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Coexpression cluster:C467: Difference between revisions

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{{Coexpression_clusters
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0.838679,0.710145,0.837984,0.725761,0.240267,0.38041,0.312897,0.27845,0.37485,0.210468,0.803871,0.692242,0.591961,0.165318,0.192521,0.349403,0.507623,0.701148,0.519713,0.196263,0.237934,0.621479,0.258889,0.752002,0.704624,0.345556,0.316926,0.246307,0.60389,0.759758,0.761849,0.408769,0.876747,0.880478,0.797125,0.814368,0.803769,0.29033,0.777157,0.324782,0.0568831,0.531289,0.587875,0.383724,0.207838,0.284102,0.784927,0.573443,0.696107,0.62601,0.344713,0.828709,0.733486,0.39491,0.510182,0.468821,0.925842,0.202425,0.821425,0.451581,0.0760947,0.546215,0.320004,0.320851,0.682393,0.433678,0.252507,0.320659,0.932716,0.165929,0.810215,0.42716,0.844731,0.183969,0.4476,0.514645,0.371276,0.597501,0.369981,0.538566,0.381461,0.42605,0.251247,0.554795,0.270785,0.384359,0.481683,0.230538,0.637576,0.798214,0.102832,0.213971,0.798393,0.656939,0.62998,0.873762,0.790478,0.271194,0.916294,0.151382,0.7457,0.903199,0.88347,0.628059,0.706525,0.0811475,0.788886,0.906223,0.848712,0.297589,0.57753,0.248535,0.262347,0.211967,0.448259,0.187057,0.901365,0.676205,0.326937,0.716128,0.830946,0.497294,0.937871,0.833214,0.224556,0.506147,0.466831,0.745372,0.732468,0.341299,0.649123,0.095206,0.890164,0.52549,0.828321,0.392372,0.69814,0.81746,0.869961,0.80097,0.956705|tfbs_overrepresentation_for_novel_motifs=1.66689,1.17433,0.324717,0.18689,0.563528,0.185775,1.93979,0.295736,0.536019,0.702947,1.53091,0.748251,0.662693,0.6536,0.264653,0.0881735,0.416635,0.0529639,0.441013,0.68534,0.324802,0.0742512,1.02103,0.0748199,1.85586,0.289541,1.20782,1.01519,0.571039,0.509878,0.902438,0.448071,1.00927,0.410119,0.831295,0.369277,0.0600845,0.547612,0.0504655,0.104553,0.0608563,0.859404,0.0917928,0.556551,0.805663,0.115453,0.675098,0.158699,0.0792306,0.27085,0.813183,0.249086,0.83143,0.515129,0.653159,0.658597,0.08088,0.603257,0.299101,0.60157,0.483605,1.26042,0.29166,0.393294,0.71007,0.364726,0.73513,1.08739,0.43915,0.930562,0.416257,0.130122,0.353719,0.651319,0.390033,0.179474,0.157868,0.379205,0.436366,0.382881,1.08201,0.392395,0.25519,0.553244,1.47014,0.568305,0.150398,0.750383,0.321213,1.18432,0.823081,0.579812,0.462581,0.377714,0.267495,2.07253,0.229209,0.499768,0.324895,0.117303,1.13963,1.15874,0.494867,0.419744,0.935363,0.16277,0.406348,0.228655,0.123981,0.897424,0.69516,0.492438,0.65299,0.171884,0.777703,0.215264,0.508825,0.460172,0.362802,0.169406,1.55274,0.319278,0.183912,0.263675,0.882719,0.379837,0.234914,0.466912,0.683004,1.10938,0.580435,0.466574,0.696335,0.723221,0.835304,0.463838,0.147939,0.179476,0.795107,1.6331,1.23566,0.759951,0.236178,0.496668,0.356718,1.74729,0.343142,1.4753,0.139503,0.162413,0.507246,0.885079,0.58078,1.18505,0.678325,0.959994,0.308372,0.904567,0.124164,0.349357,0.758809,0.564094,0.435692,0.109525,0.36994,0.254599,0.0377709,0.238589,1.22286|tfbs_overrepresentation_jaspar=MA0003.1;1.90648,MA0004.1;0.505176,MA0006.1;0.264032,MA0007.1;0.156885,MA0009.1;1.34126,MA0014.1;0.675348,MA0017.1;0.31911,MA0019.1;0.757112,MA0024.1;0.450307,MA0025.1;0.665335,MA0027.1;2.11401,MA0028.1;0.0843345,MA0029.1;1.17914,MA0030.1;0.457153,MA0031.1;0.401568,MA0038.1;0.678012,MA0040.1;0.472301,MA0041.1;1.02521,MA0042.1;1.49922,MA0043.1;0.543454,MA0046.1;0.533373,MA0048.1;1.16803,MA0050.1;0.160894,MA0051.1;0.238478,MA0052.1;0.475699,MA0055.1;0.51873,MA0056.1;0,MA0057.1;0.561641,MA0058.1;0.110291,MA0059.1;0.35417,MA0060.1;1.67182,MA0061.1;0.0956181,MA0063.1;0,MA0066.1;0.678752,MA0067.1;0.83875,MA0068.1;0.334888,MA0069.1;0.529912,MA0070.1;0.519883,MA0071.1;0.213282,MA0072.1;0.515863,MA0073.1;0.62605,MA0074.1;0.23792,MA0076.1;0.119431,MA0077.1;0.508982,MA0078.1;0.31524,MA0081.1;0.718628,MA0083.1;0.549943,MA0084.1;1.01907,MA0087.1;0.513678,MA0088.1;0.179504,MA0089.1;0,MA0090.1;0.402075,MA0091.1;1.56092,MA0092.1;0.146372,MA0093.1;0.268179,MA0095.1;0,MA0098.1;0,MA0100.1;0.252028,MA0101.1;0.0794742,MA0103.1;0.914326,MA0105.1;0.0246233,MA0106.1;0.272934,MA0107.1;0.046982,MA0108.2;0.398967,MA0109.1;0,MA0111.1;0.423052,MA0113.1;0.285689,MA0114.1;0.17185,MA0115.1;0.766188,MA0116.1;0.0483327,MA0117.1;0.577217,MA0119.1;0.100647,MA0122.1;0.600851,MA0124.1;0.727093,MA0125.1;0.648747,MA0130.1;0,MA0131.1;1.58054,MA0132.1;0,MA0133.1;0,MA0135.1;0.570637,MA0136.1;0.246897,MA0139.1;0.411319,MA0140.1;0.211376,MA0141.1;0.108582,MA0142.1;0.978356,MA0143.1;0.285827,MA0144.1;0.998358,MA0145.1;0.772194,MA0146.1;0.304434,MA0147.1;0.415954,MA0148.1;0.185927,MA0149.1;1.11603,MA0062.2;0.22708,MA0035.2;0.210872,MA0039.2;0.451391,MA0138.2;0.316226,MA0002.2;0.110362,MA0137.2;0.614924,MA0104.2;0.28985,MA0047.2;0.263601,MA0112.2;1.96386,MA0065.2;0.220145,MA0150.1;0.124469,MA0151.1;0,MA0152.1;0.216094,MA0153.1;0.633172,MA0154.1;0.715386,MA0155.1;0.677299,MA0156.1;0.620624,MA0157.1;0.352016,MA0158.1;0,MA0159.1;0.417407,MA0160.1;0.196462,MA0161.1;0,MA0162.1;0.595981,MA0163.1;0.283784,MA0164.1;0.801488,MA0080.2;1.43309,MA0018.2;0.274004,MA0099.2;0.216352,MA0079.2;2.3489,MA0102.2;1.05522,MA0258.1;0.0364681,MA0259.1;0.761407,MA0442.1;0}}
|full_id=C467_CD14_Monocytederived_Mesenchymal_Macrophage_Dendritic_mucinous_liver
|id=C467
}}

