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Coexpression cluster:C400: Difference between revisions

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{{Coexpression_clusters
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binding!0.0309390821853291!81846$GO:0016311!dephosphorylation!0.0313839018321994!81846$GO:0019899!enzyme binding!0.0313839018321994!81846$GO:0019226!transmission of nerve impulse!0.0313839018321994!81846$GO:0005543!phospholipid binding!0.0313839018321994!81846$GO:0006461!protein complex assembly!0.0313839018321994!81846$GO:0042802!identical protein binding!0.0313839018321994!81846$GO:0046983!protein dimerization activity!0.0313839018321994!81846$GO:0016791!phosphoric monoester hydrolase activity!0.0359928764865183!81846$GO:0042578!phosphoric ester hydrolase activity!0.043919653289134!81846$GO:0008289!lipid binding!0.043919653289134!81846$GO:0007267!cell-cell 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87,0.60105,0.00138557,0.119947,0.213274,0.122506,0.523764,0.406471,0.207772,0.346619,0.550577,0.0507345,0.152554,0.0649159,0.129922,0.132601,0.705312,0.0853787,0.648731,0.0968983,0.131358,0.731663,0.512987,0.10814,0.376235,0.0223791,0.450439,0.0369069,0.101267,0.0359171,0.137767,0.846127,0.0585588,0.953294,0.0996789,0.0386942,0.712424,0.136512,0.0783632,0.184896,0.114021,0.234518,0.416095,0.672276,0.192661,0.350244,0.439939,0.572791,0.17862,1.1433,0.15794,0.0260378,0.157319,0.409909,0.186447,0.362358,0.324749,0.198353,0.298136,0.652492,0.998973,0.367813,0.844111,0.0930654,0.383043,0.00194772,1.40012,0.0411255,0.101242,0.79122,0.311603,0.365188,0.28104,1.45272,0.32391,0.575406,2.15382,0.525521,0.00145117,0.073263,0.304817,0.257977,1.09502,0.738491,0.501948,0.389962,0.25314,0.0488346,1.19128,0.280717,0.425289,0.261356,0.0184748,0.290547,0.385331,0.420622,0.349541,1.43522,0.117458,0.336968,0.518366,0.28874,0.0429788,0.245012,0.41831,0.224609,0.394894,1.65767,0.597861,0.0991321,0.107506,0.296351,1.13513,0.563638,0.711797,1.34885,0.593569,0.797035,0.312191,1.01905,0.394066,0.601752,0.0277393,0.502548,3.03346,0.61471,0.58819,0.750477,0.0216391,1.15162,0.816851,0.711091,1.54156,1.14596,0.676716,0.181176,1.08231,0.29071,0.906885,0.278155,1.3843,1.10373,0.100478,0.0877598,0.000341566,0.50288,0.171687,0.186129,0.873115,0.246224,0.380465,0.289148,0.0721949,0.675601,0.486836,0.364552,0.256244,0.30298,1.71256,0.431755,0.539765,0.000709058|tfbs_overrepresentation_jaspar=MA0003.1;1.78232e-06,MA0004.1;0.778021,MA0006.1;0.0479067,MA0007.1;0.112494,MA0009.1;0.46676,MA0014.1;0.000159245,MA0017.1;0.226532,MA0019.1;0.619765,MA0024.1;0.378349,MA0025.1;0.584598,MA0027.1;2.02165,MA0028.1;0.198989,MA0029.1;0.394311,MA0030.1;0.384823,MA0031.1;0.33249,MA0038.1;0.186009,MA0040.1;1.03187,MA0041.1;1.93378,MA0042.1;1.22068,MA0043.1;0.467032,MA0046.1;0.457379,MA0048.1;0.0475232,MA0050.1;0.746851,MA0051.1;0.539526,MA0052.1;0.402401,MA0055.1;0.712959,MA0056.1;0,MA0057.1;0.103816,MA0058.1;1.92954,MA0059.1;0.927345,MA0060.1;0.184491,MA0061.1;0.052445,MA0063.1;0,MA0066.1;0.546967,MA0067.1;0.753856,MA0068.1;0.361473,MA0069.1;2.98321,MA0070.1;0.44448,MA0071.1;2.15236,MA0072.1;0.44064,MA0073.1;1.42013e-11,MA0074.1;0.182721,MA0076.1;0.0815705,MA0077.1;0.434073,MA0078.1;0.252504,MA0081.1;0.927903,MA0083.1;0.473254,MA0084.1;0.931415,MA0087.1;0.438554,MA0088.1;0.263813,MA0089.1;0,MA0090.1;0.619224,MA0091.1;0.124326,MA0092.1;0.338625,MA0093.1;1.11574,MA0095.1;0,MA0098.1;0,MA0100.1;1.07984,MA0101.1;0.736489,MA0103.1;0.170494,MA0105.1;0.00962152,MA0106.1;5.16876,MA0107.1;0.271434,MA0108.2;0.330055,MA0109.1;0,MA0111.1;0.0952636,MA0113.1;0.225587,MA0114.1;0.0253615,MA0115.1;0.682809,MA0116.1;0.0276251,MA0117.1;0.499451,MA0119.1;0.236164,MA0122.1;0.522217,MA0124.1;0.644657,MA0125.1;1.39486,MA0130.1;0,MA0131.1;0.26595,MA0132.1;0,MA0133.1;0,MA0135.1;0.493123,MA0136.1;1.67411,MA0139.1;0.00880521,MA0140.1;0.93427,MA0141.1;0.921371,MA0142.1;0.828623,MA0143.1;1.19813,MA0144.1;0.0952058,MA0145.1;0.104585,MA0146.1;0.000399295,MA0147.1;0.284471,MA0148.1;0.425644,MA0149.1;0.153304,MA0062.2;0.277944,MA0035.2;0.158878,MA0039.2;5.88665e-08,MA0138.2;0.705339,MA0002.2;0.330883,MA0137.2;0.206545,MA0104.2;0.183272,MA0047.2;0.59341,MA0112.2;0.0926572,MA0065.2;0.0190901,MA0150.1;0.289831,MA0151.1;0,MA0152.1;0.491228,MA0153.1;0.553438,MA0154.1;0.00908591,MA0155.1;0.0130327,MA0156.1;1.6986,MA0157.1;0.286356,MA0158.1;0,MA0159.1;0.285671,MA0160.1;0.879768,MA0161.1;0,MA0162.1;0.000113447,MA0163.1;0.000196937,MA0164.1;0.661297,MA0080.2;2.66001,MA0018.2;0.215022,MA0099.2;0.491785,MA0079.2;3.27582e-13,MA0102.2;0.967149,MA0258.1;0.420961,MA0259.1;0.300465,MA0442.1;0}}
|full_id=C400_acute_leukemia_chronic_myelodysplastic_NK_pancreas_duodenum
|id=C400
}}

