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Coexpression cluster:C632: Difference between revisions

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{{Coexpression_clusters
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00999129,0.656826,0.0248426,0.50228,0.597796,0.573511,0.0856549,0.333901,0.830598,0.589568,0.592968,0.848819,0.887251,0.267132,0.444149,0.0644178,0.478555,0.672236,0.0207004,0.357611,0.654138,0.188754,0.377079,0.146323,0.867077,0.777529,0.51179,0.50796,0.724085,0.885439,0.0945546,0.503417,0.959092,0.897747,0.421994,0.154203,0.191681,0.544092,0.114594,0.686786,0.241073,0.0204776,0.629207,0.332181,0.927969,0.81979,0.0716762,0.205213,0.345674,0.799154,0.425188,0.774553,0.0222541,0.777159,0.00867099,0.584228,0.157044,0.855887,0.642475,0.635743,0.197479,0.562905,0.275837,0.810569,0.947952,0.0942108,0.22957,0.315097,0.194365,0.657795,0.147894,0.625216,0.407454,0.622192,0.294118,0.175283,0.56305,0.628185,0.56424,0.111127,0.663217,0.00110572,0.373564,0.208482,0.392927,0.649921,0.747657,0.662256,0.937092,0.602579,0.265771,0.324651,0.329164,3.79035e-05,0.0986772,0.682601,0.0865196,0.619012,0.458936,0.0874665,0.14327,0.366902,0.461022,0.0671165,0.699036,0.450416,0.341247,0.481022,0.663924,0.382899,0.0315158,0.277689,0.297677,0.0591212,0.428828,0.520437,0.343234,0.200432,0.00809927,0.577896,0.167392,0.27322,0.0265342,0.195528,0.767906,0.650305,0.0538856,0.544167,0.449866,0.384185,0.414781,0.249171,0.678642,0.553004,0.112251,0.637063,0.46149,0.0143656,0.512216,0.605271,0.556477,0.750457,0.533477,0.108234,0.0248665,0.0714674,0.61579,0.295569,0.752335,0.170423,0.654735,0.104189,0.29571,0.0358649,0.264557,0.737348,0.437434,0.694833,0.147133,0.587939,0.0217959,0.504741,0.27326,0.139137,0.547991,0.480913,0.403339,0.69157,0.220775,0.0641588,0.378621,0.28403,0.517352,0.455187,0.10954,0.329999,0.000776247,0.409482,0.226719,0.227361,0.0424724,0.315496,0.176359,0.227215,0.108583,0.757328,0.669752,0.621034,0.711117,0.624999,0.326761,0.382401,0.266095,0.00041475,0.265087,0.402864,0.274042,0.0537304,0.474347,0.416949,0.189841,0.00443174,0.0720532,0.160298,0.491672,0.0930353,0.226079,0.793321,0.591032,0.160417,0.759521,0.748352,0.647234,0.700164,0.808646,0.744466,0.598612,0.0213739,0.761425,0.482811,0.0499434,0.659682,0.64545,0.79359,0.716075,0.00285601,0.0206641,0.682681,0.00729876,0.435373,0.636566,0.628086,0.202333,0.788583,0.738739,0.568069,0.694262,0.0778906,0.552561,0.335214,0.0969815,0.375214,0.342479,0.831075,0.584807,0.553916,0.771635,0.291242,0.432933,0.0141598,0.691105,0.594658,0.000182543,0.678211,0.394262,0.659112,0.348518|tfbs_overrepresentation_for_novel_motifs=0.18943,0.0298012,0.183956,0.297884,0.153879,0.296522,0.360887,0.569923,2.56974,0.84994,0.271739,0.398649,0.20272,1.65488,0.465119,0.506197,0.560096,1.79539,0.480243,0.983477,0.184,1.69702,0.789382,0.150321,0.623871,0.418678,0.392469,0.785331,0.156049,0.352289,0.706977,0.594213,0.096776,1.20134,0.130292,0.391855,0.12818,0.29748,0.734039,0.067669,0.129369,0.241157,1.07143,0.151865,0.664236,0.596593,0.361827,0.262957,1.73931,0.473123,0.431291,0.372023,1.55252,0.666176,0.811691,0.931445,0.15913,0.325599,1.40793,0.324748,0.632472,0.363871,0.564331,0.