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Coexpression cluster:C3045: Difference between revisions

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{{Coexpression_clusters
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complex!0.0134222261032357!5532$GO:0008287!protein serine/threonine phosphatase complex!0.03969244056313!5532$GO:0004722!protein serine/threonine phosphatase activity!0.03969244056313!5532$GO:0016567!protein ubiquitination!0.03969244056313!23291$GO:0043687!post-translational protein modification!0.03969244056313!5532;23291$GO:0032446!protein modification by small protein conjugation!0.03969244056313!23291$GO:0000151!ubiquitin ligase complex!0.03969244056313!23291$GO:0006464!protein modification process!0.03969244056313!5532;23291$GO:0043412!biopolymer modification!0.03969244056313!5532;23291$GO:0043234!protein complex!0.03969244056313!5532;23291$GO:0005516!calmodulin binding!0.03969244056313!5532$GO:0016055!Wnt receptor signaling pathway!0.03969244056313!23291$GO:0004842!ubiquitin-protein ligase activity!0.03969244056313!23291$GO:0008639!small protein conjugating enzyme activity!0.03969244056313!23291$GO:0032991!macromolecular complex!0.0485798812421496!5532;23291$GO:0019787!small conjugating protein ligase activity!0.0485798812421496!23291$GO:0006470!protein amino acid dephosphorylation!0.0485798812421496!5532|id=C3045|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001049!1.37e-27!56;UBERON:0005068!1.37e-27!56;UBERON:0006241!1.37e-27!56;UBERON:0007135!1.37e-27!56;UBERON:0007023!3.93e-26!114;UBERON:0000073!6.07e-26!53;UBERON:0002616!6.07e-26!53;UBERON:0001016!3.09e-25!89;UBERON:0001017!8.77e-25!81;UBERON:0000955!5.97e-23!68;UBERON:0006238!5.97e-23!68;UBERON:0003075!2.58e-22!82;UBERON:0007284!2.58e-22!82;UBERON:0002346!5.66e-22!86;UBERON:0002780!1.45e-21!41;UBERON:0001890!1.45e-21!41;UBERON:0003080!1.45e-21!41;UBERON:0006240!1.45e-21!41;UBERON:0010314!1.66e-18!132;UBERON:0003528!3.16e-18!34;UBERON:0002020!3.16e-18!34;UBERON:0001893!5.71e-18!34;UBERON:0001869!1.94e-17!32;UBERON:0002791!4.19e-17!32;UBERON:0004121!1.24e-16!171;UBERON:0000924!1.24e-16!171;UBERON:0006601!1.24e-16!171;UBERON:0003056!1.30e-16!61;UBERON:0002619!2.34e-15!22;UBERON:0010371!2.00e-14!104;UBERON:0001950!4.18e-14!20;UBERON:0011216!2.06e-13!223;UBERON:0000956!2.39e-13!25;UBERON:0000203!2.39e-13!25;UBERON:0000025!1.59e-12!192;UBERON:0000477!7.93e-12!373;UBERON:0004111!2.23e-11!240;UBERON:0000481!4.31e-11!342;UBERON:0000119!2.45e-09!309;UBERON:0000483!3.25e-09!306;UBERON:0000064!5.32e-08!218;UBERON:0003076!3.06e-07!15;UBERON:0003057!3.06e-07!15|pathway_enrichment=1.58091305570944e-05;0.00879764861457124;2;114;Oocyte meiosis (KEGG):04114!2.77966780871129e-05;0.00879764861457124;2;151;Wnt signaling pathway 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,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.0262794,0.195218,0.124213,0.0370716,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.0339803,0.115972,0.224568,0.246105,0.173026,0.200432,0.0102599,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.0437875,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.0377035,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.000393514,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.0385243,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.0257187,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.00475042,0.0859274,0.316866,0.171683,0.0133429,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,1.11965,0.599922,0.137917,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,0.63803,0.461452,1.72524,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,1.90788,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,1.94007,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,1.8537,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,0.853445,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.265282|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;0.118426,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;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;3.923,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;1.31954,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;1.31729,MA0145.1;0.273764,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.141,MA0035.2;0.894194,MA0039.2;1.15986,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;1.31345,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;2.76014,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.69213,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0}}
|full_id=C3045_occipital_brain_hippocampus_medial_cerebellum_temporal_amygdala
|id=C3045
}}

