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Coexpression cluster:C716: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.22923,2.64959,0.223258,0.345441,0.190185,0.344001,0.411652,2.29387,0.687431,0.149656,0.317729,0.451026,0.264598,0.401301,1.05539,0.597712,0.617549,2.05818,1.00427,0.289026,0.223306,3.1005,0.895263,1.64894,0.260754,0.471832,1.80469,1.59978,3.16712,0.454328,0.298956,0.65246,0.396376,0.566765,0.163884,1.08397,0.161511,0.912597,0.443749,1.05941,0.162847,0.285097,0.658594,0.187953,0.653532,0.24831,0.412635,0.830687,1.27426,1.06955,0.484909,0.423285,1.87173,0.725869,0.873575,0.403938,1.08263,0.978119,1.68545,0.373762,0.691524,1.06586,3.66926,0.591384,1.10114,0.559038,0.959746,1.32257,0.642589,1.16217,0.273995,0.108268,0.616727,0.871629,0.546891,0.874985,0.472331,0.575479,0.639503,0.710503,0.293113,0.590372,0.4307,0.10636,0.821696,0.328031,0.11917,0.76968,0.508983,1.42111,1.05129,0.795567,0.66846,0.130784,0.557745,0.140087,0.0830795,0.709167,0.51326,0.701432,0.145361,0.663075,0.703825,0.621018,0.54826,0.84292,0.606045,0.398205,0.260543,0.177931,1.2234,0.701175,0.624605,0.325885,1.00416,0.16034,0.393763,0.297931,0.556847,0.821661,0.863578,0.506732,0.904983,0.44095,1.11293,0.576194,0.405934,0.673222,0.905059,0.434621,0.796235,0.814941,0.919079,0.437919,1.06395,0.421703,0.293853,0.335825,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,1.35552,0.367151,0.534339,1.71519,3.00288,0.403378,1.29793,0.193536,0.796604,0.663597,0.414334,1.19239,0.494,0.530398,0.722397,0.237047,0.984474,0.778717,0.638755,0.673477,0.564971,0.429983,0.381825,0.410452,3.24883
|tfbs_overrepresentation_for_novel_motifs=0.22923,2.64959,0.223258,0.345441,0.190185,0.344001,0.411652,2.29387,0.687431,0.149656,0.317729,0.451026,0.264598,0.401301,1.05539,0.597712,0.617549,2.05818,1.00427,0.289026,0.223306,3.1005,0.895263,1.64894,0.260754,0.471832,1.80469,1.59978,3.16712,0.454328,0.298956,0.65246,0.396376,0.566765,0.163884,1.08397,0.161511,0.912597,0.443749,1.05941,0.162847,0.285097,0.658594,0.187953,0.653532,0.24831,0.412635,0.830687,1.27426,1.06955,0.484909,0.423285,1.87173,0.725869,0.873575,0.403938,1.08263,0.978119,1.68545,0.373762,0.691524,1.06586,3.66926,0.591384,1.10114,0.559038,0.959746,1.32257,0.642589,1.16217,0.273995,0.108268,0.616727,0.871629,0.546891,0.874985,0.472331,0.575479,0.639503,0.710503,0.293113,0.590372,0.4307,0.10636,0.821696,0.328031,0.11917,0.76968,0.508983,1.42111,1.05129,0.795567,0.66846,0.130784,0.557745,0.140087,0.0830795,0.709167,0.51326,0.701432,0.145361,0.663075,0.703825,0.621018,0.54826,0.84292,0.606045,0.398205,0.260543,0.177931,1.2234,0.701175,0.624605,0.325885,1.00416