Latest revision as of 11:23, 17 September 2013


Full id: C467_CD14_Monocytederived_Mesenchymal_Macrophage_Dendritic_mucinous_liver



Phase1 CAGE Peaks

Hg19::chr11:64570565..64570568,+p@chr11:64570565..64570568
+
Hg19::chr15:82336075..82336082,-p2@MEX3B
Hg19::chr16:86227253..86227256,-p@chr16:86227253..86227256
-
Hg19::chr18:43418864..43418874,-p@chr18:43418864..43418874
-
Hg19::chr19:3870787..3870791,+p@chr19:3870787..3870791
+
Hg19::chr19:49468563..49468567,+p1@FTL
Hg19::chr19:49468653..49468695,-p@chr19:49468653..49468695
-
Hg19::chr19:49469582..49469598,-p@chr19:49469582..49469598
-
Hg19::chr19:49469909..49469927,-p3@BC007552
Hg19::chr19:49469928..49469955,-p1@BC007552
Hg19::chr19:49470000..49470017,-p4@BC007552
Hg19::chr19:49470100..49470134,-p2@BC007552
Hg19::chr1:167522982..167523017,-p1@CREG1
Hg19::chr1:229478625..229478628,+p@chr1:229478625..229478628
+
Hg19::chr20:4004363..4004364,+p1@FTLP3
Hg19::chr20:4004638..4004661,+p3@FTLP3
Hg19::chr22:21058481..21058484,+p@chr22:21058481..21058484
+
Hg19::chr2:96931834..96931847,+p3@CIAO1
Hg19::chr5:139555310..139555313,+p@chr5:139555310..139555313
+
Hg19::chr9:108505287..108505289,+p@chr9:108505287..108505289
+
Hg19::chrX:30648208..30648217,+p1@FTLP2


