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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0499826791869596,0.14537956855423,0.069243541019063,0.0623294359481102,0.0977156115525172,0.186580091664016,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.05517363663028,0.0807517559145935,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0381808373167472,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C425_iPS_HES3GFP_H9_teratocarcinoma_testicular_hepatocellular_Wilms|gostat_on_coexpression_clusters=GO:0007167!enzyme linked receptor protein signaling pathway!0.0152323781567815!8822;9350$GO:0042074!cell migration involved in gastrulation!0.0152323781567815!9350$GO:0042127!regulation of cell proliferation!0.0152323781567815!8822;9350$GO:0007275!multicellular organismal development!0.0152323781567815!8822;83881;9350$GO:0030514!negative regulation of BMP signaling pathway!0.0152323781567815!9350$GO:0030510!regulation of BMP signaling pathway!0.0152323781567815!9350$GO:0009948!anterior/posterior axis specification!0.0152323781567815!9350$GO:0005615!extracellular space!0.0152323781567815!8822;9350$GO:0008543!fibroblast growth factor receptor signaling pathway!0.0165573613962069!8822$GO:0030509!BMP signaling pathway!0.0165573613962069!9350$GO:0009798!axis specification!0.0165573613962069!9350$GO:0008283!cell proliferation!0.0194524233922925!8822;9350$GO:0007369!gastrulation!0.0194524233922925!9350$GO:0032502!developmental process!0.0217456776068593!8822;83881;9350$GO:0044421!extracellular region part!0.0237867142250612!8822;9350$GO:0032501!multicellular organismal process!0.0271211765237296!8822;83881;9350$GO:0005102!receptor binding!0.0271211765237296!8822;9350$GO:0009952!anterior/posterior pattern formation!0.0308668156604865!9350$GO:0007178!transmembrane receptor protein serine/threonine kinase signaling pathway!0.0403700043055772!9350$GO:0003002!regionalization!0.0438810523001729!9350$GO:0009968!negative regulation of signal 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,0.844863,0.553496,0.512645,0.952571,0.778399,0.749389,0.920474,0.445744,0.717654,0.573425,0.866528,0.787336,0.745614,0.856835,0.902834,0.550393,0.972353|tfbs_overrepresentation_for_novel_motifs=0.0799767,0.0280497,0.264451,0.471537,0.212185,0.154482,0.204171,0.429796,0.220756,0.0680542,0.423075,0.23459,0.0561986,0.196345,0.0578138,0.239229,0.372343,1.39485,0.0136335,0.0413001,0.264528,0.286209,0.149707,0.0563145,0.098963,0.251049,1.31683,0.453775,0.0596298,0.102006,0.390674,1.03951,0.282966,0.0118701,0.172304,0.227245,0.04405,0.470785,0.334646,0.0160107,1.50383,0.114449,0.504679,0.0572029,0.0148686,0.0913173,0.204918,0.129869,0.453879,0.216063,0.261519,0.213054,0.259797,0.467708,0.602614,0.198331,0.221207,0.523348,0.38523,0.175903,0.437087,0.206544,0.0881719,0.349892,0.21901,0.32251,0.683218,1.032,0.394058,0.876356,0.107303,0.44639,0.00295624,0.600809,0.294572,0.127377,0.109933,0.336375,0.39137,0.0957994,0.0680662,0.34903,1.17144,0.0921969,0.554704,0.00918097,0.0402656,1.50433,0.281033,1.1284,0.769994,0.530777,0.416714,0.545807,0.0586689,0.586762,0.0636376,0.452776,0.776697,0.0780621,0.145304,0.41198,0.448017,0.375338,0.313482,0.133549,0.36244,0.194019,0.0988322,0.0520752,0.279145,0.445659,0.257318,0.437263,0.725188,0.0434964,0.076976,0.122878,0.32067,0.0312352,0.593343,0.279196,0.152778,0.226712,0.828974,0.33698,0.579525,0.420907,0.631927,0.13877,0.531386,1.28398,0.645033,1.19293,0.782074,0.0295274,3.17048,0.454639,0.742365,1.57584,1.1795,0.707679,0.201014,0.449766,0.84524,0.171082,0.816061,1.41836,0.732167,0.121647,0.115484,0.00451953,0.531723,0.0813765,1.12276,0.90553,0.268853,1.16157,1.11066,0.0845645,0.706553,0.515425,0.390719,0.607547,0.873572,0.218208,1.58347,0.587697,0.0209318|tfbs_overrepresentation_jaspar=MA