,0.16034,0.393763,0.297931,0.556847,0.821661,0.863578,0.506732,0.904983,0.44095,1.11293,0.576194,0.405934,0.673222,0.905059,0.434621,0.796235,0.814941,0.919079,0.437919,1.06395,0.421703,0.293853,0.335825,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,1.35552,0.367151,0.534339,1.71519,3.00288,0.403378,1.29793,0.193536,0.796604,0.663597,0.414334,1.19239,0.494,0.530398,0.722397,0.237047,0.984474,0.778717,0.638755,0.673477,0.564971,0.429983,0.381825,0.410452,3.24883
|tfbs_overrepresentation_jaspar=MA0003.1;0.371182,MA0004.1;2.3599,MA0006.1;1.66321,MA0007.1;0.305951,MA0009.1;0.756202,MA0014.1;0.898798,MA0017.1;0.220105,MA0019.1;0.45566,MA0024.1;0.654931,MA0025.1;0.886436,MA0027.1;2.35633,MA0028.1;0.201461,MA0029.1;0.673506,MA0030.1;0.662482,MA0031.1;0.600685,MA0038.1;0.414169,MA0040.1;0.67914,MA0041.1;0.338572,MA0042.1;0.310552,MA0043.1;0.756508,MA0046.1;0.745626,MA0048.1;1.00007,MA0050.1;0.311321,MA0051.1;0.410316,MA0052.1;0.682867,MA0055.1;0.400018,MA0056.1;0,MA0057.1;1.85243,MA0058.1;1.25545,MA0059.1;2.71991,MA0060.1;0.337131,MA0061.1;0.28989,MA0063.1;0,MA0066.1;0.414559,MA0067.1;1.06751,MA0068.1;0.491198,MA0069.1;0.741884,MA0070.1;0.731026,MA0071.1;0.987752,MA0072.1;0.726666,MA0073.1;0.405793,MA0074.1;1.85752,MA0076.1;0.254045,MA0077.1;0.719193,MA0078.1;0.502027,MA0081.1;0.239862,MA0083.1;0.763502,MA0084.1;1.25286,MA0087.1;0.724294,MA0088.1;0.20556,MA0089.1;0,MA0090.1;0.266215,MA0091.1;0.86696,MA0092.1;0.291716,MA0093.1;2.37826,MA0095.1;0,MA0098.1;0,MA0100.1;0.426863,MA0101.1;0.19375,MA0103.1;1.02503,MA0105.1;0.890241,MA0106.1;0.452066,MA0107.1;0.427483,MA0108.2;0.597764,MA0109.1;0,MA0111.1;0.277713,MA0113.1;0.467266,MA0114.1;0.134281,MA0115.1;0.992167,MA0116.1;2.67448,MA0117.1;1.86191,MA0119.1;0.226505,MA0122.1;0.818044,MA0124.1;0.951337,MA0125.1;0.868909,MA0130.1;0,MA0131.1;0.519055,MA0132.1;0,MA0133.1;0,MA0135.1;0.785738,MA0136.1;0.420617,MA0139.1;0.0781324,MA0140.1;0.376643,MA0141.1;0.670251,MA0142.1;0.570448,MA0143.1;0.467429,MA0144.1;0.124153,MA0145.1;3.48575,MA0146.1;4.17511,MA0147.1;3.452,MA0148.1;1.63103,MA0149.1;0.367947,MA0062.2;0.0823902,MA0035.2;0.376007,MA0039.2;0.991464,MA0138.2;1.25623,MA0002.2;0.652621,MA0137.2;0.20663,MA0104.2;2.93885,MA0047.2;1.12244,MA0112.2;1.38772,MA0065.2;0.452385,MA0150.1;0.261236,MA0151.1;0,MA0152.1;0.382565,MA0153.1;0.852412,MA0154.1;0.5526,MA0155.1;0.392911,MA0156.1;0.208455,MA0157.1;0.544523,MA0158.1;0,MA0159.1;0.143477,MA0160.1;0.940794,MA0161.1;0,MA0162.1;0.63904,MA0163.1;4.60751,MA0164.1;0.478818,MA0080.2;0.191221,MA0018.2;0.453345,MA0099.2;0.382887,MA0079.2;2.08428,MA0102.2;1.28978,MA0258.1;3.13623,MA0259.1;2.76095,MA0442.1;0
}}
}}