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:0008043ferritin complex0.0242541980461979
GO:0006357regulation of transcription from RNA polymerase II promoter0.0470088123859172



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>

Uber Anatomy
Ontology termp-valuen
musculoskeletal system2.10e-24167
bone marrow5.92e-2376
mesoderm1.44e-21315
mesoderm-derived structure1.44e-21315
presumptive mesoderm1.44e-21315
immune system4.77e-2193
hemolymphoid system5.43e-21108
skeletal element9.77e-2190
hematopoietic system2.34e-2098
blood island2.34e-2098
skeletal system3.17e-20100
bone element5.95e-2082
lateral plate mesoderm1.98e-17203
connective tissue3.21e-13371


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)
MA0003.11.90648
MA0004.10.505176
MA0006.10.264032
MA0007.10.156885
MA0009.11.34126
MA0014.10.675348
MA0017.10.31911
MA0019.10.757112
MA0024.10.450307
MA0025.10.665335
MA0027.12.11401
MA0028.10.0843345
MA0029.11.17914
MA0030.10.457153
MA0031.10.401568
MA0038.10.678012
MA0040.10.472301
MA0041.11.02521
MA0042.11.49922
MA0043.10.543454
MA0046.10.533373
MA0048.11.16803
MA0050.10.160894
MA0051.10.238478
MA0052.10.475699
MA0055.10.51873
MA0056.10
MA0057.10.561641
MA0058.10.110291
MA0059.10.35417
MA0060.11.67182
MA0061.10.0956181
MA0063.10
MA0066.10.678752
MA0067.10.83875
MA0068.10.334888
MA0069.10.529912
MA0070.10.519883
MA0071.10.213282
MA0072.10.515863
MA0073.10.62605
MA0074.10.23792
MA0076.10.119431
MA0077.10.508982
MA0078.10.31524
MA0081.10.718628
MA0083.10.549943
MA0084.11.01907
MA0087.10.513678
MA0088.10.179504
MA0089.10
MA0090.10.402075
MA0091.11.56092
MA0092.10.146372
MA0093.10.268179
MA0095.10
MA0098.10
MA0100.10.252028
MA0101.10.0794742
MA0103.10.914326
MA0105.10.0246233
MA0106.10.272934
MA0107.10.046982
MA0108.20.398967
MA0109.10
MA0111.10.423052
MA0113.10.285689
MA0114.10.17185
MA0115.10.766188
MA0116.10.0483327
MA0117.10.577217
MA0119.10.100647
MA0122.10.600851
MA0124.10.727093
MA0125.10.648747
MA0130.10
MA0131.11.58054
MA0132.10
MA0133.10
MA0135.10.570637
MA0136.10.246897
MA0139.10.411319
MA0140.10.211376
MA0141.10.108582
MA0142.10.978356
MA0143.10.285827
MA0144.10.998358
MA0145.10.772194
MA0146.10.304434
MA0147.10.415954
MA0148.10.185927
MA0149.11.11603
MA0062.20.22708
MA0035.20.210872
MA0039.20.451391
MA0138.20.316226
MA0002.20.110362
MA0137.20.614924
MA0104.20.28985
MA0047.20.263601
MA0112.21.96386
MA0065.20.220145
MA0150.10.124469
MA0151.10
MA0152.10.216094
MA0153.10.633172
MA0154.10.715386
MA0155.10.677299
MA0156.10.620624
MA0157.10.352016
MA0158.10
MA0159.10.417407
MA0160.10.196462
MA0161.10
MA0162.10.595981
MA0163.10.283784
MA0164.10.801488
MA0080.21.43309
MA0018.20.274004
MA0099.20.216352
MA0079.22.3489
MA0102.21.05522
MA0258.10.0364681
MA0259.10.761407
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
CHD2#110694.433152643192947.30842829241517e-050.00114745180762409
CTCF#10664123.063003641757169.61865604962896e-050.0013695471290623
EP300#203392.903117882667090.001797884834934830.0110270903380173
HEY1#23462132.501021121922580.0003339397910464340.00339991595214452
RDBP#7936321.94834342714640.0003351363455256030.00341143321543357
SP1#666792.442163447774670.006047090263267070.02709361046784



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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