Latest revision as of 12:18, 17 September 2013


Full id: C3045_occipital_brain_hippocampus_medial_cerebellum_temporal_amygdala



Phase1 CAGE Peaks

Hg19::chr10:75255724..75255792,-p1@PPP3CB
Hg19::chr2:86790580..86790591,-p4@CHMP3
p4@RNF103-CHMP3
Hg19::chr5:171433662..171433686,-p2@FBXW11


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
1.58091305570944e-050.008797648614571242114Oocyte meiosis (KEGG):04114
2.77966780871129e-050.008797648614571242151Wnt signaling pathway (KEGG):04310



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:0005955calcineurin complex0.0134222261032357
GO:0008287protein serine/threonine phosphatase complex0.03969244056313
GO:0004722protein serine/threonine phosphatase activity0.03969244056313
GO:0016567protein ubiquitination0.03969244056313
GO:0043687post-translational protein modification0.03969244056313
GO:0032446protein modification by small protein conjugation0.03969244056313
GO:0000151ubiquitin ligase complex0.03969244056313
GO:0006464protein modification process0.03969244056313
GO:0043412biopolymer modification0.03969244056313
GO:0043234protein complex0.03969244056313
GO:0005516calmodulin binding0.03969244056313
GO:0016055Wnt receptor signaling pathway0.03969244056313
GO:0004842ubiquitin-protein ligase activity0.03969244056313
GO:0008639small protein conjugating enzyme activity0.03969244056313
GO:0032991macromolecular complex0.0485798812421496
GO:0019787small conjugating protein ligase activity0.0485798812421496
GO:0006470protein amino acid dephosphorylation0.0485798812421496



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 tube1.37e-2756
neural rod1.37e-2756
future spinal cord1.37e-2756
neural keel1.37e-2756
adult organism3.93e-26114
regional part of nervous system6.07e-2653
regional part of brain6.07e-2653
nervous system3.09e-2589
central nervous system8.77e-2581
brain5.97e-2368
future brain5.97e-2368
neural plate2.58e-2282
presumptive neural plate2.58e-2282
neurectoderm5.66e-2286
regional part of forebrain1.45e-2141
forebrain1.45e-2141
anterior neural tube1.45e-2141
future forebrain1.45e-2141
structure with developmental contribution from neural crest1.66e-18132
brain grey matter3.16e-1834
gray matter3.16e-1834
telencephalon5.71e-1834
cerebral hemisphere1.94e-1732
regional part of telencephalon4.19e-1732
ectoderm-derived structure1.24e-16171
ectoderm1.24e-16171
presumptive ectoderm1.24e-16171
pre-chordal neural plate1.30e-1661
regional part of cerebral cortex2.34e-1522
ecto-epithelium2.00e-14104
neocortex4.18e-1420
organ system subdivision2.06e-13223
cerebral cortex2.39e-1325
pallium2.39e-1325
tube1.59e-12192
anatomical cluster7.93e-12373
anatomical conduit2.23e-11240
multi-tissue structure4.31e-11342
cell layer2.45e-09309
epithelium3.25e-09306
organ part5.32e-08218
posterior neural tube3.06e-0715
chordal neural plate3.06e-0715


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
MA0014.10.118426
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
MA0060.10.492218
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
MA0073.13.923
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
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
MA0144.11.31729
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.21.15986
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
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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#9774321.65264761012189.8473954032885e-050.0013882993095627
EGR1#195834.988179094810140.008056488137383440.031899441353459
ELK4#2005210.8237877723120.01091284719516480.0401722480073249
FAM48A#555781385.056250.002594789661407470.014348347405503
IRF1#365937.63716375356390.002244692747297240.0127589782211264
JUND#372736.994663941871030.002921845042734990.0156129227126221
MAX#414936.452555509007120.003721913834265510.0185667252071482
MEF2A#4205212.4954872730960.008235029478029740.0324709572113092
MYC#460935.22228187160940.007020843755740150.0293159243965195
NFKB1#479035.488063424193840.006049381815655430.0268527451311305
NRF1#4899312.21027944771090.0005492172401020010.00469276767888513
PAX5#507936.669565531177830.003370290999677260.0172223222289507
POU2F2#545239.106124057742520.001324165192682130.00879344366748451
SIX5#147912211.3911435703060.009873820081429030.0370566298506672
STAT1#6772213.80439166479950.006770931708444080.0287424028247852



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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