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Coexpression cluster:C1912: Difference between revisions

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61742,0.422872,0.00848325,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,5.58769e-06,0.168186,0.108081,0.123829,0.205215,0.00103241,0.00268881,0.109077,0.144842,0.0604892,0.214671,0.00695007,0.442567,0.109896,0.0354176,0.00227842,0.0150771,0.389061,0.00651415,0.0698238,0.445995,0.385709,0.278202,0.426488,1.16831e-06,0.0001062,0.253154,0.319519,0.0537766,0.430805,0.362154,0.0289453,0.185476,0.336314,0.0676318,0.184651,0.303359,0.297596,0.42392,0.425912,0.380826,0.259046,7.96686e-05,0.151046,0.483953,1.85829e-08,0.321735,0.15463,1.85896e-05,0.470121,0.0400826,0.0343725,0.0165533,8.62944e-06,1.87608e-05,0.162633,0.0090162,2.22465e-05,0.0337021,1.25233e-08,0.0858973,0.319112,0.00721116
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,1.70183,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,1.54297,0.500405,0.770467,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,1.0713,0.0526856,0.413782,0.654459,0.388123,0.815792,0.415749,0.580638,0.132849,0.451846,0.218848,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.05625,1.23387,0.741483,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,1.57121,1.18161,0.251545,0.963115,2.64291,1.96782,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.99322,0.28626,1.06255,3.27673,0.211081,0.389604,1.01316,1.05685,2.22024,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,1.80913,1.48307,0.918767,2.89249,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,2.59164,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,3.51312,3.03281,0.398598,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,1.70183,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,1.54297,0.500405,0.770467,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,1.0713,0.0526856,0.413782,0.654459,0.388123,0.815792,0.415749,0.580638,0.132849,0.451846,0.218848,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.05625,1.23387,0.741483,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,1.57121,1.18161,0.251545,0.963115,2.64291,1.96782,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.99322,0.28626,1.06255,3.27673,0.211081,0.389604,1.01316,1.05685,2.22024,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,1.80913,1.48307,0.918767,2.89249,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,2.59164,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,3.51312,3.03281,0.398598,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
|tfbs_overrepresentation_jaspar=MA0003.1;0.136928,MA0004.1;0.626788,MA0006.1;1.14863,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.0418333,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;1.18667,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.0140295,MA0074.1;0.730989,MA0076.1;2.29573,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;1.76068,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;2.17426,MA0035.2;0.691506,MA0039.2;0.0118463,MA0138.2;0.837782,MA0002.2;0.83106,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;1.3196,MA0156.1;2.09554,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.469165,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.00207114,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;1.02361,MA0442.1;0
}}
}}

Revision as of 20:16, 22 January 2013


Full id: C1912_uterus_cervix_rectum_cerebellum_neuroepithelioma_sacrococcigeal_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr2:66662249..66662267,+p2@MEIS1
Hg19::chr2:66662281..66662308,+p1@MEIS1
Hg19::chr2:66662396..66662407,+p4@MEIS1
Hg19::chr2:66662510..66662521,+p6@MEIS1
Hg19::chr2:66789201..66789212,+p@chr2:66789201..66789212
+


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

No GOStat results

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>

Cell Type
Ontology termp-valuen
smooth muscle cell1.82e-1043
smooth muscle myoblast1.82e-1043
muscle precursor cell8.08e-0958
myoblast8.08e-0958
multi-potent skeletal muscle stem cell8.08e-0958
muscle cell8.36e-0955
contractile cell5.77e-0859
electrically responsive cell4.03e-0761
electrically active cell4.03e-0761
Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.40e-15342
multi-cellular organism1.96e-13656
anatomical cluster4.28e-13373
adult organism3.37e-12114
anatomical conduit8.48e-11240
organ system subdivision5.37e-10223
organism subdivision1.56e-09264
epithelium1.71e-09306
muscle tissue1.73e-0964
musculature1.73e-0964
musculature of body1.73e-0964
dense mesenchyme tissue2.08e-0973
paraxial mesoderm3.35e-0972
presumptive paraxial mesoderm3.35e-0972
somite3.37e-0971
presomitic mesoderm3.37e-0971
presumptive segmental plate3.37e-0971
dermomyotome3.37e-0971
trunk paraxial mesoderm3.37e-0971
anatomical system5.30e-09624
anatomical group5.64e-09625
germ layer6.62e-09560
germ layer / neural crest6.62e-09560
embryonic tissue6.62e-09560
presumptive structure6.62e-09560
germ layer / neural crest derived structure6.62e-09560
epiblast (generic)6.62e-09560
neurectoderm6.79e-0986
skeletal muscle tissue6.90e-0962
striated muscle tissue6.90e-0962
myotome6.90e-0962
embryonic structure8.42e-09564
cell layer9.18e-09309
tube2.43e-08192
trunk3.45e-08199
multilaminar epithelium3.91e-0883
trunk mesenchyme4.77e-08122
ectoderm-derived structure7.44e-08171
ectoderm7.44e-08171
presumptive ectoderm7.44e-08171
epithelial vesicle9.56e-0878
neural plate9.61e-0882
presumptive neural plate9.61e-0882
developing anatomical structure1.53e-07581
mesenchyme1.72e-07160
entire embryonic mesenchyme1.72e-07160
organ part2.04e-07218
splanchnic layer of lateral plate mesoderm2.09e-0783
embryo2.34e-07592
anatomical space4.74e-0795
organ5.07e-07503
smooth muscle tissue5.59e-0715
structure with developmental contribution from neural crest5.79e-07132


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)
MA0003.10.136928
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.11.18667
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.12.29573
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.11.76068
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.22.17426
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.3196
MA0156.12.09554
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.00207114
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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
CEBPB#105146.376918100659850.001113944176677320.00765742222523545
ELF1#199743.406478367046030.01235066105299550.0447397138397487
ELK4#2005412.98854532677446.83810524411663e-050.00109116099861008
EP300#203345.419153380978560.00209386927943890.0121227126600876
FOSL2#2355413.54416048364945.7953819349229e-050.000965025341041793
FOXA1#316948.865135799508360.0003075468591372710.00316857910835922
GABPB1#255345.654147068945740.001776696502096670.0109112316819049
GTF2F1#2962410.19172870140610.000177833889427640.00215937606998411
HDAC2#3066410.7324961893010.0001450965797478750.00188667102742633
HSF1#32974131.4325333333336.79362350565572e-095.3227250210591e-07
JUND#372745.595731153496820.001849593301755460.0109370215627923
MAX#414945.16204440720570.002526309009485180.0140022919196318
MYC#460944.177825497287520.005691969036823440.0256887582315718
NR3C1#2908411.97841866493849.4122920812787e-050.00136624096271948
REST#597847.720022972902420.0005286363773650570.00457417188199082
RFX5#599349.638328661756080.000221480125815720.00249796575162721
SIN3A#2594244.327107781452110.004977052855762880.0232488783971294
SMARCB1#6598414.60217262492594.30486693344344e-050.000768671563791929
SP1#666744.558705102512720.00407573565781680.0194901903098319
SRF#6722411.03774260973420.0001299255814846750.00171048755889046
SUZ12#23512440.09262472885037.78750287036555e-073.41443749906846e-05
TCF12#693848.507571921749140.0003614215578492260.00361279728945399
USF1#739145.089199421766370.00266867775360040.0147234039042933
YY1#752843.928936599883080.007193866269917620.0298510151123972
ZNF263#1012746.577473309608540.0009875103237900160.00709413885722283



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1912&oldid=2570423"