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Coexpression cluster:C853: Difference between revisions

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13572,0.167775,0.168268,1.78684e-06,0.237199,0.00876024,0.168156,1.16282e-10,0.0824214,0.546774,0.0333049,4.2278e-07,0.503708,0.246187,0.291231,0.198269,0.00104171,0.197483,0.308086,0.20448,1.42224e-08,0.00128849,0.319783,0.139615,0.206257,0.268704,9.14679e-06,0.383259,0.000142318,0.689269,0.675716,4.14603e-09,0.0018739,0.638663,7.61043e-05,0.52491,3.27688e-05,5.31985e-08,0.622646,0.479007,2.91591e-08,0.0846975,0.375599,2.75711e-06,0.536945,0.523194,0.0277872,0.593153,0.000423841,0.336551,0.00157002,0.00178511,0.335207,0.514691,8.23607e-07,0.668131,0.670422,0.249066,0.450988,0.571064,6.02395e-08,0.733696,0.573814,0.539957,0.285349,0.2588,0.000352012,1.48464e-09,0.00291717,0.65176,0.217989,0.650689,0.298817,2.80137e-05,0.475347,2.94055e-05,0.555097,0.000511364,0.536392,0.775775
|tfbs_overrepresentation_for_novel_motifs=0.280498,2.37683,0.273994,0.404877,0.237701,0.403356,3.076,0.140612,0.138703,0.0921938,0.375531,0.515448,0.348369,2.0398,1.23932,0.256724,0.68716,0.191625,1.22644,0.400542,0.274046,0.111654,0.396189,0.233338,0.314616,0.537051,4.25038,0.39419,0.240354,0.590419,0.355553,2.88046,0.165252,1.72495,0.20845,0.359459,3.28419,0.404426,1.65036,0.125439,0.597291,0.340749,0.127662,1.91686,0.413441,0.301189,0.47544,0.365597,0.518466,0.675323,0.550604,0.486559,2.87924,0.797754,0.947672,0.466348,0.244111,0.435652,1.47951,1.10913,0.762758,0.477672,0.430344,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.445273,0.0579262,0.945703,0.339984,0.0955465,0.610619,0.644006,0.709631,0.309107,0.11972,0.659298,0.49429,0.439665,0.89511,0.0102458,0.0463436,0.971783,0.575506,1.4989,1.12715,0.868602,0.739223,1.56172,0.238337,0.18161,0.115206,0.780743,0.579925,0.0696508,0.187593,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.22412,0.7752,0.772599,0.269151,0.384185,1.07963,0.204477,0.0136871,1.66701,0.624851,0.173291,0.937551,0.57318,0.400807,0.504966,1.18924,2.63171,0.468435,0.744085,0.979528,0.182384,0.869279,0.358161,0.993705,0.50181,1.13991,0.0752959,0.350108,1.02211,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.896414,0.168379,0.052013,0.0287097,0.869654,0.821366,0.477214,1.26919,2.35803,0.225815,0.314669,0.28899,1.05976,0.851493,0.708865,0.291837,0.633206,0.493542,0.479645,0.473159,0.140569
|tfbs_overrepresentation_for_novel_motifs=0.280498,2.37683,0.273994,0.404877,0.237701,0.403356,3.076,0.140612,0.138703,0.0921938,0.375531,0.515448,0.348369,2.0398,1.23932,0.256724,0.68716,0.191625,1.22644,0.400542,0.274046,0.111654,0.396189,0.233338,0.314616,0.537051,4.25038,0.39419,0.240354,0.590419,0.355553,2.88046,0.165252,1.72495,0.20845,0.359459,3.28419,0.404426,1.65036,0.125439,0.597291,0.340749,0.127662,1.91686,0.413441,0.301189,0.47544,0.365597,0.518466,0.675323,0.550604,0.486559,2.87924,0.797754,0.947672,0.466348,0.244111,0.435652,1.47951,1.10913,0.762758,0.477672,0.430344,