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Coexpression cluster:C3751: Difference between revisions

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{{Coexpression_clusters
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2,0.193601,0.220904,0.222977,0.341681,0.0542164,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.0377094,0.203781,0.21382,0.207559,0.141867,0.193031,0.0339803,0.115972,0.0273485,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.00467879,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.0215087,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.00172878,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,1.23863,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,1.96502,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,1.39264,2.05816,0.598234,0.777097,0.259059,0.63803,0.151453,2.89234,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.78399,2.0644,2.8077,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,0.886337,1.45054,3.91579,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.95969,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,2.84649,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,2.82894,0.684398,0.830777,1.58942,1.44883,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,3.25952,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,3.36921,1.54007,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,2.6906,1.69998,1.11698,0.960047,0.524529,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;5.30359,MA0004.1;0.826076,MA0006.1;3.80603,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.24048,MA0017.1;2.76432,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;3.37768,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;4.88467,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;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;3.60951,MA0101.1;0.646932,MA0103.1;1.52002,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;2.32521,MA0115.1;1.57693,MA0116.1;2.36034,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;0.752137,MA0146.1;0.107247,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.0526989,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;2.13692,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;1.51687,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;1.43223,MA0163.1;0.776149,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=C3751_Mesenchymal_Renal_Reticulocytes_Alveolar_neuroblastoma_nonsmall_Neurons
|id=C3751
}}

Latest revision as of 12:32, 17 September 2013


Full id: C3751_Mesenchymal_Renal_Reticulocytes_Alveolar_neuroblastoma_nonsmall_Neurons



Phase1 CAGE Peaks

Hg19::chr19:12912626..12912647,-p3@PRDX2
Hg19::chr19:12912657..12912669,-p2@PRDX2
Hg19::chr19:12912688..12912699,-p4@PRDX2


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
anatomical cluster2.36e-26373
epithelium3.86e-23306
cell layer7.58e-23309
multi-tissue structure7.32e-20342
tube1.42e-16192
anatomical conduit1.04e-15240
vasculature9.63e-1478
vascular system9.63e-1478
epithelial tube4.87e-13117
organ part9.21e-13218
ectoderm-derived structure1.69e-12171
ectoderm1.69e-12171
presumptive ectoderm1.69e-12171
epithelial vesicle5.24e-1278
structure with developmental contribution from neural crest5.53e-12132
neural plate8.06e-1282
presumptive neural plate8.06e-1282
splanchnic layer of lateral plate mesoderm1.21e-1183
mesenchyme1.75e-11160
entire embryonic mesenchyme1.75e-11160
neurectoderm2.69e-1186
vessel3.25e-1168
circulatory system3.81e-11112
pre-chordal neural plate4.71e-1161
ecto-epithelium6.09e-11104
dense mesenchyme tissue3.48e-1073
cardiovascular system3.78e-10109
paraxial mesoderm4.64e-1072
presumptive paraxial mesoderm4.64e-1072
epithelial tube open at both ends4.94e-1059
blood vessel4.94e-1059
blood vasculature4.94e-1059
vascular cord4.94e-1059
nervous system6.78e-1089
skeletal muscle tissue7.05e-1062
striated muscle tissue7.05e-1062
myotome7.05e-1062
somite7.75e-1071
presomitic mesoderm7.75e-1071
presumptive segmental plate7.75e-1071
dermomyotome7.75e-1071
trunk paraxial mesoderm7.75e-1071
central nervous system9.26e-1081
multilaminar epithelium1.27e-0983
muscle tissue2.87e-0964
musculature2.87e-0964
musculature of body2.87e-0964
unilaminar epithelium5.60e-09148
multi-cellular organism5.67e-09656
compound organ9.34e-0968
artery2.58e-0842
arterial blood vessel2.58e-0842
arterial system2.58e-0842
trunk mesenchyme4.00e-08122
embryo4.15e-08592
developing anatomical structure1.18e-07581
nephron epithelium1.74e-0715
renal tubule1.74e-0715
nephron tubule1.74e-0715
nephron1.74e-0715
uriniferous tubule1.74e-0715
nephrogenic mesenchyme1.74e-0715
organism subdivision2.38e-07264
excretory tube2.52e-0716
kidney epithelium2.52e-0716
regional part of nervous system2.76e-0753
regional part of brain2.76e-0753
brain2.89e-0768
future brain2.89e-0768
neural tube5.34e-0756
neural rod5.34e-0756
future spinal cord5.34e-0756
neural keel5.34e-0756
cerebral hemisphere5.47e-0732
cerebral cortex9.53e-0725
pallium9.53e-0725


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)
MA0003.15.30359
MA0004.10.826076
MA0006.13.80603
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.12.76432
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
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.14.88467
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
MA0073.10.211629
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
MA0100.13.60951
MA0101.10.646932
MA0103.11.52002
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
MA0115.11.57693
MA0116.12.36034
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
MA0145.10.752137
MA0146.10.107247
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.22.13692
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.776149
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
BRCA1#672320.18423064322380.0001215704860271640.00164167313035828
CCNT2#90536.336201576962630.003930750035764890.0189951694884902
CTCF#1066435.360256373075030.0064925092527670.0279375045877687
E2F6#187635.017155731697390.00791769806886330.0322083223733744
EGR1#195834.988179094810140.008056488137383440.0320513318825304
ELF1#199734.258097958807540.01295179875054610.0462104710886951
EP300#203336.77394172622320.003216880500103790.0167423024144287
FOXA1#3169311.08141974938550.000734755275698670.005811215921143
GTF2F1#2962312.73966087675770.0004835525047438590.00433714703220061
HMGN3#932438.178547723350590.001827766942164210.0108664058560192
JUND#372736.994663941871030.002921845042734990.015671455136514
MAX#414936.452555509007120.003721913834265510.0186424132625224
MXI1#460139.96157162875930.001011470541259020.00720088424393667
MYC#460935.22228187160940.007020843755740150.0294383290912858
NANOG#79923329.24477848101273.99627955670032e-050.00073752861039446
NFKB1#479035.488063424193840.006049381815655430.0269547074297213
PAX5#507936.669565531177830.003370290999677260.017284905800201
POU2F2#545239.106124057742520.001324165192682130.00881923911475856
REST#597839.650028716128020.001112636247114590.00767216539102077
RFX5#5993312.04791082719510.0005717246050312580.00484386679847972
RXRA#6256320.07461713913330.0001235730348432220.00165205378724927
SIN3A#2594235.408884726815140.006318961977991520.027660256926923
SIX5#147912317.0867153554590.0002004060546325010.00239640576365512
SP1#666735.69838137814090.005403962701712170.0246370028201553
TAF7#6879311.43306940492390.0006690181981945830.00542734127708902
TCF12#6938310.63446490218640.0008313523990202070.00629216705567587
TCF7L2#6934310.77017656313730.0008003181298398380.00613508699077678
USF1#739136.361499277207960.00388404057290560.0190184871955407
YY1#752834.911170749853860.008441455341808260.0329244185100315
ZBTB7A#5134137.35190930787590.002516255860282270.014012009906266
ZEB1#6935316.88843201754390.0002075486917327580.002426800024169
ZNF263#1012738.221841637010680.001799043925565870.0109378477437521



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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