534578,0.379438,0.503101,0.896916,1.25738,0.584559,1.09778,0.652781,0.278952,0.103789,0.80977,0.196336,0.402042,0.368241,0.519091,0.581542,0.213774,0.493088,0.533593,0.37913,0.0800936,0.760489,0.557435,0.656421,2.36937,0.454557,1.35556,0.98765,0.734737,0.609873,0.101133,0.154399,0.353375,0.0605346,0.649779,0.458696,1.26286,1.21087,0.6046,0.644537,0.563483,0.492631,0.268065,0.548871,0.348037,0.218314,0.142849,0.19228,0.641937,0.179896,0.279418,0.940917,0.12714,0.145638,0.704759,0.500972,0.336456,0.801818,0.452379,0.294241,0.388967,1.04884,0.519787,0.355419,0.614537,0.842806,0.719563,0.735394,0.256408,0.856671,0.386057,1.00021,0.323556,0.249339,0.288795,0.95886,1.80749,1.40745,0.922589,0.356906,0.646464,0.494226,0.318465,0.47912,1.64894,0.238532,0.0991414,0.230014,0.13139,0.735758,0.0728391,0.363452,1.12781,0.440071,0.870811,0.218554,1.08507,0.921409,0.718143,0.580811,0.199028,0.508869,0.378443,0.306931,0.35974,1.8632|tfbs_overrepresentation_jaspar=MA0003.1;0.923172,MA0004.1;3.87082,MA0006.1;0.152601,MA0007.1;2.05002,MA0009.1;0.695988,MA0014.1;0.856585,MA0017.1;0.181071,MA0019.1;0.403106,MA0024.1;0.59663,MA0025.1;0.824398,MA0027.1;2.28954,MA0028.1;0.492785,MA0029.1;0.614815,MA0030.1;0.604021,MA0031.1;0.543644,MA0038.1;0.363295,MA0040.1;0.620334,MA0041.1;0.291389,MA0042.1;0.264992,MA0043.1;0.69629,MA0046.1;0.685589,MA0048.1;0.267987,MA0050.1;0.265714,MA0051.1;0.944936,MA0052.1;0.623986,MA0055.1;0.45122,MA0056.1;0,MA0057.1;0.477843,MA0058.1;4.08876,MA0059.1;5.94708,MA0060.1;0.266757,MA0061.1;0.224865,MA0063.1;0,MA0066.1;0.953901,MA0067.1;1.00375,MA0068.1;0.0444239,MA0069.1;1.6324,MA0070.1;0.671241,MA0071.1;0.329767,MA0072.1;0.666958,MA0073.1;0.629368,MA0074.1;0.358953,MA0076.1;0.212295,MA0077.1;0.65962,MA0078.1;0.447828,MA0081.1;0.199203,MA0083.1;0.703169,MA0084.1;1.18798,MA0087.1;0.664629,MA0088.1;0.14098,MA0089.1;0,MA0090.1;0.635809,MA0091.1;0.278153,MA0092.1;0.247341,MA0093.1;7.18889,MA0095.1;0,MA0098.1;0,MA0100.1;0.979866,MA0101.1;0.1571,MA0103.1;0.448026,MA0105.1;1.03343,MA0106.1;0.399649,MA0107.1;0.107387,MA0108.2;0.540797,MA0109.1;0,MA0111.1;0.660878,MA0113.1;0.414278,MA0114.1;0.339925,MA0115.1;0.929032,MA0116.1;1.1824,MA0117.1;0.732,MA0119.1;0.18693,MA0122.1;0.756889,MA0124.1;0.888592,MA0125.1;0.807083,MA0130.1;0,MA0131.1;0.464307,MA0132.1;0,MA0133.1;0,MA0135.1;0.725055,MA0136.1;0.369468,MA0139.1;0.789887,MA0140.1;0.327488,MA0141.1;0.197753,MA0142.1;0.514195,MA0143.1;0.414436,MA0144.1;0.652118,MA0145.1;0.324645,MA0146.1;0.382098,MA0147.1;3.80431,MA0148.1;1.46178,MA0149.1;0.319221,MA0062.2;0.473181,MA0035.2;0.326883,MA0039.2;0.364185,MA0138.2;0.44894,MA0002.2;0.531015,MA0137.2;0.168782,MA0104.2;3.92728,MA0047.2;1.78642,MA0112.2;0.515321,MA0065.2;0.846317,MA0150.1;0.218956,MA0151.1;0,MA0152.1;0.333125,MA0153.1;0.790794,MA0154.1;0.42076,MA0155.1;1.81542,MA0156.1;0.508404,MA0157.1;0.489002,MA0158.1;0,MA0159.1;0.361202,MA0160.1;0.30953,MA0161.1;0,MA0162.1;0.165836,MA0163.1;0.317359,MA0164.1;0.425415,MA0080.2;0.46983,MA0018.2;0.400879,MA0099.2;0.333432,MA0079.2;1.10125,MA0102.2;1.22472,MA0258.1;0.300766,MA0259.1;1.79733,MA0442.1;0}}
|full_id=C632_Monocytederived_Macrophage_Dendritic_CD14_Keratinocyte_basal_tenocyte
|id=C632
}}

