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Coexpression cluster:C1091: Difference between revisions

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{{Coexpression_clusters
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,0.19223,0.555925,0.637689,0.450635,0.597407,0.907465,0.543352,0.81316,0.322799,0.774423,0.250594,0.491486,0.264925,0.341703,0.715078,1.1906,1.46316,0.385586,0.619829,0.421276,0.470396,0.304828,0.777139,0.429397,0.810962,0.628961,0.154814,0.269459,7.49887,0.266487,1.20926,0.244807,3.00164,0.268162,0.413601,0.0547276,0.299183,5.73559,0.371118,0.555735,0.440085,0.186577,0.822946,0.63387,0.567337,0.0927889,0.887323,1.03948,1.34776,0.308962,0.514077,2.49031,0.513089,0.85167,0.558065,0.556977,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,0.429044,0.799673,0.730167,0.797419,0.989108,0.167664,0.745864,0.575394,0.19474,0.986227,0.237806,1.4112,1.24284,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,0.239285,0.946574,0.87,0.664183,2.31367,0.246049,0.822041,0.864454,0.778061,1.67288,0.446229,0.762347,0.539961,0.385342,0.782066,1.65974,0.861701,0.336372,0.459808,1.17281,0.732093,0.279527,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,1.94293,0.960022,0.432175,1.08604,0.583225,1.23359,0.364369,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.999704,0.0510299,0.960402,1.63059,0.557588,1.36372,0.643609,0.786331,0.385642,0.941217,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,1.79865,0.553354,0.664626|tfbs_overrepresentation_jaspar=MA0003.1;0.797136,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.275152,MA0017.1;0.896777,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.316923,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.835832,MA0056.1;0,MA0057.1;0.632427,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.165998,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.823119,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.326687,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.770971,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.825856,MA0103.1;0.792149,MA0105.1;0.279181,MA0106.1;0.59853,MA0107.1;0.666147,MA0108.2;0.753643,MA0109.1;0,MA0111.1;1.84219,MA0113.1;0.614917,MA0114.1;1.89851,MA0115.1;1.1606,MA0116.1;0.673701,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;4.42548,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;1.7555,MA0146.1;0.934908,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.284736,MA0138.2;2.6595,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;2.83822,MA0065.2;1.78056,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.577214,MA0155.1;2.75898,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.682702,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.194027,MA0163.1;2.76433,MA0164.1;1.51849,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;11.5801,MA0102.2;1.46209,MA0258.1;0.603127,MA0259.1;0.25092,MA0442.1;0}}
|full_id=C1091_Neutrophils_Mesenchymal_Monocytederived_Smooth_Hepatic_Prostate_leiomyoma
|id=C1091
}}

Latest revision as of 11:37, 17 September 2013


Full id: C1091_Neutrophils_Mesenchymal_Monocytederived_Smooth_Hepatic_Prostate_leiomyoma



Phase1 CAGE Peaks

Hg19::chr7:143078652..143078754,+p2@ZYX
Hg19::chr7:143079397..143079426,+p6@ZYX
Hg19::chr7:143079458..143079487,+p4@ZYX
Hg19::chr7:143079496..143079519,+p7@ZYX
Hg19::chr7:143079687..143079742,+p8@ZYX
Hg19::chr7:143079960..143079978,+p3@ZYX
Hg19::chr7:143085915..143085937,+p@chr7:143085915..143085937
+
Hg19::chr7:143085953..143085988,+p@chr7:143085953..143085988
+