0003.1;0.00111053,MA0004.1;0.13931,MA0006.1;0.0576274,MA0007.1;1.89025,MA0009.1;0.495012,MA0014.1;0.00481891,MA0017.1;0.259379,MA0019.1;0.238234,MA0024.1;0.404839,MA0025.1;2.53478,MA0027.1;2.05626,MA0028.1;0.0643724,MA0029.1;0.421158,MA0030.1;0.41146,MA0031.1;0.357843,MA0038.1;0.594428,MA0040.1;1.09053,MA0041.1;0.459457,MA0042.1;1.32287,MA0043.1;1.23939,MA0046.1;0.485466,MA0048.1;0.0201022,MA0050.1;0.131853,MA0051.1;0.203156,MA0052.1;0.429421,MA0055.1;0.0385267,MA0056.1;0,MA0057.1;0.0582452,MA0058.1;0.086794,MA0059.1;0.291213,MA0060.1;0.0880744,MA0061.1;0.17524,MA0063.1;0,MA0066.1;0.595133,MA0067.1;0.78548,MA0068.1;0.0418736,MA0069.1;0.482095,MA0070.1;0.472333,MA0071.1;0.179775,MA0072.1;0.468422,MA0073.1;7.48886e-05,MA0074.1;1.10877,MA0076.1;0.094817,MA0077.1;0.461731,MA0078.1;0.275364,MA0081.1;0.0862369,MA0083.1;0.501617,MA0084.1;0.964138,MA0087.1;1.17726,MA0088.1;0.0540176,MA0089.1;0,MA0090.1;0.335123,MA0091.1;0.434924,MA0092.1;0.118775,MA0093.1;0.0588752,MA0095.1;0,MA0098.1;0,MA0100.1;0.215803,MA0101.1;0.217713,MA0103.1;0.768241,MA0105.1;0.0469725,MA0106.1;0.235406,MA0107.1;0.316679,MA0108.2;3.46368,MA0109.1;0,MA0111.1;0.109681,MA0113.1;0.247415,MA0114.1;0.306489,MA0115.1;0.71383,MA0116.1;0.588414,MA0117.1;0.528241,MA0119.1;0.269691,MA0122.1;0.551352,MA0124.1;0.675302,MA0125.1;0.598285,MA0130.1;0,MA0131.1;0.289284,MA0132.1;0,MA0133.1;0,MA0135.1;0.521813,MA0136.1;0.211008,MA0139.1;0.057952,MA0140.1;0.526893,MA0141.1;0.288855,MA0142.1;1.58842,MA0143.1;1.28085,MA0144.1;0.27852,MA0145.1;0.573071,MA0146.1;0.00808278,MA0147.1;0.0356084,MA0148.1;0.469347,MA0149.1;0.17166,MA0062.2;0.0628366,MA0035.2;1.00893,MA0039.2;0.126946,MA0138.2;0.757929,MA0002.2;0.20101,MA0137.2;0.237908,MA0104.2;0.0196756,MA0047.2;0.643013,MA0112.2;0.358584,MA0065.2;0.815716,MA0150.1;0.0992631,MA0151.1;0,MA0152.1;0.182375,MA0153.1;0.583009,MA0154.1;0.351815,MA0155.1;0.203574,MA0156.1;0.240796,MA0157.1;0.310364,MA0158.1;0,MA0159.1;0.944104,MA0160.1;0.493256,MA0161.1;0,MA0162.1;0.0322127,MA0163.1;0.01442,MA0164.1;0.712784,MA0080.2;0.0589108,MA0018.2;0.236412,MA0099.2;0.182613,MA0079.2;0.000214137,MA0102.2;1.00004,MA0258.1;0.783032,MA0259.1;0.348068,MA0442.1;0}}
|full_id=C425_iPS_HES3GFP_H9_teratocarcinoma_testicular_hepatocellular_Wilms
|gostat_on_coexpression_clusters=GO:0007167!enzyme linked receptor protein signaling pathway!0.0152323781567815!8822;9350$GO:0042074!cell migration involved in gastrulation!0.0152323781567815!9350$GO:0042127!regulation of cell proliferation!0.0152323781567815!8822;9350$GO:0007275!multicellular organismal development!0.0152323781567815!8822;83881;9350$GO:0030514!negative regulation of BMP signaling pathway!0.0152323781567815!9350$GO:0030510!regulation of BMP signaling pathway!0.0152323781567815!9350$GO:0009948!anterior/posterior axis specification!0.0152323781567815!9350$GO:0005615!extracellular space!0.0152323781567815!8822;9350$GO:0008543!fibroblast growth factor receptor signaling pathway!0.0165573613962069!8822$GO:0030509!BMP signaling pathway!0.0165573613962069!9350$GO:0009798!axis specification!0.0165573613962069!9350$GO:0008283!cell proliferation!0.0194524233922925!8822;9350$GO:0007369!gastrulation!0.0194524233922925!9350$GO:0032502!developmental process!0.0217456776068593!8822;83881;9350$GO:0044421!extracellular region part!0.0237867142250612!8822;9350$GO:0032501!multicellular organismal process!0.0271211765237296!8822;83881;9350$GO:0005102!receptor binding!0.0271211765237296!8822;9350$GO:0009952!anterior/posterior pattern formation!0.0308668156604865!9350$GO:0007178!transmembrane receptor protein serine/threonine kinase signaling pathway!0.0403700043055772!9350$GO:0003002!regionalization!0.0438810523001729!9350$GO:0009968!negative regulation of signal transduction!0.0499201251580985!9350
|id=C425
}}