Latest revision as of 11:22, 17 September 2013


Full id: C400_acute_leukemia_chronic_myelodysplastic_NK_pancreas_duodenum



Phase1 CAGE Peaks

Hg19::chr11:10066331..10066341,-p14@SBF2
Hg19::chr13:21651405..21651425,+p@chr13:21651405..21651425
+
Hg19::chr13:44990601..44990610,-p@chr13:44990601..44990610
-
Hg19::chr13:91807411..91807446,+p@chr13:91807411..91807446
+
Hg19::chr15:91832784..91832813,+p@chr15:91832784..91832813
+
Hg19::chr17:73494290..73494299,+p@chr17:73494290..73494299
+
Hg19::chr17:73494308..73494321,+p@chr17:73494308..73494321
+
Hg19::chr1:120342510..120342533,-p@chr1:120342510..120342533
-
Hg19::chr1:200119992..200120017,+p@chr1:200119992..200120017
+
Hg19::chr20:11561982..11561988,-p@chr20:11561982..11561988
-
Hg19::chr20:11562071..11562078,-p@chr20:11562071..11562078
-
Hg19::chr21:40361134..40361189,-p@chr21:40361134..40361189
-
Hg19::chr2:117207734..117207758,+p@chr2:117207734..117207758
+
Hg19::chr3:71808686..71808697,-p@chr3:71808686..71808697
-
Hg19::chr4:77177483..77177500,+p@chr4:77177483..77177500
+
Hg19::chr4:77177512..77177526,+p@chr4:77177512..77177526
+
Hg19::chr4:80118672..80118679,+p2@ENST00000512130
Hg19::chr4:80118699..80118734,+p1@ENST00000512130
Hg19::chr4:80127830..80127850,+p@chr4:80127830..80127850
+
Hg19::chr5:150155709..150155730,-p@chr5:150155709..150155730
-
Hg19::chr6:142507003..142507014,+p@chr6:142507003..142507014
+
Hg19::chr6:156491058..156491081,-p@chr6:156491058..156491081
-
Hg19::chr6:156491142..156491148,-p@chr6:156491142..156491148
-
Hg19::chr6:156491164..156491167,-p@chr6:156491164..156491167
-
Hg19::chr8:54090128..54090133,+p1@ENST00000529837
Hg19::chr8:94710802..94710816,+p3@FAM92A1


