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Coexpression cluster:C1191: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.79738,2.46405,1.00019,0.529489,0.90845,0.52784,0.604235,0.226729,0.224331,0.443077,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,3.97473,0.19568,1.10853,0.384762,0.23059,0.520063,0.897212,0.430372,0.670692,0.957451,0.517892,0.346214,0.898182,1.1974,0.864517,0.257226,0.186138,0.309012,0.232776,0.305874,0.529001,0.773034,0.207499,0.307642,1.16235,0.0729319,0.340293,0.794027,0.415364,0.60533,0.486696,0.0670664,0.915545,0.684981,0.617179,1.79619,0.941629,1.09491,1.45196,1.65331,0.562713,0.150585,0.561701,0.905643,0.60771,1.19465,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.168304,0.156354,3.06919,0.850825,3.87752,0.200147,1.87399,0.625403,0.229431,1.04131,0.310394,0.097572,0.88003,1.69317,1.65172,1.27705,2.315,0.881388,0.73028,0.343884,0.277058,0.194299,0.924148,0.715799,1.92468,0.28424,0.875714,0.918549,0.831244,1.78098,0.493026,0.815341,0.589207,1.09919,1.57162,1.02467,0.915771,0.379203,0.507004,1.22894,0.304323,0.155979,2.07616,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.76179,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,1.15519,0.26104,0.106334,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.695791,0.602897,0.033943
|tfbs_overrepresentation_jaspar=MA0003.1;0.546816,MA0004.1;0.502801,MA0006.1;1.62096,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.367415,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;2.03099,MA0031.1;1.8966,MA0038.1;2.51051,MA0040.1;2.0669,MA0041.1;0.521615,MA0042.1;3.14308,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;1.8235,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.0407081,MA0056.1;0,MA0057.1;3.10865,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.575931,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;3.58082,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.0022316,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;4.56507,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;4.12807,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.104569,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;1.65047,MA0140.1;1.38735,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;1.30855,MA0145.1;0.581146,MA0146.1;0.0127148,MA0147.1;0.768766,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.243958,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;1.70023,MA0104.2;0.636673,MA0047.2;0.636643,MA0112.2;0.0758925,MA0065.2;0.996317,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;5.24111,MA0155.1;0.071478,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.485816,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.263996,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:45, 22 January 2013


Full id: C1191_Melanocyte_retina_spinal_locus_medulla_teratocarcinoma_sacrococcigeal



Phase1 CAGE Peaks

Hg19::chr13:78492927..78492943,-p2@EDNRB
Hg19::chr13:78492955..78492973,-p1@EDNRB
Hg19::chr13:78493559..78493593,-p4@EDNRB
Hg19::chr13:78493594..78493623,-p5@EDNRB
Hg19::chr13:78493657..78493668,-p8@EDNRB
Hg19::chr13:78493676..78493690,-p7@EDNRB
Hg19::chr13:78493703..78493726,-p3@EDNRB


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
melanocyte1.04e-0910
melanoblast1.04e-0910
fat cell4.88e-0715
pigment cell7.41e-0714
Uber Anatomy
Ontology termp-valuen
adult organism8.00e-50114
neural tube2.24e-3456
neural rod2.24e-3456
future spinal cord2.24e-3456
neural keel2.24e-3456
regional part of nervous system1.57e-3153
regional part of brain1.57e-3153
central nervous system2.89e-3081
regional part of forebrain8.05e-2641
forebrain8.05e-2641
anterior neural tube8.05e-2641
future forebrain8.05e-2641
nervous system1.09e-2489
neural plate1.84e-2482
presumptive neural plate1.84e-2482
brain4.67e-2468
future brain4.67e-2468
brain grey matter1.70e-2234
gray matter1.70e-2234
neurectoderm3.20e-2286
telencephalon5.72e-2234
regional part of telencephalon1.11e-2032
cerebral hemisphere1.73e-2032
structure with developmental contribution from neural crest6.09e-19132
ecto-epithelium7.45e-18104
organ system subdivision8.35e-18223
anatomical cluster3.97e-15373
anatomical conduit4.92e-15240
pre-chordal neural plate5.73e-1561
cerebral cortex5.88e-1525
pallium5.88e-1525
regional part of cerebral cortex5.08e-1422
ectoderm-derived structure4.27e-13171
ectoderm4.27e-13171
presumptive ectoderm4.27e-13171
tube1.45e-12192
neocortex2.19e-1220
multi-cellular organism4.81e-11656
multi-tissue structure1.37e-10342
epithelium8.76e-10306
posterior neural tube1.37e-0915
chordal neural plate1.37e-0915
embryo1.53e-09592
cell layer2.28e-09309
neural nucleus2.80e-099
nucleus of brain2.80e-099
germ layer5.55e-09560
germ layer / neural crest5.55e-09560
embryonic tissue5.55e-09560
presumptive structure5.55e-09560
germ layer / neural crest derived structure5.55e-09560
epiblast (generic)5.55e-09560
embryonic structure6.29e-09564
basal ganglion6.39e-099
nuclear complex of neuraxis6.39e-099
aggregate regional part of brain6.39e-099
collection of basal ganglia6.39e-099
cerebral subcortex6.39e-099
anatomical system1.55e-08624
anatomical group1.99e-08625
developing anatomical structure6.15e-08581
telencephalic nucleus1.95e-077
brainstem4.91e-076
segmental subdivision of hindbrain5.82e-0712
hindbrain5.82e-0712
presumptive hindbrain5.82e-0712


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)
MA0003.10.546816
MA0004.10.502801
MA0006.11.62096
MA0007.10.483857
MA0009.10.973289
MA0014.10.367415
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.12.03099
MA0031.11.8966
MA0038.12.51051
MA0040.12.0669
MA0041.10.521615
MA0042.13.14308
MA0043.10.973609
MA0046.10.962263
MA0048.11.8235
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.13.10865
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.13.58082
MA0071.10.567661
MA0072.10.942461
MA0073.10.0022316
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.14.56507
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.14.12807
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.65047
MA0140.11.38735
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.11.30855
MA0145.10.581146
MA0146.10.0127148
MA0147.10.768766
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.243958
MA0138.20.704862
MA0002.20.213296
MA0137.21.70023
MA0104.20.636673
MA0047.20.636643
MA0112.20.0758925
MA0065.20.996317
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.15.24111
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.485816
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.263996
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
TRIM28#10155513.27894646090188.62103642667186e-060.00023410619432272



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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