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Coexpression cluster:C418: Difference between revisions

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{{Coexpression_clusters
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regulation of cell growth!0.039468234767104!58189$GO:0045792!negative regulation of cell size!0.039468234767104!58189$GO:0045926!negative regulation of growth!0.039468234767104!58189$GO:0001558!regulation of cell growth!0.0498755484983084!58189$GO:0004867!serine-type endopeptidase inhibitor activity!0.0498755484983084!58189$GO:0016049!cell growth!0.0498755484983084!58189$GO:0040008!regulation of growth!0.0498755484983084!58189$GO:0008361!regulation of cell 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771051,0.174147,0.785658,0.279009,0.434406,0.360297,0.321937,0.049645,0.289869,0.873883,0.40917,0.656007,0.579256,0.615853,0.0937863,0.868288,0.762566,0.613632,0.272023,0.668878,0.1095,0.95345,0.809846,0.179153,0.916155,0.394809,0.334071,0.667946,0.816905,0.0944129,0.130418,0.917279,0.248613,0.296011,0.865306,0.306722,0.720561,0.533358,0.426987,0.642001,0.0640739,0.032983,0.022767,0.119212,0.71486,0.113494,0.898958,0.757791,0.689901,0.915843,0.8776,0.0752977,0.802337,0.0111165,0.847687,0.598206,0.935973,0.607593,0.510875,0.560848,0.069712,0.368167,0.369103,0.744723,0.491808,0.292816,0.368891,0.622781,0.920233,0.861711,0.251432,0.00776918,0.256423,0.506646,0.577077,0.424465,0.294891,0.423054,0.601773,0.435547,0.483649,0.318655,0.00312844,0.313355,0.00293305,0.542667,0.268004,0.701284,0.567788,0.559125,0.940116,0.688653,0.720186,0.921516,0.705191,0.844425,0.883624,0.342219,0.43978,0.224435,0.525737,0.255119,0.691923,0.428522,0.854091,0.843017,0.000692015,0.657048,0.635971,0.641475,0.607287,0.878949,0.639657,0.109904,0.260355,0.936552,0.302474,0.429467,0.441869,0.624512,0.559017,0.642135,0.881424,0.577814,0.568247,0.527024,0.392029,0.791885,0.176622,0.73971,0.459206,0.738258,0.588303,0.877271,0.0805518,0.759718,0.14737,0.437713,0.853655,0.320082|tfbs_overrepresentation_for_novel_motifs=0.0737355,0.748423,0.528759,0.880383,0.196868,0.446495,0.565195,0.397511,1.32584,0.0567872,0.401546,1.85477,0.279201,0.18622,0.195296,0.222896,0.359143,0.32265,5.19625,2.23345,0.0704756,1.54141,0.14085,0.0512902,0.635488,0.239737,3.99102,1.98331,2.19032,0.0302434,1.22178,1.00986,0.107025,0.746804,0.363331,1.07225,0.0397666,0.146177,0.310421,0.574327,0.360494,0.705426,1.11564,0.429731,0.488146,0.0845678,0.566947,0.38574,0.405707,0.442908,0.69748,1.10838,0.58467,0.453481,0.587358,1.05153,0.452131,0.499803,0.350885,0.166299,0.423157,0.196176,1.74807,0.336984,0.208359,0.309988,0.667509,1.01514,0.380596,0.859886,0.0999006,0.215242,0.0150978,0.585564,0.268256,0.113577,2.33683,0.323653,0.37794,0.0888599,0.1613,0.336133,0.208117,0.0828649,0.539768,0.00197079,0.456145,0.00500612,0.269174,1.11136,0.753896,0.516018,0.402998,0.814489,0.0535122,1.25595