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Coexpression cluster:C3109: Difference between revisions

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{{Coexpression_clusters
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cation channel activity!0.00153206738976007!55800;782$GO:0005244!voltage-gated ion channel activity!0.00153206738976007!55800;782$GO:0022832!voltage-gated channel activity!0.00153206738976007!55800;782$GO:0005261!cation channel activity!0.00187461200335429!55800;782$GO:0046873!metal ion transmembrane transporter activity!0.00187461200335429!55800;782$GO:0022836!gated channel activity!0.00187461200335429!55800;782$GO:0005216!ion channel activity!0.00195450256590777!55800;782$GO:0030001!metal ion transport!0.00195450256590777!55800;782$GO:0022838!substrate specific channel activity!0.00195450256590777!55800;782$GO:0015267!channel activity!0.00195450256590777!55800;782$GO:0022803!passive transmembrane transporter activity!0.00195450256590777!55800;782$GO:0006812!cation transport!0.00257593431578316!55800;782$GO:0008324!cation transmembrane transporter activity!0.00257593431578316!55800;782$GO:0005248!voltage-gated sodium channel activity!0.0047167129409244!55800$GO:0015075!ion transmembrane transporter activity!0.00513488797003193!55800;782$GO:0006811!ion transport!0.00513488797003193!55800;782$GO:0022891!substrate-specific transmembrane transporter activity!0.00600986352552187!55800;782$GO:0005891!voltage-gated calcium channel complex!0.00616847909776799!782$GO:0022857!transmembrane transporter activity!0.00621379523318357!55800;782$GO:0022892!substrate-specific transporter activity!0.00688725467743432!55800;782$GO:0005272!sodium channel activity!0.00814285141353296!55800$GO:0005245!voltage-gated calcium channel activity!0.00913501136980657!782$GO:0031402!sodium ion binding!0.0125145366795723!55800$GO:0005262!calcium channel activity!0.014861404268176!782$GO:0003012!muscle system process!0.0190081598302255!782$GO:0006936!muscle contraction!0.0190081598302255!782$GO:0006814!sodium ion transport!0.0191893628056703!55800$GO:0006816!calcium ion transport!0.0195707371948487!782$GO:0005886!plasma membrane!0.0221460263117811!55800;782$GO:0031420!alkali metal ion binding!0.0221460263117811!55800$GO:0006810!transport!0.0228914222139489!55800;782$GO:0015674!di-, tri-valent inorganic cation transport!0.0228914222139489!782$GO:0051234!establishment of localization!0.0228914222139489!55800;782$GO:0051179!localization!0.0260924446112384!55800;782$GO:0015672!monovalent inorganic cation 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,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.0285999,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.0532009,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.0246892,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.0166394,0.0969345,0.202137,0.0541163,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.0229018,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.0440463,0.0445413,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.056548,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,1.94915,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,1.55576,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,0.427404,0.596053,0.855276,1.39264,1.18324,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,1.10051,1.87308,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,0.507157,0.82001,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.698641,1.37083,3.10872,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.265282|tfbs_overrepresentation_jaspar=MA0003.1;0.708947,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;4.7105,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;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,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;3.33427,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;2.03569,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;1.15387,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;1.16674,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;9.73446,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;2.15877,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;0.277623,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;1.38935,MA0160.1;0.871361,MA0161.1;0,MA0162.1;2.76014,MA0163.1;1.84145,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;7.52072,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3109_skeletal_occipital_temporal_postcentral_paracentral_insula_parietal
|id=C3109
}}

Latest revision as of 12:19, 17 September 2013


Full id: C3109_skeletal_occipital_temporal_postcentral_paracentral_insula_parietal



Phase1 CAGE Peaks

Hg19::chr11:123525613..123525633,-p6@SCN3B
Hg19::chr17:37353856..37353900,-p1@CACNB1
Hg19::chr17:37353907..37353930,-p2@CACNB1


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:0022843voltage-gated cation channel activity0.00153206738976007
GO:0005244voltage-gated ion channel activity0.00153206738976007
GO:0022832voltage-gated channel activity0.00153206738976007
GO:0005261cation channel activity0.00187461200335429
GO:0046873metal ion transmembrane transporter activity0.00187461200335429
GO:0022836gated channel activity0.00187461200335429
GO:0005216ion channel activity0.00195450256590777
GO:0030001metal ion transport0.00195450256590777
GO:0022838substrate specific channel activity0.00195450256590777
GO:0015267channel activity0.00195450256590777
GO:0022803passive transmembrane transporter activity0.00195450256590777
GO:0006812cation transport0.00257593431578316
GO:0008324cation transmembrane transporter activity0.00257593431578316
GO:0005248voltage-gated sodium channel activity0.0047167129409244
GO:0015075ion transmembrane transporter activity0.00513488797003193
GO:0006811ion transport0.00513488797003193
GO:0022891substrate-specific transmembrane transporter activity0.00600986352552187
GO:0005891voltage-gated calcium channel complex0.00616847909776799
GO:0022857transmembrane transporter activity0.00621379523318357
GO:0022892substrate-specific transporter activity0.00688725467743432
GO:0005272sodium channel activity0.00814285141353296
GO:0005245voltage-gated calcium channel activity0.00913501136980657
GO:0031402sodium ion binding0.0125145366795723
GO:0005262calcium channel activity0.014861404268176
GO:0003012muscle system process0.0190081598302255
GO:0006936muscle contraction0.0190081598302255
GO:0006814sodium ion transport0.0191893628056703
GO:0006816calcium ion transport0.0195707371948487
GO:0005886plasma membrane0.0221460263117811
GO:0031420alkali metal ion binding0.0221460263117811
GO:0006810transport0.0228914222139489
GO:0015674di-, tri-valent inorganic cation transport0.0228914222139489
GO:0051234establishment of localization0.0228914222139489
GO:0051179localization0.0260924446112384
GO:0015672monovalent inorganic cation transport0.0449431125566352



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
nervous system1.09e-2289
central nervous system7.64e-2281
neural tube1.59e-1956
neural rod1.59e-1956
future spinal cord1.59e-1956
neural keel1.59e-1956
brain2.82e-1868
future brain2.82e-1868
regional part of nervous system2.83e-1853
regional part of brain2.83e-1853
adult organism1.01e-16114
structure with developmental contribution from neural crest5.02e-16132
ectoderm-derived structure1.11e-15171
ectoderm1.11e-15171
presumptive ectoderm1.11e-15171
cerebral hemisphere2.28e-1532
telencephalon2.58e-1534
brain grey matter3.41e-1534
gray matter3.41e-1534
regional part of forebrain4.31e-1541
forebrain4.31e-1541
anterior neural tube4.31e-1541
future forebrain4.31e-1541
neural plate2.48e-1482
presumptive neural plate2.48e-1482
regional part of telencephalon2.56e-1432
regional part of cerebral cortex1.98e-1322
neurectoderm3.06e-1386
ecto-epithelium4.14e-13104
neocortex2.30e-1220
cerebral cortex9.71e-1225
pallium9.71e-1225
organ system subdivision1.08e-11223
pre-chordal neural plate3.69e-1061
epithelium5.27e-08306
multi-tissue structure5.46e-08342
anatomical cluster6.22e-08373
cell layer1.03e-07309


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.14.7105
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
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
MA0073.13.33427
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
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
MA0108.21.15387
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
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.19.73446
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
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
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.27.52072
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EGR1#195834.988179094810140.008056488137383440.0319091192149945



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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