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
somatic cell1.57e-26588
mesodermal cell7.08e-19121
multi fate stem cell5.97e-17427
somatic stem cell1.41e-16433
stem cell7.12e-16441
animal cell1.23e-15679
eukaryotic cell1.23e-15679
defensive cell3.03e-1348
phagocyte3.03e-1348
contractile cell3.20e-1259
classical monocyte1.91e-1142
CD14-positive, CD16-negative classical monocyte1.91e-1142
muscle precursor cell3.84e-1158
myoblast3.84e-1158
multi-potent skeletal muscle stem cell3.84e-1158
smooth muscle cell5.24e-1143
smooth muscle myoblast5.24e-1143
muscle cell6.35e-1155
native cell8.30e-11722
myeloid leukocyte1.08e-1072
monopoietic cell1.08e-1059
monocyte1.08e-1059
monoblast1.08e-1059
promonocyte1.08e-1059
electrically responsive cell1.85e-1061
electrically active cell1.85e-1061
embryonic cell2.24e-10250
stuff accumulating cell3.03e-1087
fibroblast3.85e-1076
macrophage dendritic cell progenitor4.33e-1061
granulocyte monocyte progenitor cell3.26e-0967
lining cell4.67e-0958
barrier cell4.67e-0958
myeloid lineage restricted progenitor cell5.28e-0966
vascular associated smooth muscle cell9.33e-0932
endothelial cell1.59e-0836
connective tissue cell3.50e-08361
meso-epithelial cell1.15e-0745
mesenchymal cell4.75e-07354
Uber Anatomy
Ontology termp-valuen
mesoderm3.13e-34315
mesoderm-derived structure3.13e-34315
presumptive mesoderm3.13e-34315
lateral plate mesoderm4.61e-23203
musculoskeletal system2.08e-20167
vasculature3.50e-1678
vascular system3.50e-1678
cardiovascular system6.38e-15109
vessel6.71e-1568
epithelial vesicle1.25e-1478
epithelial tube open at both ends2.42e-1459
blood vessel2.42e-1459
blood vasculature2.42e-1459
vascular cord2.42e-1459
circulatory system5.12e-14112
splanchnic layer of lateral plate mesoderm2.24e-1383
artery2.97e-1342
arterial blood vessel2.97e-1342
arterial system2.97e-1342
somite2.28e-1271
presomitic mesoderm2.28e-1271
presumptive segmental plate2.28e-1271
dermomyotome2.28e-1271
trunk paraxial mesoderm2.28e-1271
dense mesenchyme tissue3.80e-1273
multilaminar epithelium3.99e-1283
paraxial mesoderm6.09e-1272
presumptive paraxial mesoderm6.09e-1272
multi-cellular organism1.34e-11656
trunk mesenchyme1.57e-11122
anatomical system7.28e-11624
anatomical group1.39e-10625
skeletal muscle tissue3.60e-1062
striated muscle tissue3.60e-1062
myotome3.60e-1062
muscle tissue3.75e-1064
musculature3.75e-1064
musculature of body3.75e-1064
unilaminar epithelium3.79e-10148
systemic artery7.67e-1033
systemic arterial system7.67e-1033
embryonic structure8.96e-10564
epithelial tube1.10e-09117
skeletal system1.16e-09100
germ layer1.65e-09560
germ layer / neural crest1.65e-09560
embryonic tissue1.65e-09560
presumptive structure1.65e-09560
germ layer / neural crest derived structure1.65e-09560
epiblast (generic)1.65e-09560
mesenchyme3.78e-09160
entire embryonic mesenchyme3.78e-09160
bone marrow3.84e-0976
skeletal element6.54e-0990
immune system1.45e-0893
developing anatomical structure1.69e-08581
hemolymphoid system3.72e-08108
embryo5.53e-08592
bone element7.68e-0882
connective tissue2.43e-07371
hematopoietic system5.92e-0798


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)
MA0003.10.797136
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.275152
MA0017.10.896777
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.835832
MA0056.10
MA0057.10.632427
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.823119
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.326687
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.825856
MA0103.10.792149
MA0105.10.279181
MA0106.10.59853
MA0107.10.666147
MA0108.20.753643
MA0109.10
MA0111.11.84219
MA0113.10.614917
MA0114.11.89851
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.14.42548
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.11.7555
MA0146.10.934908
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.284736
MA0138.22.6595
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.22.83822
MA0065.21.78056
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.12.75898
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.194027
MA0163.12.76433
MA0164.11.51849
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.211.5801
MA0102.21.46209
MA0258.10.603127
MA0259.10.25092
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
EGR1#195853.117611934256340.01051390990388360.0389245741386635



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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