,0.15207,0.438691,0.272612,0.687221,0.13295,0.398316,1.10755,0.362101,2.25517,0.394926,0.349366,0.18395,0.306554,0.178841,0.075464,0.431643,0.0680411,0.415422,0.70928,0.353647,0.43082,2.40842,0.308176,0.116148,0.578146,0.267369,0.442338,0.215895,0.812657,1.5605,0.555018,1.04926,0.616494,2.74435,0.516623,0.117129,0.629526,0.213587,0.765929,1.71258,0.112299,0.432429,0.726382,1.55835,1.16239,0.691851,1.06196,2.89883,0.302448,0.161608,0.289694,1.40098,1.15177,1.16461,0.197065,0.0143922,0.516957,0.188592,0.569975,0.888975,0.714117,0.0480206,0.0919218,0.961075,5.37232,1.25113,3.59741,0.273059,0.314905,0.207576,0.749935,1.07066,0.127529|tfbs_overrepresentation_jaspar=MA0003.1;0.152235,MA0004.1;0.409228,MA0006.1;0.431998,MA0007.1;0.120068,MA0009.1;0.480543,MA0014.1;0.379799,MA0017.1;0.242343,MA0019.1;1.87392,MA0024.1;0.391254,MA0025.1;0.599238,MA0027.1;2.03861,MA0028.1;0.213776,MA0029.1;0.407394,MA0030.1;0.397801,MA0031.1;0.912186,MA0038.1;0.195728,MA0040.1;2.7903,MA0041.1;0.437147,MA0042.1;0.778983,MA0043.1;0.480818,MA0046.1;0.47108,MA0048.1;0.243139,MA0050.1;0.123567,MA0051.1;0.192868,MA0052.1;1.87776,MA0055.1;1.24924,MA0056.1;0,MA0057.1;0.0501,MA0058.1;0.274844,MA0059.1;0.972405,MA0060.1;0.017391,MA0061.1;0.536938,MA0063.1;0,MA0066.1;0.570377,MA0067.1;0.769322,MA0068.1;0.105313,MA0069.1;0.467738,MA0070.1;0.458064,MA0071.1;0.978531,MA0072.1;1.1512,MA0073.1;1.19268e-05,MA0074.1;0.19236,MA0076.1;0.0879186,MA0077.1;0.44756,MA0078.1;0.263604,MA0081.1;0.27336,MA0083.1;0.487092,MA0084.1;0.947429,MA0087.1;0.452083,MA0088.1;0.634322,MA0089.1;0,MA0090.1;5.92348,MA0091.1;1.92403,MA0092.1;0.357807,MA0093.1;0.198309,MA0095.1;0,MA0098.1;0,MA0100.1;0.592379,MA0101.1;0.202181,MA0103.1;0.411939,MA0105.1;0.501682,MA0106.1;0.637762,MA0107.1;0.539977,MA0108.2;1.62457,MA0109.1;0,MA0111.1;1.13254,MA0113.1;1.23797,MA0114.1;0.524336,MA0115.1;0.697973,MA0116.1;0.126338,MA0117.1;0.513502,MA0119.1;0.0722294,MA0122.1;0.53644,MA0124.1;1.58599,MA0125.1;0.583056,MA0130.1;0,MA0131.1;0.277285,MA0132.1;0,MA0133.1;0,MA0135.1;0.507125,MA0136.1;1.72893,MA0139.1;0.140093,MA0140.1;0.168354,MA0141.1;0.270862,MA0142.1;0.319458,MA0143.1;0.236302,MA0144.1;0.0245926,MA0145.1;0.21721,MA0146.1;0.0536518,MA0147.1;0.561572,MA0148.1;1.41112,MA0149.1;0.162171,MA0062.2;0.0113502,MA0035.2;0.50217,MA0039.2;0.0064561,MA0138.2;0.730951,MA0002.2;0.359117,MA0137.2;0.832275,MA0104.2;0.0172311,MA0047.2;1.81274,MA0112.2;0.196276,MA0065.2;0.745387,MA0150.1;0.0921806,MA0151.1;0,MA0152.1;0.513688,MA0153.1;0.567879,MA0154.1;0.488003,MA0155.1;0.177814,MA0156.1;0.487034,MA0157.1;1.46654,MA0158.1;0,MA0159.1;0.0320844,MA0160.1;0.916248,MA0161.1;0,MA0162.1;0.00361818,MA0163.1;0.0474539,MA0164.1;0.245213,MA0080.2;0.766855,MA0018.2;0.225392,MA0099.2;0.172833,MA0079.2;4.195e-05,MA0102.2;0.983247,MA0258.1;0.733928,MA0259.1;0.587878,MA0442.1;0}}
|full_id=C418_normal_Melanocyte_Hep2_cervical_umbilical_osteosarcoma_gall
|id=C418
}}

