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Coexpression cluster:C486: Difference between revisions

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{{Coexpression_clusters
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telophase!0.00551925114800423!8379$GO:0051326!telophase!0.00551925114800423!8379$GO:0000089!mitotic metaphase!0.00827838931830998!8379$GO:0051323!metaphase!0.00827838931830998!8379$GO:0051322!anaphase!0.0091976688152717!8379$GO:0000090!mitotic anaphase!0.0091976688152717!8379$GO:0000299!integral to membrane of membrane fraction!0.0126128318365972!23209$GO:0030225!macrophage differentiation!0.0151734731405287!1053$GO:0007093!mitotic cell cycle checkpoint!0.0330872449633977!8379$GO:0002573!myeloid leukocyte differentiation!0.0330872449633977!1053$GO:0006909!phagocytosis!0.0410950816486348!1053$GO:0000075!cell cycle checkpoint!0.0477251694968636!8379$GO:0042089!cytokine biosynthetic process!0.0477251694968636!1053$GO:0007088!regulation of mitosis!0.0477251694968636!8379$GO:0042107!cytokine metabolic process!0.0477251694968636!1053$GO:0009059!macromolecule biosynthetic process!0.0477251694968636!23209;1053$GO:0030099!myeloid cell 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.402165,0.231499,0.295178,0.0382459,0.853653,0.443376,0.732022,0.00178617,0.384162,0.415478,0.139993,0.342865,0.561059,0.341641,0.503294,0.352504,0.394885,0.582219,0.00671515,0.248521,0.0101759,0.0225833,0.211091,0.600795,0.0593004,0.891475,0.882305,0.932759,0.074503,0.575861,0.120631,0.413017,0.80499,0.656078,0.0117861,0.710279,0.623643,0.308409,0.591322,0.670178,0.76842,0.755179,0.630922,0.8189,0.710781,0.044531,0.0731045,0.217876,0.539632,0.746817,0.738766,0.619286,0.878628,0.112204,0.315334,0.47773,0.463264,0.91905,0.481656,0.771273,0.471824,0.43392,0.694466,0.696673,0.299342,0.595141,0.373236,0.322893,0.490576,0.215172,0.706399,0.0963263,0.455078,0.842076,0.767893,0.317129|tfbs_overrepresentation_for_novel_motifs=0.38505,0.946977,0.117015,0.212191,0.643195,0.21101,0.267678,0.154541,0.349778,0.282303,0.189673,0.301621,0.259152,0.258863,1.57751,0.343795,0.450873,0.0660543,0.52649,0.202562,0.373792,0.206387,0.205464,0.630143,0.14499,0.3198,1.01201,0.589279,0.651136,0.61444,0.174693,0.483059,1.14885,0.263718,0.262221,0.679792,0.0741766,0.6081,0.226317,0.132023,0.2603,0.163791,0.243154,0.0919607,0.429714,0.833707,0.74012,0.53703,0.78545,0.651467,0.331306,0.27764,0.991471,0.551494,0.691633,0.261104,1.62192,0.665859,0.613944,0.235655,0.519357,0.270343,0.985086,0.426924,0.284296,1.0283,0.774525,1.12911,0.473932,0.971498,0.155159,1.02248,0.0433928,0.689771,0.0237,0.701812,0.955383,0.412445,0.471083,0.141103,1.24363,0.426001,0.284019,0.361652,0.642096,0.0337108,0.356951,2.08417,0.352635,1.2264,0.863265,0.617268,0.497892,0.201541,0.645099,1.24924,0.521585,0.535841,0.356444,0.309213,0.49381,0.492893,0.530844,1.15092,0.387815,0.186536,0.440324,0.256236,0.14483,0.288337,0.390957,0.528368,1.21021,0.196252,1.91278,0.544005,0.466326,0.173882,0.395564,1.67865,0.682065,0.925065,0.209033,0.795647,0.923346,0.413094,1.33772,0.502315,0.721838,0.219699,0.617901,0.176632,0.73532,3.05451,0.875585,2.48667,0.508946,1.11539,0.83506,1.67608,1.2779,0.799588,0.264127,1.31902,0.389296,0.23014,0.979522,1.51807,0.161595,0.0534036,0.623601,0.0148103,0.618251,0.332338,1.3642,1.0011,0.339339,0.607655,0.145027,0.127152,3.11841,0.601304,0.470393,0.805591,0.402913,0.283401,0.720567,0.266654,1.57488|tfbs_overrepresentation_jaspar=MA0003.1;0.0417237,MA0004.1;0.193314,MA0006.1;0.308609,MA0007.1;0.180248,MA0009.1;1.41914,MA0014.1;0.00883981,MA0017.1;0.367718,MA0019.1;0.824541,MA0024.1;1.21812,MA0025.1;0.70396,MA0027.1;2.15732,MA0028.1;0.680413,MA0029.1;0.50258,MA0030.1;1.23309,MA0031.1;1.11067,MA0038.1;0.269828,MA0040.1;0.507819,MA0041.1;0.206566,MA0042.1;0.183918,MA0043.1;0.580321,MA0046.1;0.570066,MA0048.1;0.270045,MA0050.1;0.184533,MA0051.1;0.266537,MA0052.1;0.511289,MA0055.1;0.317307,MA0056.1;0,MA0057.1;0.122328,MA0058.1;0.12994,MA0059.1;0.405044,MA0060.1;0.0387582,MA0061.1;0.290613,MA0063.1;0,MA0066.1;1.36491,MA0067.1;0.879057,MA0068.1;0.409781,MA0069.1;0.566544,MA0070.1;0.556335,MA0071.1;0.674412,MA0072.1;0.552241,MA0073.1;1.28654e-06,MA0074.1;0.265952,MA0076.1;0.432406,MA0077.1;0.545231,MA0078.1;0.346453,MA0081.1;0.405301,MA0083.1;0.586921,MA0084.1;1.06048,MA0087.1;0.550016,MA0088.1;0.398465,MA0089.1;0,MA0090.1;0.149167,MA0091.1;0.195166,MA0092.1;0.168981,MA0093.1;0.0941737,MA0095.1;0,MA0098.1;0,MA0100.1;0.768006,MA0101.1;0.317957,MA0103.1;1.03031,MA0105.1;0.220534,MA0106.1;0.817478,MA0107.1;0.0591705,MA0108.2;1.10489,MA0109.1;0,MA0111.1;0.15804,MA0113.1;0.315797,MA0114.1;0.207884,MA0115.1;0.805883,MA0116.1;1.74683,MA0117.1;0.614633,MA0119.1;1.2467,MA0122.1;0.638621,MA0124.1;0.766407,MA0125.1;0.687166,MA0130.1;0,MA0131.1;0.361613,MA0132.1;0,MA0133.1;0,MA0135.1;0.60795,MA0136.1;1.38399,MA0139.1;0.108841,MA0140.1;0.238066,MA0141.1;1.30232,MA0142.1;0.407878,MA0143.1;0.315941,MA0144.1;0.189563,MA0145.1;1.59211,MA0146.1;0.205334,MA0147.1;0.485912,MA0148.1;0.606512,MA0149.1;0.230803,MA0062.2;0.826291,MA0035.2;0.237534,MA0039.2;0.0934976,MA0138.2;0.347473,MA0002.2;1.32966,MA0137.2;0.697429,MA0104.2;0.34888,MA0047.2;0.292798,MA0112.2;0.632219,MA0065.2;0.963917,MA0150.1;0.145358,MA0151.1;0,MA0152.1;0.243034,MA0153.1;0.67139,MA0154.1;1.9317,MA0155.1;0.124291,MA0156.1;0.106343,MA0157.1;0.384449,MA0158.1;0,MA0159.1;1.77332,MA0160.1;0.632864,MA0161.1;0,MA0162.1;0.0505942,MA0163.1;0.10617,MA0164.1;0.870085,MA0080.2;1.07751,MA0018.2;0.30364,MA0099.2;1.26491,MA0079.2;5.95052e-06,MA0102.2;1.09681,MA0258.1;0.706831,MA0259.1;0.0662172,MA0442.1;0}}
|full_id=C486_acute_Neural_chronic_neuroectodermal_caudate_Astrocyte_myelodysplastic
|id=C486
}}