Latest revision as of 11:27, 17 September 2013


Full id: C632_Monocytederived_Macrophage_Dendritic_CD14_Keratinocyte_basal_tenocyte



Phase1 CAGE Peaks

Hg19::chr18:3466261..3466312,+p@chr18:3466261..3466312
+
Hg19::chr20:57571799..57571828,+p@chr20:57571799..57571828
+
Hg19::chr8:11702366..11702398,+p@chr8:11702366..11702398
+
Hg19::chr8:11702610..11702625,+p@chr8:11702610..11702625
+
Hg19::chr8:11704610..11704653,+p@chr8:11704610..11704653
+
Hg19::chr8:11705180..11705213,+p@chr8:11705180..11705213
+
Hg19::chr8:11705214..11705244,+p@chr8:11705214..11705244
+
Hg19::chr8:11705265..11705300,+p@chr8:11705265..11705300
+
Hg19::chr8:11706577..11706604,+p@chr8:11706577..11706604
+
Hg19::chr8:11710161..11710184,+p@chr8:11710161..11710184
+
Hg19::chr8:11710828..11710871,+p@chr8:11710828..11710871
+
Hg19::chr8:11710864..11710931,-p3@CTSB
Hg19::chr8:11710941..11710962,-p8@CTSB
Hg19::chr8:11725589..11725605,-p1@CTSB