Latest revision as of 11:22, 17 September 2013


Full id: C425_iPS_HES3GFP_H9_teratocarcinoma_testicular_hepatocellular_Wilms



Phase1 CAGE Peaks

Hg19::chr13:48611649..48611658,+p4@NUDT15
Hg19::chr13:48611665..48611708,+p3@NUDT15
Hg19::chr13:93868779..93868791,+p@chr13:93868779..93868791
+
Hg19::chr15:74643092..74643103,+p@chr15:74643092..74643103
+
Hg19::chr1:178235815..178235824,-p@chr1:178235815..178235824
-
Hg19::chr1:196539193..196539198,-p@chr1:196539193..196539198
-
Hg19::chr1:226411361..226411366,+p1@MIXL1
Hg19::chr2:82240962..82240967,-p@chr2:82240962..82240967
-
Hg19::chr3:162430587..162430591,+p@chr3:162430587..162430591
+
Hg19::chr3:54673186..54673191,-p@chr3:54673186..54673191
-
Hg19::chr4:111540901..111540905,+p@chr4:111540901..111540905
+
Hg19::chr4:88852761..88852767,+p@chr4:88852761..88852767
+
Hg19::chr4:88853035..88853041,+p@chr4:88853035..88853041
+
Hg19::chr6:160649974..160649978,+p@chr6:160649974..160649978
+
Hg19::chr7:125557914..125557920,+p1@ENST00000411856
Hg19::chr7:125564060..125564062,+p@chr7:125564060..125564062
+
Hg19::chr7:125566765..125566770,+p@chr7:125566765..125566770
+
Hg19::chr8:21899898..21899901,+p1@FGF17
Hg19::chr8:81213028..81213032,+p1@ENST00000472088
Hg19::chr9:14722725..14722738,-p1@CER1
Hg19::chr9:5098356..5098369,+p1@ENST00000431069
Hg19::chr9:6020363..6020368,+p@chr9:6020363..6020368
+
Hg19::chrY:15863548..15863573,+p1@KALP
Hg19::chrY:21589521..21589522,+p@chrY:21589521..21589522
+


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:0007167enzyme linked receptor protein signaling pathway0.0152323781567815
GO:0042074cell migration involved in gastrulation0.0152323781567815
GO:0042127regulation of cell proliferation0.0152323781567815
GO:0007275multicellular organismal development0.0152323781567815
GO:0030514negative regulation of BMP signaling pathway0.0152323781567815
GO:0030510regulation of BMP signaling pathway0.0152323781567815
GO:0009948anterior/posterior axis specification0.0152323781567815
GO:0005615extracellular space0.0152323781567815
GO:0008543fibroblast growth factor receptor signaling pathway0.0165573613962069
GO:0030509BMP signaling pathway0.0165573613962069
GO:0009798axis specification0.0165573613962069
GO:0008283cell proliferation0.0194524233922925
GO:0007369gastrulation0.0194524233922925
GO:0032502developmental process0.0217456776068593
GO:0044421extracellular region part0.0237867142250612
GO:0032501multicellular organismal process0.0271211765237296
GO:0005102receptor binding0.0271211765237296
GO:0009952anterior/posterior pattern formation0.0308668156604865
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0403700043055772
GO:0003002regionalization0.0438810523001729
GO:0009968negative regulation of signal transduction0.0499201251580985