Latest revision as of 11:22, 17 September 2013


Full id: C418_normal_Melanocyte_Hep2_cervical_umbilical_osteosarcoma_gall



Phase1 CAGE Peaks

Hg19::chr16:84328230..84328235,+p10@WFDC1
Hg19::chr16:84328254..84328265,+p8@WFDC1
Hg19::chr16:84328292..84328340,+p2@WFDC1
Hg19::chr16:84328345..84328375,+p5@WFDC1
Hg19::chr16:84328382..84328416,+p3@WFDC1
Hg19::chr16:84328429..84328455,+p4@WFDC1
Hg19::chr16:84328459..84328512,+p1@WFDC1
Hg19::chr16:84353062..84353074,+p@chr16:84353062..84353074
+
Hg19::chr16:84353087..84353097,+p@chr16:84353087..84353097
+
Hg19::chr16:84353122..84353133,+p@chr16:84353122..84353133
+
Hg19::chr16:84363141..84363156,+p@chr16:84363141..84363156
+
Hg19::chr16:86229885..86229905,+p@chr16:86229885..86229905
+
Hg19::chr16:86229916..86229943,+p@chr16:86229916..86229943
+
Hg19::chr16:86532148..86532166,-p@chr16:86532148..86532166
-
Hg19::chr16:86546627..86546642,+p@chr16:86546627..86546642
+
Hg19::chr1:192735472..192735488,-p@chr1:192735472..192735488
-
Hg19::chr1:204839198..204839211,+p@chr1:204839198..204839211
+
Hg19::chr1:204839218..204839235,+p4@NFASC
Hg19::chr20:49253425..49253427,-p14@FAM65C
Hg19::chr20:49253452..49253461,-p12@FAM65C
Hg19::chr20:49269691..49269695,+p1@ENST00000435177
Hg19::chr7:54879609..54879616,-p@chr7:54879609..54879616
-
Hg19::chr7:54879626..54879647,-p@chr7:54879626..54879647
-
Hg19::chr7:54879666..54879725,-p@chr7:54879666..54879725
-
Hg19::chr8:53477984..53477997,-p1@FAM150A


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:0030308negative regulation of cell growth0.039468234767104
GO:0045792negative regulation of cell size0.039468234767104
GO:0045926negative regulation of growth0.039468234767104
GO:0001558regulation of cell growth0.0498755484983084
GO:0004867serine-type endopeptidase inhibitor activity0.0498755484983084
GO:0016049cell growth0.0498755484983084
GO:0040008regulation of growth0.0498755484983084
GO:0008361regulation of cell size0.0498755484983084