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
somatic cell2.66e-17588
monopoietic cell7.15e-1359
monocyte7.15e-1359
monoblast7.15e-1359
promonocyte7.15e-1359
mesodermal cell1.20e-12121
macrophage dendritic cell progenitor3.79e-1261
defensive cell4.67e-1148
phagocyte4.67e-1148
embryonic cell7.96e-11250
myeloid lineage restricted progenitor cell3.04e-1066
stuff accumulating cell7.52e-1087
muscle precursor cell2.37e-0958
myoblast2.37e-0958
multi-potent skeletal muscle stem cell2.37e-0958
granulocyte monocyte progenitor cell4.16e-0967
contractile cell8.92e-0959
muscle cell1.56e-0855
fibroblast2.04e-0876
smooth muscle cell2.74e-0843
smooth muscle myoblast2.74e-0843
multi fate stem cell4.60e-08427
classical monocyte6.91e-0842
CD14-positive, CD16-negative classical monocyte6.91e-0842
somatic stem cell1.17e-07433
non-terminally differentiated cell1.31e-07106
animal cell2.54e-07679
eukaryotic cell2.54e-07679
electrically responsive cell7.74e-0761
electrically active cell7.74e-0761
Uber Anatomy
Ontology termp-valuen
mesoderm1.85e-24315
mesoderm-derived structure1.85e-24315
presumptive mesoderm1.85e-24315
musculoskeletal system9.51e-19167
multi-cellular organism9.57e-19656
anatomical system8.93e-18624
anatomical group1.80e-17625
lateral plate mesoderm2.10e-16203
embryonic structure2.94e-12564
developing anatomical structure9.47e-12581
germ layer1.25e-11560
germ layer / neural crest1.25e-11560
embryonic tissue1.25e-11560
presumptive structure1.25e-11560
germ layer / neural crest derived structure1.25e-11560
epiblast (generic)1.25e-11560
multilaminar epithelium1.64e-1083
splanchnic layer of lateral plate mesoderm3.11e-1083
embryo5.17e-10592
skeletal system6.97e-10100
unilaminar epithelium7.14e-10148
bone marrow2.69e-0976
artery3.07e-0942
arterial blood vessel3.07e-0942
arterial system3.07e-0942
skeletal element3.14e-0990
epithelial tube3.64e-09117
vasculature5.94e-0978
vascular system5.94e-0978
circulatory system7.28e-09112
epithelial vesicle9.57e-0978
immune system1.00e-0893
cardiovascular system1.21e-08109
dense mesenchyme tissue1.37e-0873
vessel1.59e-0868
somite1.74e-0871
presomitic mesoderm1.74e-0871
presumptive segmental plate1.74e-0871
dermomyotome1.74e-0871
trunk paraxial mesoderm1.74e-0871
paraxial mesoderm2.39e-0872
presumptive paraxial mesoderm2.39e-0872
epithelial tube open at both ends3.58e-0859
blood vessel3.58e-0859
blood vasculature3.58e-0859
vascular cord3.58e-0859
bone element6.29e-0882
muscle tissue1.07e-0764
musculature1.07e-0764
musculature of body1.07e-0764
skeletal muscle tissue1.10e-0762
striated muscle tissue1.10e-0762
myotome1.10e-0762
trunk mesenchyme1.12e-07122
systemic artery1.75e-0733
systemic arterial system1.75e-0733
hemolymphoid system8.70e-07108
Disease
Ontology termp-valuen
ovarian cancer8.89e-0714


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)
MA0003.10.923172
MA0004.13.87082
MA0006.10.152601
MA0007.12.05002
MA0009.10.695988
MA0014.10.856585
MA0017.10.181071
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.492785
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.267987
MA0050.10.265714
MA0051.10.944936
MA0052.10.623986
MA0055.10.45122
MA0056.10
MA0057.10.477843
MA0058.14.08876
MA0059.15.94708
MA0060.10.266757
MA0061.10.224865
MA0063.10
MA0066.10.953901
MA0067.11.00375
MA0068.10.0444239
MA0069.11.6324
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.10.629368
MA0074.10.358953
MA0076.10.212295
MA0077.10.65962
MA0078.10.447828
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.14098
MA0089.10
MA0090.10.635809
MA0091.10.278153
MA0092.10.247341
MA0093.17.18889
MA0095.10
MA0098.10
MA0100.10.979866
MA0101.10.1571
MA0103.10.448026
MA0105.11.03343
MA0106.10.399649
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.660878
MA0113.10.414278
MA0114.10.339925
MA0115.10.929032
MA0116.11.1824
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.789887
MA0140.10.327488
MA0141.10.197753
MA0142.10.514195
MA0143.10.414436
MA0144.10.652118
MA0145.10.324645
MA0146.10.382098
MA0147.13.80431
MA0148.11.46178
MA0149.10.319221
MA0062.20.473181
MA0035.20.326883
MA0039.20.364185
MA0138.20.44894
MA0002.20.531015
MA0137.20.168782
MA0104.23.92728
MA0047.21.78642
MA0112.20.515321
MA0065.20.846317
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.42076
MA0155.11.81542
MA0156.10.508404
MA0157.10.489002
MA0158.10
MA0159.10.361202
MA0160.10.30953
MA0161.10
MA0162.10.165836
MA0163.10.317359
MA0164.10.425415
MA0080.20.46983
MA0018.20.400879
MA0099.20.333432
MA0079.21.10125
MA0102.21.22472
MA0258.10.300766
MA0259.11.79733
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
BCL3#60237.402950600801070.006944266328473380.0293731412692654
FOSL2#235544.837200172731910.007541622873992410.0310914440191408
POLR2A#5430121.840674151335490.003085141629167310.0162625097970325



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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