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.445273,0.0579262,0.945703,0.339984,0.0955465,0.610619,0.644006,0.709631,0.309107,0.11972,0.659298,0.49429,0.439665,0.89511,0.0102458,0.0463436,0.971783,0.575506,1.4989,1.12715,0.868602,0.739223,1.56172,0.238337,0.18161,0.115206,0.780743,0.579925,0.0696508,0.187593,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.22412,0.7752,0.772599,0.269151,0.384185,1.07963,0.204477,0.0136871,1.66701,0.624851,0.173291,0.937551,0.57318,0.400807,0.504966,1.18924,2.63171,0.468435,0.744085,0.979528,0.182384,0.869279,0.358161,0.993705,0.50181,1.13991,0.0752959,0.350108,1.02211,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.896414,0.168379,0.052013,0.0287097,0.869654,0.821366,0.477214,1.26919,2.35803,0.225815,0.314669,0.28899,1.05976,0.851493,0.708865,0.291837,0.633206,0.493542,0.479645,0.473159,0.140569
|tfbs_overrepresentation_jaspar=MA0003.1;0.115024,MA0004.1;0.380329,MA0006.1;0.236135,MA0007.1;0.363007,MA0009.1;0.828613,MA0014.1;0.284587,MA0017.1;2.92614,MA0019.1;0.520264,MA0024.1;0.725404,MA0025.1;0.960689,MA0027.1;2.43535,MA0028.1;0.25013,MA0029.1;0.744375,MA0030.1;0.733118,MA0031.1;0.669876,MA0038.1;0.477043,MA0040.1;0.750125,MA0041.1;0.397617,MA0042.1;0.367902,MA0043.1;0.828925,MA0046.1;0.817858,MA0048.1;0.0613414,MA0050.1;0.368721,MA0051.1;0.473017,MA0052.1;0.753928,MA0055.1;0.014035,MA0056.1;0,MA0057.1;2.25468,MA0058.1;0.293055,MA0059.1;0.291897,MA0060.1;0.138988,MA0061.1;0.118318,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;4.99908,MA0069.1;0.814052,MA0070.1;0.803003,MA0071.1;0.440254,MA0072.1;0.798564,MA0073.1;65.0341,MA0074.1;0.4723,MA0076.1;0.307383,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;0.292043,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;0.873421,MA0089.1;0,MA0090.1;0.320494,MA0091.1;0.382762,MA0092.1;0.347826,MA0093.1;0.238771,MA0095.1;0,MA0098.1;0,MA0100.1;0.49029,MA0101.1;0.241637,MA0103.1;1.20737,MA0105.1;0.0508589,MA0106.1;0.516528,MA0107.1;0.179177,MA0108.2;0.666881,MA0109.1;0,MA0111.1;1.59097,MA0113.1;0.532314,MA0114.1;0.174997,MA0115.1;1.06753,MA0116.1;0.182037,MA0117.1;0.865782,MA0119.1;0.277531,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;0.585907,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;0.109245,MA0140.1;0.437738,MA0141.1;1.43869,MA0142.1;0.638837,MA0143.1;0.532484,MA0144.1;0.163394,MA0145.1;0.945459,MA0146.1;0.00275056,MA0147.1;0.184931,MA0148.1;0.403564,MA0149.1;0.428597,MA0062.2;0.114378,MA0035.2;0.437071,MA0039.2;2.12191,MA0138.2;0.569505,MA0002.2;0.129981,MA0137.2;0.255808,MA0104.2;0.138396,MA0047.2;0.504873,MA0112.2;1.29974,MA0065.2;0.340764,MA0150.1;0.315136,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;0.0494985,MA0155.1;0.12484,MA0156.1;0.257809,MA0157.1;0.612166,MA0158.1;0,MA0159.1;1.64451,MA0160.1;1.88551,MA0161.1;0,MA0162.1;0.0377269,MA0163.1;5.06176,MA0164.1;0.544294,MA0080.2;0.238846,MA0018.2;0.517858,MA0099.2;3.99523,MA0079.2;13.0917,MA0102.2;1.36707,MA0258.1;3.60118,MA0259.1;0.191914,MA0442.1;0
}}
}}