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
larynx4.16e-379
subdivision of digestive tract1.12e-25118
digestive system1.66e-24145
digestive tract1.66e-24145
primitive gut1.66e-24145
endoderm-derived structure5.19e-23160
endoderm5.19e-23160
presumptive endoderm5.19e-23160
upper respiratory tract2.85e-2019
intestine6.96e-1717
organ system subdivision9.51e-14223
cloaca1.56e-1314
anal region1.56e-1314
embryonic cloaca1.56e-1314
terminal part of digestive tract1.56e-1314
primitive urogenital sinus1.56e-1314
proctodeum1.56e-1314
respiratory primordium3.32e-1338
endoderm of foregut3.32e-1338
hindgut1.40e-1219
genitourinary system1.46e-1215
gastrointestinal system3.59e-1125
colon4.49e-119
respiratory tract5.07e-1054
orifice2.57e-0936
organ segment3.55e-0998
multi-tissue structure3.71e-09342
prostate gland4.15e-0911
male accessory sex gland4.15e-0911
embryonic cloacal epithelium4.15e-0911
epithelium of hindgut4.15e-0911
urogenital sinus epithelium4.15e-0911
prostate bud4.15e-0911
prostate field4.15e-0911
respiratory system5.09e-0974
large intestine5.28e-0911
segment of respiratory tract1.95e-0847
sex gland2.54e-0812
male reproductive gland2.54e-0812
small intestine5.99e-084
adult organism7.53e-08114
mixed endoderm/mesoderm-derived structure9.79e-0829
anatomical cluster1.33e-07373
foregut3.60e-0787
organ3.65e-07503
organ part6.00e-07218


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)
MA0003.10.152235
MA0004.10.409228
MA0006.10.431998
MA0007.10.120068
MA0009.10.480543
MA0014.10.379799
MA0017.10.242343
MA0019.11.87392
MA0024.10.391254
MA0025.10.599238
MA0027.12.03861
MA0028.10.213776
MA0029.10.407394
MA0030.10.397801
MA0031.10.912186
MA0038.10.195728
MA0040.12.7903
MA0041.10.437147
MA0042.10.778983
MA0043.10.480818
MA0046.10.47108
MA0048.10.243139
MA0050.10.123567
MA0051.10.192868
MA0052.11.87776
MA0055.11.24924
MA0056.10
MA0057.10.0501
MA0058.10.274844
MA0059.10.972405
MA0060.10.017391
MA0061.10.536938
MA0063.10
MA0066.10.570377
MA0067.10.769322
MA0068.10.105313
MA0069.10.467738
MA0070.10.458064
MA0071.10.978531
MA0072.11.1512
MA0073.11.19268e-05
MA0074.10.19236
MA0076.10.0879186
MA0077.10.44756
MA0078.10.263604
MA0081.10.27336
MA0083.10.487092
MA0084.10.947429
MA0087.10.452083
MA0088.10.634322
MA0089.10
MA0090.15.92348
MA0091.11.92403
MA0092.10.357807
MA0093.10.198309
MA0095.10
MA0098.10
MA0100.10.592379
MA0101.10.202181
MA0103.10.411939
MA0105.10.501682
MA0106.10.637762
MA0107.10.539977
MA0108.21.62457
MA0109.10
MA0111.11.13254
MA0113.11.23797
MA0114.10.524336
MA0115.10.697973
MA0116.10.126338
MA0117.10.513502
MA0119.10.0722294
MA0122.10.53644
MA0124.11.58599
MA0125.10.583056
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.11.72893
MA0139.10.140093
MA0140.10.168354
MA0141.10.270862
MA0142.10.319458
MA0143.10.236302
MA0144.10.0245926
MA0145.10.21721
MA0146.10.0536518
MA0147.10.561572
MA0148.11.41112
MA0149.10.162171
MA0062.20.0113502
MA0035.20.50217
MA0039.20.0064561
MA0138.20.730951
MA0002.20.359117
MA0137.20.832275
MA0104.20.0172311
MA0047.21.81274
MA0112.20.196276
MA0065.20.745387
MA0150.10.0921806
MA0151.10
MA0152.10.513688
MA0153.10.567879
MA0154.10.488003
MA0155.10.177814
MA0156.10.487034
MA0157.11.46654
MA0158.10
MA0159.10.0320844
MA0160.10.916248
MA0161.10
MA0162.10.00361818
MA0163.10.0474539
MA0164.10.245213
MA0080.20.766855
MA0018.20.225392
MA0099.20.172833
MA0079.24.195e-05
MA0102.20.983247
MA0258.10.733928
MA0259.10.587878
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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