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><br><br>

Cell Type
Ontology termp-valuen
embryonic stem cell9.05e-1095
melanocyte2.04e-2010
melanoblast2.04e-2010
neuron8.39e-166
neuroblast8.39e-166
electrically signaling cell8.39e-166
pigment cell8.46e-1514
neuronal stem cell4.18e-128
neurecto-epithelial cell1.45e-1020
neurectodermal cell3.14e-0959
columnar/cuboidal epithelial cell5.50e-0827
ectodermal cell1.26e-0772


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)
MA0003.10.00111053
MA0004.10.13931
MA0006.10.0576274
MA0007.11.89025
MA0009.10.495012
MA0014.10.00481891
MA0017.10.259379
MA0019.10.238234
MA0024.10.404839
MA0025.12.53478
MA0027.12.05626
MA0028.10.0643724
MA0029.10.421158
MA0030.10.41146
MA0031.10.357843
MA0038.10.594428
MA0040.11.09053
MA0041.10.459457
MA0042.11.32287
MA0043.11.23939
MA0046.10.485466
MA0048.10.0201022
MA0050.10.131853
MA0051.10.203156
MA0052.10.429421
MA0055.10.0385267
MA0056.10
MA0057.10.0582452
MA0058.10.086794
MA0059.10.291213
MA0060.10.0880744
MA0061.10.17524
MA0063.10
MA0066.10.595133
MA0067.10.78548
MA0068.10.0418736
MA0069.10.482095
MA0070.10.472333
MA0071.10.179775
MA0072.10.468422
MA0073.17.48886e-05
MA0074.11.10877
MA0076.10.094817
MA0077.10.461731
MA0078.10.275364
MA0081.10.0862369
MA0083.10.501617
MA0084.10.964138
MA0087.11.17726
MA0088.10.0540176
MA0089.10
MA0090.10.335123
MA0091.10.434924
MA0092.10.118775
MA0093.10.0588752
MA0095.10
MA0098.10
MA0100.10.215803
MA0101.10.217713
MA0103.10.768241
MA0105.10.0469725
MA0106.10.235406
MA0107.10.316679
MA0108.23.46368
MA0109.10
MA0111.10.109681
MA0113.10.247415
MA0114.10.306489
MA0115.10.71383
MA0116.10.588414
MA0117.10.528241
MA0119.10.269691
MA0122.10.551352
MA0124.10.675302
MA0125.10.598285
MA0130.10
MA0131.10.289284
MA0132.10
MA0133.10
MA0135.10.521813
MA0136.10.211008
MA0139.10.057952
MA0140.10.526893
MA0141.10.288855
MA0142.11.58842
MA0143.11.28085
MA0144.10.27852
MA0145.10.573071
MA0146.10.00808278
MA0147.10.0356084
MA0148.10.469347
MA0149.10.17166
MA0062.20.0628366
MA0035.21.00893
MA0039.20.126946
MA0138.20.757929
MA0002.20.20101
MA0137.20.237908
MA0104.20.0196756
MA0047.20.643013
MA0112.20.358584
MA0065.20.815716
MA0150.10.0992631
MA0151.10
MA0152.10.182375
MA0153.10.583009
MA0154.10.351815
MA0155.10.203574
MA0156.10.240796
MA0157.10.310364
MA0158.10
MA0159.10.944104
MA0160.10.493256
MA0161.10
MA0162.10.0322127
MA0163.10.01442
MA0164.10.712784
MA0080.20.0589108
MA0018.20.236412
MA0099.20.182613
MA0079.20.000214137
MA0102.21.00004
MA0258.10.783032
MA0259.10.348068
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
NANOG#7992367.311194620253160.0001260976518292320.00167978477798382



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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