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:0051262protein tetramerization0.010518466187841
GO:0046839phospholipid dephosphorylation0.010518466187841
GO:0019902phosphatase binding0.010518466187841
GO:0042552myelination0.010518466187841
GO:0007272ensheathment of neurons0.010518466187841
GO:0008366axon ensheathment0.010518466187841
GO:0001508regulation of action potential0.010518466187841
GO:0030258lipid modification0.010518466187841
GO:0004437inositol or phosphatidylinositol phosphatase activity0.010518466187841
GO:0051259protein oligomerization0.010518466187841
GO:0005774vacuolar membrane0.010518466187841
GO:0044437vacuolar part0.010518466187841
GO:0019208phosphatase regulator activity0.0124401090490811
GO:0042803protein homodimerization activity0.0222578257724849
GO:0005773vacuole0.0306350327720868
GO:0035091phosphoinositide binding0.0309390821853291
GO:0016311dephosphorylation0.0313839018321994
GO:0019899enzyme binding0.0313839018321994
GO:0019226transmission of nerve impulse0.0313839018321994
GO:0005543phospholipid binding0.0313839018321994
GO:0006461protein complex assembly0.0313839018321994
GO:0042802identical protein binding0.0313839018321994
GO:0046983protein dimerization activity0.0313839018321994
GO:0016791phosphoric monoester hydrolase activity0.0359928764865183
GO:0042578phosphoric ester hydrolase activity0.043919653289134
GO:0008289lipid binding0.043919653289134
GO:0007267cell-cell signaling0.0467487386126265



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>

Uber Anatomy
Ontology termp-valuen
temporal lobe8.99e-116
Disease
Ontology termp-valuen
myeloid leukemia1.20e-0931
chronic leukemia1.47e-098
leukemia6.83e-0839


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)
MA0003.11.78232e-06
MA0004.10.778021
MA0006.10.0479067
MA0007.10.112494
MA0009.10.46676
MA0014.10.000159245
MA0017.10.226532
MA0019.10.619765
MA0024.10.378349
MA0025.10.584598
MA0027.12.02165
MA0028.10.198989
MA0029.10.394311
MA0030.10.384823
MA0031.10.33249
MA0038.10.186009
MA0040.11.03187
MA0041.11.93378
MA0042.11.22068
MA0043.10.467032
MA0046.10.457379
MA0048.10.0475232
MA0050.10.746851
MA0051.10.539526
MA0052.10.402401
MA0055.10.712959
MA0056.10
MA0057.10.103816
MA0058.11.92954
MA0059.10.927345
MA0060.10.184491
MA0061.10.052445
MA0063.10
MA0066.10.546967
MA0067.10.753856
MA0068.10.361473
MA0069.12.98321
MA0070.10.44448
MA0071.12.15236
MA0072.10.44064
MA0073.11.42013e-11
MA0074.10.182721
MA0076.10.0815705
MA0077.10.434073
MA0078.10.252504
MA0081.10.927903
MA0083.10.473254
MA0084.10.931415
MA0087.10.438554
MA0088.10.263813
MA0089.10
MA0090.10.619224
MA0091.10.124326
MA0092.10.338625
MA0093.11.11574
MA0095.10
MA0098.10
MA0100.11.07984
MA0101.10.736489
MA0103.10.170494
MA0105.10.00962152
MA0106.15.16876
MA0107.10.271434
MA0108.20.330055
MA0109.10
MA0111.10.0952636
MA0113.10.225587
MA0114.10.0253615
MA0115.10.682809
MA0116.10.0276251
MA0117.10.499451
MA0119.10.236164
MA0122.10.522217
MA0124.10.644657
MA0125.11.39486
MA0130.10
MA0131.10.26595
MA0132.10
MA0133.10
MA0135.10.493123
MA0136.11.67411
MA0139.10.00880521
MA0140.10.93427
MA0141.10.921371
MA0142.10.828623
MA0143.11.19813
MA0144.10.0952058
MA0145.10.104585
MA0146.10.000399295
MA0147.10.284471
MA0148.10.425644
MA0149.10.153304
MA0062.20.277944
MA0035.20.158878
MA0039.25.88665e-08
MA0138.20.705339
MA0002.20.330883
MA0137.20.206545
MA0104.20.183272
MA0047.20.59341
MA0112.20.0926572
MA0065.20.0190901
MA0150.10.289831
MA0151.10
MA0152.10.491228
MA0153.10.553438
MA0154.10.00908591
MA0155.10.0130327
MA0156.11.6986
MA0157.10.286356
MA0158.10
MA0159.10.285671
MA0160.10.879768
MA0161.10
MA0162.10.000113447
MA0163.10.000196937
MA0164.10.661297
MA0080.22.66001
MA0018.20.215022
MA0099.20.491785
MA0079.23.27582e-13
MA0102.20.967149
MA0258.10.420961
MA0259.10.300465
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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