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Coexpression cluster:C4488: Difference between revisions

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{{Coexpression_clusters
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7491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,1.26332,0.845342,0.635379,1.7611,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,1.11965,1.46099,0.137917,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.718382,0.63803,0.901413,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,2.06667,0.388177,0.891404,1.25741,2.16722,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,3.36921,2.3415,1.99724,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,2.85375,1.11698,0.960047,0.524529,0.936473,18.3121|tfbs_overrepresentation_jaspar=MA0003.1;2.61626,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;1.88666,MA0009.1;1.3275,MA0014.1;6.45108,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;5.1975,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;1.70054,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;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;1.12079,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;11.6487,MA0146.1;7.1063,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;4.75888,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;2.13189,MA0047.2;0.973066,MA0112.2;4.7367,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;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;0.387745,MA0164.1;2.32251,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;1.22771,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4488_Alveolar_Renal_Mesenchymal_leiomyoma_Hepatocyte_tubular_small
|id=C4488
}}

Latest revision as of 12:46, 17 September 2013


Full id: C4488_Alveolar_Renal_Mesenchymal_leiomyoma_Hepatocyte_tubular_small



Phase1 CAGE Peaks

Hg19::chr5:179233795..179233828,-p2@MGAT4B
Hg19::chr5:179233829..179233834,-p6@MGAT4B
Hg19::chr5:179233835..179233873,-p1@MGAT4B


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>

Cell Type
Ontology termp-valuen
embryonic cell6.08e-31250
animal cell1.09e-30679
eukaryotic cell1.09e-30679
epithelial cell3.20e-29253
mesodermal cell3.62e-26121
somatic cell1.13e-20588
native cell1.28e-18722
lining cell2.68e-1458
barrier cell2.68e-1458
contractile cell1.34e-1159
smooth muscle cell1.91e-1143
smooth muscle myoblast1.91e-1143
squamous epithelial cell4.36e-1163
muscle precursor cell5.48e-1158
myoblast5.48e-1158
multi-potent skeletal muscle stem cell5.48e-1158
vascular associated smooth muscle cell2.50e-1032
muscle cell5.42e-1055
meso-epithelial cell9.99e-1045
epithelial cell of nephron4.66e-0915
electrically responsive cell9.71e-0961
electrically active cell9.71e-0961
endothelial cell1.07e-0836
endodermal cell2.12e-0858
non-terminally differentiated cell2.32e-08106
mesothelial cell8.61e-0819
kidney cell1.04e-0717
kidney epithelial cell1.04e-0717
kidney tubule cell3.31e-0710
nephron tubule epithelial cell3.31e-0710
kidney cortical cell3.81e-0712
renal cortical epithelial cell3.81e-0712
endothelial cell of vascular tree4.18e-0724
endo-epithelial cell5.18e-0742
Uber Anatomy
Ontology termp-valuen
epithelial tube9.62e-25117
trunk1.10e-17199
vasculature5.41e-1678
vascular system5.41e-1678
vessel8.26e-1668
unilaminar epithelium6.22e-15148
organism subdivision1.04e-14264
artery1.82e-1442
arterial blood vessel1.82e-1442
arterial system1.82e-1442
splanchnic layer of lateral plate mesoderm3.32e-1483
circulatory system5.89e-14112
cardiovascular system6.33e-14109
mesenchyme1.36e-13160
entire embryonic mesenchyme1.36e-13160
epithelial tube open at both ends1.57e-1359
blood vessel1.57e-1359
blood vasculature1.57e-1359
vascular cord1.57e-1359
trunk mesenchyme3.72e-12122
systemic artery2.29e-1133
systemic arterial system2.29e-1133
epithelial vesicle1.76e-1078
subdivision of trunk1.86e-10112
multilaminar epithelium8.04e-1083
nephron epithelium4.66e-0915
renal tubule4.66e-0915
nephron tubule4.66e-0915
nephron4.66e-0915
uriniferous tubule4.66e-0915
nephrogenic mesenchyme4.66e-0915
skeletal muscle tissue1.70e-0862
striated muscle tissue1.70e-0862
myotome1.70e-0862
muscle tissue2.22e-0864
musculature2.22e-0864
musculature of body2.22e-0864
somite4.25e-0871
presomitic mesoderm4.25e-0871
presumptive segmental plate4.25e-0871
dermomyotome4.25e-0871
trunk paraxial mesoderm4.25e-0871
excretory tube5.95e-0816
kidney epithelium5.95e-0816
parenchyma6.01e-0815
trunk region element9.22e-08101
paraxial mesoderm1.47e-0772
presumptive paraxial mesoderm1.47e-0772
dense mesenchyme tissue2.07e-0773
nephron tubule epithelium3.31e-0710
abdominal segment of trunk3.33e-0760
abdomen3.33e-0760
cortex of kidney3.81e-0712
renal parenchyma3.81e-0712
urinary system structure4.63e-0747
mesoderm5.45e-07315
mesoderm-derived structure5.45e-07315
presumptive mesoderm5.45e-07315
aorta8.89e-0721
aortic system8.89e-0721
renal system9.00e-0748


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
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.16.45108
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
MA0073.15.1975
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
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
MA0100.10.956299
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.111.6487
MA0146.17.1063
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.24.75888
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.24.7367
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.387745
MA0164.12.32251
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
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
CCNT2#90536.336201576962630.003930750035764890.0190852442113087
E2F6#187635.017155731697390.00791769806886330.0323874537292031
EGR1#195834.988179094810140.008056488137383440.0322059084659033
ELF1#199734.258097958807540.01295179875054610.0464405160060522
HMGN3#932438.178547723350590.001827766942164210.0109048929833013
HNF4G#3174328.75342252644684.20470658818262e-050.000759486944592191
IRF1#365937.63716375356390.002244692747297240.0128597622509587
JUND#372736.994663941871030.002921845042734990.0157426008263619
MYC#460935.22228187160940.007020843755740150.0295653361157109
NFKB1#479035.488063424193840.006049381815655430.0270574469997961
PAX5#507936.669565531177830.003370290999677260.0173522219233568
SIN3A#2594235.408884726815140.006318961977991520.0277918836864927
SP1#666735.69838137814090.005403962701712170.0247602202598981
TAF7#6879311.43306940492390.0006690181981945830.00544935202006271
TCF7L2#6934310.77017656313730.0008003181298398380.00616449776254465
YY1#752834.911170749853860.008441455341808260.0330850435112062
ZEB1#6935316.88843201754390.0002075486917327580.00243525197347236



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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