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Coexpression cluster:C4718: Difference between revisions

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{{Coexpression_clusters
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3,0.295769,0.286691,0.347036,0.141729,0.0037817,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=1.66899,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,1.55576,1.00813,0.795576,1.21459,1.3235,0.439574,0.599922,0.843849,2.47502,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,1.44641,1.72524,0.939121,1.89324,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.06461,1.81344,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,5.52876,0.82001,1.76229,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,2.84649,1.05794,0.946807,0.569121,1.22626,1.27082,1.1798,1.09802,1.90788,1.16312,0.921547,0.743661,1.50815,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,2.29164,0.318511,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.265282|tfbs_overrepresentation_jaspar=MA0003.1;2.61626,MA0004.1;3.20493,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.758317,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;1.58389,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;2.37507,MA0056.1;0,MA0057.1;0.333427,MA0058.1;4.13609,MA0059.1;4.12962,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;1.04561,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0185922,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;3.82193,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;1.52002,MA0105.1;0.846801,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;1.96087,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;5.85055,MA0146.1;0.348055,MA0147.1;2.37462,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;3.37171,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;2.13189,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;2.02721,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;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;1.54885,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;3.52796,MA0442.1;0}}
|full_id=C4718_cerebellum_pancreas_occipital_pharyngeal_Hepatocyte_cervical_rectal
|id=C4718
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4718_cerebellum_pancreas_occipital_pharyngeal_Hepatocyte_cervical_rectal



Phase1 CAGE Peaks

Hg19::chr8:110656917..110656960,-p4@SYBU
Hg19::chr8:110656962..110656982,-p3@SYBU
Hg19::chr8:110656995..110657075,-p1@SYBU


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell2.30e-08253
endodermal cell4.73e-0858
Uber Anatomy
Ontology termp-valuen
adult organism1.89e-33114
organ system subdivision1.13e-31223
neural tube1.12e-2356
neural rod1.12e-2356
future spinal cord1.12e-2356
neural keel1.12e-2356
regional part of nervous system3.06e-2253
regional part of brain3.06e-2253
anatomical cluster1.33e-21373
central nervous system2.92e-2081
brain8.92e-2068
future brain8.92e-2068
neural plate1.09e-1982
presumptive neural plate1.09e-1982
ecto-epithelium1.37e-19104
neurectoderm7.28e-1886
regional part of forebrain1.37e-1741
forebrain1.37e-1741
anterior neural tube1.37e-1741
future forebrain1.37e-1741
nervous system2.79e-1789
multi-tissue structure5.27e-17342
ectoderm-derived structure8.98e-17171
ectoderm8.98e-17171
presumptive ectoderm8.98e-17171
organ part4.92e-16218
brain grey matter1.32e-1534
gray matter1.32e-1534
telencephalon3.06e-1534
cerebral hemisphere8.74e-1532
regional part of telencephalon1.49e-1432
regional part of cerebral cortex2.50e-1422
pre-chordal neural plate6.30e-1461
neocortex2.72e-1320
digestive system3.10e-13145
digestive tract3.10e-13145
primitive gut3.10e-13145
anatomical conduit3.33e-12240
organ5.20e-12503
endoderm-derived structure5.84e-12160
endoderm5.84e-12160
presumptive endoderm5.84e-12160
cerebral cortex1.17e-1125
pallium1.17e-1125
subdivision of digestive tract1.48e-11118
structure with developmental contribution from neural crest1.60e-11132
respiratory system3.24e-0974
organ segment1.93e-0898
foregut3.39e-0887
respiratory primordium3.51e-0838
endoderm of foregut3.51e-0838
tube3.77e-08192
posterior neural tube2.66e-0715
chordal neural plate2.66e-0715
respiratory tract7.31e-0754
Disease
Ontology termp-valuen
carcinoma2.01e-10106
cell type cancer3.16e-07143


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)
MA0003.12.61626
MA0004.13.20493
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0055.12.37507
MA0056.10
MA0057.10.333427
MA0058.14.13609
MA0059.14.12962
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
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
MA0093.13.82193
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.10.846801
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
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.15.85055
MA0146.10.348055
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
MA0102.21.88331
MA0258.10.519674
MA0259.13.52796
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#90536.336201576962630.003930750035764890.0191216918806302
CTCF#1066435.360256373075030.0064925092527670.0281380684641768
E2F1#186934.907389214879320.008460985347239390.0327826692146294
E2F6#187635.017155731697390.00791769806886330.0324433642739334
EGR1#195834.988179094810140.008056488137383440.0322590025909669
EP300#203336.77394172622320.003216880500103790.0168523165404464
ESR1#2099330.76860329615453.43136389821584e-050.000679371022115192
HMGN3#932438.178547723350590.001827766942164210.010925489450131
MAX#414936.452555509007120.003721913834265510.0187439945480208
MXI1#460139.96157162875930.001011470541259020.0072354090314076
MYC#460935.22228187160940.007020843755740150.0296142932554825
NRF1#4899312.21027944771090.0005492172401020010.00473616541483056
PAX5#507936.669565531177830.003370290999677260.0173710616253908
RAD21#5885310.35503389545630.0009004912073565420.00668845752116562
SIN3A#2594235.408884726815140.006318961977991520.0278340814010737
SMC3#9126315.04493284493280.0002935825420371870.00310905162318209
SRF#6722313.79717826216780.0003806615025800190.00376547704754258
TCF7L2#6934310.77017656313730.0008003181298398380.00617542853064964
TFAP2A#7020316.5186343730450.0002218033880766340.00249487604171627
TFAP2C#7022310.80922860986020.0007916746575753130.00618921398027608
USF1#739136.361499277207960.00388404057290560.0191233883364929
USF2#7392312.99219738506960.0004558979393427810.00423306586833399
YY1#752834.911170749853860.008441455341808260.0331322918727916
ZEB1#6935316.88843201754390.0002075486917327580.00243826522113358



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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