Latest revision as of 11:24, 17 September 2013


Full id: C486_acute_Neural_chronic_neuroectodermal_caudate_Astrocyte_myelodysplastic



Phase1 CAGE Peaks

Hg19::chr10:105793289..105793301,-p@chr10:105793289..105793301
-
Hg19::chr10:105793325..105793341,-p@chr10:105793325..105793341
-
Hg19::chr10:105793354..105793360,-p@chr10:105793354..105793360
-
Hg19::chr14:23588242..23588262,-p1@CEBPE
Hg19::chr14:23588275..23588288,-p1@CU690200
Hg19::chr14:23588458..23588473,-p2@CEBPE
Hg19::chr16:1537839..1537851,-p@chr16:1537839..1537851
-
Hg19::chr16:1537876..1537921,+p@chr16:1537876..1537921
+
Hg19::chr17:56359033..56359070,-p@chr17:56359033..56359070
-
Hg19::chr22:50523663..50523686,-p7@MLC1
Hg19::chr22:50523689..50523719,-p5@MLC1
Hg19::chr7:2119411..2119445,-p15@MAD1L1
Hg19::chr8:130559296..130559308,+p@chr8:130559296..130559308
+
Hg19::chr8:130695974..130696000,+p@chr8:130695974..130696000
+
Hg19::chr9:100947946..100947962,-p@chr9:100947946..100947962
-
Hg19::chr9:100947965..100947975,-p@chr9:100947965..100947975
-
Hg19::chr9:127148331..127148341,-p@chr9:127148331..127148341
-
Hg19::chr9:127149681..127149698,-p@chr9:127149681..127149698
-
Hg19::chr9:127149714..127149721,-p@chr9:127149714..127149721
-


