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Coexpression cluster:C4665: Difference between revisions

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{{Coexpression_clusters
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0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.00371523,0.00186843,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.00940743,0.141729,0.263159,0.255956,0.200105,0.227491,0.00569858,0.253509,0.177664,0.28365,0.264413,0.131761,0.0136582,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.00084829,0.224257,0.0935776,0.327622,0.225752,0.207791,0.00475042,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,4.27237,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,2.90305,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,0.599922,1.36391,1.45286,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,2.07812,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,2.42838,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,7.6454,1.45054,8.74621,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,3.76231,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,9.40451,0.560075,0.450952,1.27663,2.40384,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,5.65686,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,2.36218,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,1.54007,7.72083,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,2.56478|tfbs_overrepresentation_jaspar=MA0003.1;3.22681,MA0004.1;0.826076,MA0006.1;2.61424,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;2.44638,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;0.557638,MA0056.1;0,MA0057.1;3.3282,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;5.87909,MA0074.1;0.935474,MA0076.1;1.74184,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;0.531867,MA0145.1;0.273764,MA0146.1;2.3244,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.141,MA0035.2;0.894194,MA0039.2;4.04548,MA0138.2;1.04628,MA0002.2;1.20011,MA0137.2;0.666381,MA0104.2;2.13189,MA0047.2;0.973066,MA0112.2;1.34467,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;7.07944,MA0163.1;2.48891,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;23.8753,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0}}
|full_id=C4665_CD14_amygdala_brain_temporal_medial_occipital_hippocampus
|id=C4665
}}

Latest revision as of 14:17, 17 September 2013


Full id: C4665_CD14_amygdala_brain_temporal_medial_occipital_hippocampus



Phase1 CAGE Peaks

Hg19::chr7:150783530..150783552,+p2@AGAP3
Hg19::chr7:150783553..150783570,+p1@AGAP3
Hg19::chr7:150783576..150783596,+p3@AGAP3


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

Uber Anatomy
Ontology termp-valuen
neural tube1.65e-2456
neural rod1.65e-2456
future spinal cord1.65e-2456
neural keel1.65e-2456
regional part of nervous system2.60e-2353
regional part of brain2.60e-2353
central nervous system6.94e-2281
nervous system2.53e-2189
neurectoderm4.57e-2186
neural plate1.31e-2082
presumptive neural plate1.31e-2082
regional part of forebrain3.82e-1941
forebrain3.82e-1941
anterior neural tube3.82e-1941
future forebrain3.82e-1941
brain4.88e-1968
future brain4.88e-1968
pre-chordal neural plate6.86e-1861
telencephalon1.18e-1634
brain grey matter1.99e-1634
gray matter1.99e-1634
tube2.99e-16192
germ layer4.12e-16560
germ layer / neural crest4.12e-16560
embryonic tissue4.12e-16560
presumptive structure4.12e-16560
germ layer / neural crest derived structure4.12e-16560
epiblast (generic)4.12e-16560
ecto-epithelium5.51e-16104
developing anatomical structure7.01e-16581
cerebral hemisphere1.17e-1532
regional part of telencephalon1.53e-1532
embryonic structure3.07e-15564
embryo1.01e-14592
regional part of cerebral cortex8.17e-1422
multi-cellular organism2.24e-13656
neocortex1.16e-1220
anatomical system1.58e-12624
anatomical group2.72e-12625
cerebral cortex5.51e-1225
pallium5.51e-1225
structure with developmental contribution from neural crest6.64e-12132
bone marrow7.56e-1276
cell layer2.32e-11309
epithelium3.43e-11306
anatomical conduit3.47e-11240
ectoderm-derived structure3.56e-11171
ectoderm3.56e-11171
presumptive ectoderm3.56e-11171
bone element1.51e-1082
immune system1.21e-0893
anatomical cluster2.36e-08373
skeletal element3.03e-0890
skeletal system4.16e-08100
organ1.07e-07503
lateral plate mesoderm1.09e-07203
blood vessel endothelium3.95e-0718
endothelium3.95e-0718
cardiovascular system endothelium3.95e-0718


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)
MA0003.13.22681
MA0004.10.826076
MA0006.12.61424
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
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
MA0055.10.557638
MA0056.10
MA0057.13.3282
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
MA0073.15.87909
MA0074.10.935474
MA0076.11.74184
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
MA0144.10.531867
MA0145.10.273764
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.24.04548
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.21.34467
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
MA0162.17.07944
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.223.8753
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
CCNT2#90536.336201576962630.003930750035764890.0191110098685
E2F4#1874312.66806031528440.0004917987006298980.00438924666681644
E2F6#187635.017155731697390.00791769806886330.0324242821869589
EBF1#187938.9064668465690.00141523283560980.00919074133305884
EGR1#195834.988179094810140.008056488137383440.0322416969222589
ELF1#199734.258097958807540.01295179875054610.0464868001136945
EP300#203336.77394172622320.003216880500103790.0168447120857528
ETS1#211339.728760922202340.001085840092584840.00765106284101118
GABPB1#255337.067683836182170.002832212825417420.0154784654774343
HMGN3#932438.178547723350590.001827766942164210.0109186153218949
IRF1#365937.63716375356390.002244692747297240.0128710588467649
MYC#460935.22228187160940.007020843755740150.029601142505581
PAX5#507936.669565531177830.003370290999677260.0173642060932018
POU2F2#545239.106124057742520.001324165192682130.00885594829396318
REST#597839.650028716128020.001112636247114590.00771188060873378
SIN3A#2594235.408884726815140.006318961977991520.0278235199637192
SMARCB1#6598318.25271578115740.000164397760679890.00203937970396093
YY1#752834.911170749853860.008441455341808260.0331186008430921
ZBTB7A#5134137.35190930787590.002516255860282270.0140901423940818
ZNF263#1012738.221841637010680.001799043925565870.0110109205662315



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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