase activity0.00398252561133767
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.00398252561133767
GO:0016817hydrolase activity, acting on acid anhydrides0.00398252561133767
GO:0051649establishment of cellular localization0.0040439511919829
GO:0051641cellular localization0.0040439511919829
GO:0005856cytoskeleton0.00608515578786366
GO:0006996organelle organization and biogenesis0.00672161565731717
GO:0005200structural constituent of cytoskeleton0.0159025179172436
GO:0043234protein complex0.0200923685812479
GO:0043232intracellular non-membrane-bound organelle0.0200923685812479
GO:0043228non-membrane-bound organelle0.0200923685812479
GO:0019904protein domain specific binding0.0200923685812479
GO:0016043cellular component organization and biogenesis0.024117104410547
GO:0032553ribonucleotide binding0.0257609028649648
GO:0032555purine ribonucleotide binding0.0257609028649648
GO:0017076purine nucleotide binding0.0259211692716775
GO:0030182neuron differentiation0.0259211692716775
GO:0032991macromolecular complex0.0259211692716775
GO:0016787hydrolase activity0.0259211692716775
GO:0007067mitosis0.0259211692716775
GO:0006810transport0.0259211692716775
GO:0048699generation of neurons0.0259211692716775
GO:0000087M phase of mitotic cell cycle0.0259211692716775
GO:0044446intracellular organelle part0.0259211692716775
GO:0044422organelle part0.0259211692716775
GO:0051234establishment of localization0.0259211692716775
GO:0022008neurogenesis0.0262332920829515
GO:0000166nucleotide binding0.026251361438029
GO:0051179localization0.0283173817486308
GO:0000279M phase0.0285313078467313
GO:0000278mitotic cell cycle0.029711842062198
GO:0022403cell cycle phase0.0328788603232456
GO:0044267cellular protein metabolic process0.0402331255801294
GO:0044260cellular macromolecule metabolic process0.0404174924579409
GO:0019538protein metabolic process0.0424714515947361



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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
cell layer1.59e-33309
epithelium2.40e-32306
tube6.08e-24192
central nervous system7.85e-2181
anatomical cluster9.88e-20373
vasculature1.51e-1978
vascular system1.51e-1978
nervous system3.40e-1989
anatomical conduit7.57e-19240
epithelial vesicle1.43e-1878
multi-cellular organism1.67e-18656
neural plate5.69e-1882
presumptive neural plate5.69e-1882
brain6.53e-1868
future brain6.53e-1868
ecto-epithelium7.17e-18104
anatomical system1.73e-17624
anatomical group2.82e-17625
structure with developmental contribution from neural crest5.29e-17132
dense mesenchyme tissue9.27e-1773
neurectoderm1.09e-1686
developing anatomical structure1.18e-16581
paraxial mesoderm1.55e-1672
presumptive paraxial mesoderm1.55e-1672
embryo1.63e-16592
somite3.20e-1671
presomitic mesoderm3.20e-1671
presumptive segmental plate3.20e-1671
dermomyotome3.20e-1671
trunk paraxial mesoderm3.20e-1671
neural tube7.41e-1656
neural rod7.41e-1656
future spinal cord7.41e-1656
neural keel7.41e-1656
artery1.28e-1542
arterial blood vessel1.28e-1542
arterial system1.28e-1542
ectoderm-derived structure1.87e-15171
ectoderm1.87e-15171
presumptive ectoderm1.87e-15171
vessel1.91e-1568
epithelial tube open at both ends2.05e-1559
blood vessel2.05e-1559
blood vasculature2.05e-1559
vascular cord2.05e-1559
cardiovascular system3.05e-15109
skeletal muscle tissue3.11e-1562
striated muscle tissue3.11e-1562
myotome3.11e-1562
regional part of nervous system3.14e-1553
regional part of brain3.14e-1553
multilaminar epithelium5.59e-1583
embryonic structure7.78e-15564
muscle tissue1.58e-1464
musculature1.58e-1464
musculature of body1.58e-1464
germ layer4.31e-14560
germ layer / neural crest4.31e-14560
embryonic tissue4.31e-14560
presumptive structure4.31e-14560
germ layer / neural crest derived structure4.31e-14560
epiblast (generic)4.31e-14560
multi-tissue structure7.69e-14342
pre-chordal neural plate9.14e-1461
circulatory system9.25e-14112
splanchnic layer of lateral plate mesoderm3.92e-1283
epithelial tube5.21e-12117
brain grey matter1.83e-1134
gray matter1.83e-1134
telencephalon1.89e-1134
systemic artery2.00e-1133
systemic arterial system2.00e-1133
unilaminar epithelium2.54e-11148
cerebral hemisphere7.23e-1132
regional part of forebrain7.29e-1141
forebrain7.29e-1141
anterior neural tube7.29e-1141
future forebrain7.29e-1141
regional part of telencephalon1.57e-1032
mesenchyme1.53e-09160
entire embryonic mesenchyme1.53e-09160
cerebral cortex2.26e-0925


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
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
MA0073.10.211629
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
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.22.59836
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
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
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
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
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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

No analysis results for this cluster

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:C3284&oldid=2571795"