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

GO IDGO nameFDR corrected p-value
GO:0000093mitotic telophase0.00551925114800423
GO:0051326telophase0.00551925114800423
GO:0000089mitotic metaphase0.00827838931830998
GO:0051323metaphase0.00827838931830998
GO:0051322anaphase0.0091976688152717
GO:0000090mitotic anaphase0.0091976688152717
GO:0000299integral to membrane of membrane fraction0.0126128318365972
GO:0030225macrophage differentiation0.0151734731405287
GO:0007093mitotic cell cycle checkpoint0.0330872449633977
GO:0002573myeloid leukocyte differentiation0.0330872449633977
GO:0006909phagocytosis0.0410950816486348
GO:0000075cell cycle checkpoint0.0477251694968636
GO:0042089cytokine biosynthetic process0.0477251694968636
GO:0007088regulation of mitosis0.0477251694968636
GO:0042107cytokine metabolic process0.0477251694968636
GO:0009059macromolecule biosynthetic process0.0477251694968636
GO:0030099myeloid cell differentiation0.0477251694968636
GO:0005819spindle0.0477251694968636



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><br>uberon_data<br>disease_data<br>

Disease
Ontology termp-valuen
syndrome4.10e-231
hematopoietic system disease2.90e-122
myeloid leukemia6.57e-1231
leukemia1.52e-0939
hematologic cancer2.24e-0751
immune system cancer2.24e-0751
cardiovascular system disease9.11e-074


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)
MA0003.10.0417237
MA0004.10.193314
MA0006.10.308609
MA0007.10.180248
MA0009.11.41914
MA0014.10.00883981
MA0017.10.367718
MA0019.10.824541
MA0024.11.21812
MA0025.10.70396
MA0027.12.15732
MA0028.10.680413
MA0029.10.50258
MA0030.11.23309
MA0031.11.11067
MA0038.10.269828
MA0040.10.507819
MA0041.10.206566
MA0042.10.183918
MA0043.10.580321
MA0046.10.570066
MA0048.10.270045
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.10.317307
MA0056.10
MA0057.10.122328
MA0058.10.12994
MA0059.10.405044
MA0060.10.0387582
MA0061.10.290613
MA0063.10
MA0066.11.36491
MA0067.10.879057
MA0068.10.409781
MA0069.10.566544
MA0070.10.556335
MA0071.10.674412
MA0072.10.552241
MA0073.11.28654e-06
MA0074.10.265952
MA0076.10.432406
MA0077.10.545231
MA0078.10.346453
MA0081.10.405301
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.10.398465
MA0089.10
MA0090.10.149167
MA0091.10.195166
MA0092.10.168981
MA0093.10.0941737
MA0095.10
MA0098.10
MA0100.10.768006
MA0101.10.317957
MA0103.11.03031
MA0105.10.220534
MA0106.10.817478
MA0107.10.0591705
MA0108.21.10489
MA0109.10
MA0111.10.15804
MA0113.10.315797
MA0114.10.207884
MA0115.10.805883
MA0116.11.74683
MA0117.10.614633
MA0119.11.2467
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.11.38399
MA0139.10.108841
MA0140.10.238066
MA0141.11.30232
MA0142.10.407878
MA0143.10.315941
MA0144.10.189563
MA0145.11.59211
MA0146.10.205334
MA0147.10.485912
MA0148.10.606512
MA0149.10.230803
MA0062.20.826291
MA0035.20.237534
MA0039.20.0934976
MA0138.20.347473
MA0002.21.32966
MA0137.20.697429
MA0104.20.34888
MA0047.20.292798
MA0112.20.632219
MA0065.20.963917
MA0150.10.145358
MA0151.10
MA0152.10.243034
MA0153.10.67139
MA0154.11.9317
MA0155.10.124291
MA0156.10.106343
MA0157.10.384449
MA0158.10
MA0159.11.77332
MA0160.10.632864
MA0161.10
MA0162.10.0505942
MA0163.10.10617
MA0164.10.870085
MA0080.21.07751
MA0018.20.30364
MA0099.21.26491
MA0079.25.95052e-06
MA0102.21.09681
MA0258.10.706831
MA0259.10.0662172
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
SPI1#668873.022645503139950.005284523421607440.0244749597174838



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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