Revision as of 19:30, 22 January 2013


Full id: C853_Neutrophils_leiomyoma_Smooth_Monocytederived_CD14_Osteoblast_Prostate



Phase1 CAGE Peaks

Hg19::chr1:26607267..26607285,+p@chr1:26607267..26607285
+
Hg19::chr1:26607290..26607307,+p@chr1:26607290..26607307
+
Hg19::chr1:26607342..26607393,+p@chr1:26607342..26607393
+
Hg19::chr1:26607542..26607556,+p@chr1:26607542..26607556
+
Hg19::chr1:26607565..26607584,+p@chr1:26607565..26607584
+
Hg19::chr1:26607589..26607601,+p@chr1:26607589..26607601
+
Hg19::chr1:26607604..26607669,+p@chr1:26607604..26607669
+
Hg19::chr1:26607679..26607701,+p@chr1:26607679..26607701
+
Hg19::chr1:26607704..26607714,+p@chr1:26607704..26607714
+
Hg19::chr1:26607717..26607763,+p@chr1:26607717..26607763
+


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 cell9.54e-33588
somatic stem cell7.03e-29433
multi fate stem cell3.73e-28427
stem cell4.26e-27441
defensive cell2.77e-2248
phagocyte2.77e-2248
myeloid leukocyte1.30e-2072
classical monocyte7.80e-2042
CD14-positive, CD16-negative classical monocyte7.80e-2042
myeloid lineage restricted progenitor cell7.88e-1966
connective tissue cell2.63e-18361
granulocyte monocyte progenitor cell5.36e-1867
mesenchymal cell1.25e-17354
monopoietic cell1.73e-1759
monocyte1.73e-1759
monoblast1.73e-1759
promonocyte1.73e-1759
macrophage dendritic cell progenitor4.53e-1761
native cell1.11e-16722
animal cell3.53e-15679
eukaryotic cell3.53e-15679
stuff accumulating cell5.72e-1587
motile cell3.90e-13386
myeloid cell4.14e-11108
common myeloid progenitor4.14e-11108
mesodermal cell7.13e-10121
muscle precursor cell6.50e-0958
myoblast6.50e-0958
multi-potent skeletal muscle stem cell6.50e-0958
smooth muscle cell1.30e-0843
smooth muscle myoblast1.30e-0843
contractile cell2.48e-0859
muscle cell2.90e-0855
vascular associated smooth muscle cell8.98e-0832
leukocyte2.45e-07136
fibroblast2.57e-0776
hematopoietic lineage restricted progenitor cell2.61e-07120
electrically responsive cell2.92e-0761
electrically active cell2.92e-0761
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm3.10e-25203
mesoderm1.01e-24315
mesoderm-derived structure1.01e-24315
presumptive mesoderm1.01e-24315
musculoskeletal system8.62e-24167
bone marrow2.57e-1876
connective tissue1.66e-17371
skeletal system8.44e-16100
hematopoietic system9.47e-1698
blood island9.47e-1698
skeletal element9.96e-1690
hemolymphoid system1.43e-15108
immune system1.47e-1593
bone element4.46e-1582
epithelial vesicle4.50e-1078
artery4.93e-1042
arterial blood vessel4.93e-1042
arterial system4.93e-1042
multilaminar epithelium1.26e-0983
somite5.62e-0971
presomitic mesoderm5.62e-0971
presumptive segmental plate5.62e-0971
dermomyotome5.62e-0971
trunk paraxial mesoderm5.62e-0971
dense mesenchyme tissue7.24e-0973
paraxial mesoderm1.14e-0872
presumptive paraxial mesoderm1.14e-0872
cardiovascular system1.46e-08109
splanchnic layer of lateral plate mesoderm1.47e-0883
systemic artery4.35e-0833
systemic arterial system4.35e-0833
epithelial tube open at both ends4.75e-0859
blood vessel4.75e-0859
blood vasculature4.75e-0859
vascular cord4.75e-0859
circulatory system6.26e-08112
vessel1.16e-0768
skeletal muscle tissue2.86e-0762
striated muscle tissue2.86e-0762
myotome2.86e-0762
vasculature4.50e-0778
vascular system4.50e-0778
muscle tissue8.20e-0764
musculature8.20e-0764
musculature of body8.20e-0764


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)
MA0003.10.115024
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.284587
MA0017.12.92614
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.014035
MA0056.10
MA0057.12.25468
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.14.99908
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.165.0341
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.873421
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.11.20737
MA0105.10.0508589
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.11.59097
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.10.437738
MA0141.11.43869
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.945459
MA0146.10.00275056
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.22.12191
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.21.29974
MA0065.20.340764
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.0494985
MA0155.10.12484
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.64451
MA0160.11.88551
MA0161.10
MA0162.10.0377269
MA0163.15.06176
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.23.99523
MA0079.213.0917
MA0102.21.36707
MA0258.13.60118
MA0259.10.191914
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
FOSL1#8061311.91407391491190.001676457234327950.0104798896927023



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C853&oldid=2569364"