Revision as of 19:23, 22 January 2013


Full id: C716_Melanocyte_Monocytederived_melanoma_Macrophage_Renal_CD14_Dendritic



Phase1 CAGE Peaks

Hg19::chr7:2671611..2671658,+p2@TTYH3
Hg19::chr7:2695761..2695776,+p10@TTYH3
Hg19::chr7:2696064..2696098,+p8@TTYH3
Hg19::chr7:2697935..2697953,+p@chr7:2697935..2697953
+
Hg19::chr7:2697957..2697994,+p@chr7:2697957..2697994
+
Hg19::chr7:2698019..2698038,+p@chr7:2698019..2698038
+
Hg19::chr7:2698048..2698063,+p@chr7:2698048..2698063
+
Hg19::chr7:2698578..2698617,+p9@TTYH3
Hg19::chr7:2701358..2701440,+p4@TTYH3
Hg19::chr7:2701441..2701465,+p14@TTYH3
Hg19::chr7:2701486..2701509,+p11@TTYH3
Hg19::chr7:2701540..2701595,+p6@TTYH3


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 cell3.14e-21250
somatic cell6.13e-20588
animal cell1.04e-15679
eukaryotic cell1.04e-15679
mesodermal cell4.12e-15121
endothelial cell2.36e-1236
lining cell2.77e-1158
barrier cell2.77e-1158
non-terminally differentiated cell2.21e-10106
stuff accumulating cell3.73e-1087
ectodermal cell9.96e-1072
meso-epithelial cell9.97e-1045
neurectodermal cell1.25e-0959
native cell4.26e-08722
defensive cell4.54e-0848
phagocyte4.54e-0848
electrically responsive cell5.45e-0861
electrically active cell5.45e-0861
contractile cell7.61e-0859
monopoietic cell1.57e-0759
monocyte1.57e-0759
monoblast1.57e-0759
promonocyte1.57e-0759
smooth muscle cell2.37e-0743
smooth muscle myoblast2.37e-0743
fibroblast5.86e-0776
kidney cell6.28e-0717
kidney epithelial cell6.28e-0717
pigment cell7.20e-0714
macrophage dendritic cell progenitor9.81e-0761
Uber Anatomy
Ontology termp-valuen
anatomical system3.15e-20624
multi-cellular organism3.71e-20656
anatomical group8.58e-20625
developing anatomical structure1.42e-17581
embryo2.89e-17592
embryonic structure1.82e-15564
germ layer2.64e-15560
germ layer / neural crest2.64e-15560
embryonic tissue2.64e-15560
presumptive structure2.64e-15560
germ layer / neural crest derived structure2.64e-15560
epiblast (generic)2.64e-15560
mesoderm1.88e-13315
mesoderm-derived structure1.88e-13315
presumptive mesoderm1.88e-13315
vasculature3.98e-1378
vascular system3.98e-1378
lateral plate mesoderm6.69e-12203
epithelial tube2.28e-11117
vessel1.69e-1068
cell layer3.48e-10309
epithelial tube open at both ends5.82e-1059
blood vessel5.82e-1059
blood vasculature5.82e-1059
vascular cord5.82e-1059
epithelium1.05e-09306
musculoskeletal system1.18e-09167
splanchnic layer of lateral plate mesoderm1.37e-0983
artery1.44e-0942
arterial blood vessel1.44e-0942
arterial system1.44e-0942
anatomical cluster4.79e-09373
cardiovascular system4.86e-09109
circulatory system3.93e-08112
organ1.98e-07503
epithelial vesicle2.00e-0778
systemic artery3.72e-0733
systemic arterial system3.72e-0733
tube6.09e-07192


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)
MA0003.10.371182
MA0004.12.3599
MA0006.11.66321
MA0007.10.305951
MA0009.10.756202
MA0014.10.898798
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.11.00007
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.400018
MA0056.10
MA0057.11.85243
MA0058.11.25545
MA0059.12.71991
MA0060.10.337131
MA0061.10.28989
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.491198
MA0069.10.741884
MA0070.10.731026
MA0071.10.987752
MA0072.10.726666
MA0073.10.405793
MA0074.11.85752
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.20556
MA0089.10
MA0090.10.266215
MA0091.10.86696
MA0092.10.291716
MA0093.12.37826
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.11.02503
MA0105.10.890241
MA0106.10.452066
MA0107.10.427483
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.134281
MA0115.10.992167
MA0116.12.67448
MA0117.11.86191
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.0781324
MA0140.10.376643
MA0141.10.670251
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.13.48575
MA0146.14.17511
MA0147.13.452
MA0148.11.63103
MA0149.10.367947
MA0062.20.0823902
MA0035.20.376007
MA0039.20.991464
MA0138.21.25623
MA0002.20.652621
MA0137.20.20663
MA0104.22.93885
MA0047.21.12244
MA0112.21.38772
MA0065.20.452385
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.5526
MA0155.10.392911
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.143477
MA0160.10.940794
MA0161.10
MA0162.10.63904
MA0163.14.60751
MA0164.10.478818
MA0080.20.191221
MA0018.20.453345
MA0099.20.382887
MA0079.22.08428
MA0102.21.28978
MA0258.13.13623
MA0259.12.76095
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

No analysis results for this cluster

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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