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Coexpression cluster:C2525: Difference between revisions

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{{Coexpression_clusters
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0.106889,0.128632,0.0845989,0.159153,0.00365225,0.13698,0.0874421,0.100355,4.10228e-05,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.0805224,0.362662,0.111581,0.184359,0.334474,0.00761927,0.257476,0.291176,0.00142707,3.49391e-06,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.00499935,0.150674,0.251128,0.246177,4.39467e-07,0.0104945,0.000664446,0.213257,0.287217,0.122782,0.0991993,0.289049,0.266974,0.125746,0.112897,0.0150081,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.00445319,0.321965,0.264707,0.0229223|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,1.33003,0.806311,0.682839,1.09415,0.433165,0.911389,0.49475,2.67722,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.0946706,0.61613,1.92371,0.694903,0.173425,0.538016,2.09659,0.83543,0.25073,1.17354,2.95463,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,2.95051,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.6318,0.291738,2.1528,1.89266,1.51507,1.24792,1.11156,1.12407,0.535192,0.456994,1.66879,1.15558,0.939507,0.272395,0.465545,1.1057,4.20395,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,1.1313,2.93345,3.53462,0.736652,1.99225,1.57854,1.0102,0.814847,1.11673,1.36323,4.07559,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,1.811,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,2.79075,0.383416,1.92786,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,2.44698,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;2.54431,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;1.01899,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;2.94475,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;2.47057,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;2.05538,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.257871,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.02191,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.20937,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2525_neuroblastoma_nonsmall_Neurons_Neural_temporal_duodenum_brain
|id=C2525
}}

Latest revision as of 12:07, 17 September 2013


Full id: C2525_neuroblastoma_nonsmall_Neurons_Neural_temporal_duodenum_brain



Phase1 CAGE Peaks

Hg19::chr1:151032739..151032748,+p6@MLLT11
Hg19::chr1:151032782..151032801,+p4@MLLT11
Hg19::chr1:151032833..151032850,+p3@MLLT11
Hg19::chr1:151032860..151032918,+p1@MLLT11


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>

Uber Anatomy
Ontology termp-valuen
cell layer1.70e-30309
epithelium9.98e-30306
central nervous system1.02e-2981
nervous system4.49e-2989
brain1.11e-2768
future brain1.11e-2768
tube2.35e-27192
neural tube3.22e-2456
neural rod3.22e-2456
future spinal cord3.22e-2456
neural keel3.22e-2456
ectoderm-derived structure6.43e-24171
ectoderm6.43e-24171
presumptive ectoderm6.43e-24171
anatomical cluster1.56e-23373
neural plate1.61e-2382
presumptive neural plate1.61e-2382
regional part of nervous system2.13e-2353
regional part of brain2.13e-2353
neurectoderm8.24e-2386
structure with developmental contribution from neural crest1.60e-22132
anatomical conduit2.20e-22240
ecto-epithelium1.18e-21104
pre-chordal neural plate1.00e-1861
regional part of forebrain1.47e-1841
forebrain1.47e-1841
anterior neural tube1.47e-1841
future forebrain1.47e-1841
brain grey matter5.92e-1734
gray matter5.92e-1734
cerebral hemisphere6.68e-1732
telencephalon2.04e-1634
regional part of telencephalon6.16e-1632
multi-tissue structure7.34e-16342
vasculature1.31e-1478
vascular system1.31e-1478
cerebral cortex7.40e-1425
pallium7.40e-1425
regional part of cerebral cortex1.19e-1322
artery1.19e-1242
arterial blood vessel1.19e-1242
arterial system1.19e-1242
neocortex1.25e-1220
splanchnic layer of lateral plate mesoderm1.81e-1283
epithelial tube open at both ends3.50e-1259
blood vessel3.50e-1259
blood vasculature3.50e-1259
vascular cord3.50e-1259
vessel1.37e-1168
skeletal muscle tissue1.08e-1062
striated muscle tissue1.08e-1062
myotome1.08e-1062
systemic artery1.72e-1033
systemic arterial system1.72e-1033
circulatory system2.33e-10112
multilaminar epithelium4.84e-1083
muscle tissue6.26e-1064
musculature6.26e-1064
musculature of body6.26e-1064
cardiovascular system7.29e-10109
epithelial vesicle8.63e-1078
paraxial mesoderm1.50e-0972
presumptive paraxial mesoderm1.50e-0972
dense mesenchyme tissue1.50e-0973
epithelial tube2.76e-09117
multi-cellular organism2.95e-09656
somite4.02e-0971
presomitic mesoderm4.02e-0971
presumptive segmental plate4.02e-0971
dermomyotome4.02e-0971
trunk paraxial mesoderm4.02e-0971
anatomical system4.42e-09624
organ part4.51e-09218
anatomical group6.09e-09625
embryo1.56e-08592
developing anatomical structure2.05e-08581
organ system subdivision4.13e-08223
embryonic structure1.68e-07564
posterior neural tube6.97e-0715
chordal neural plate6.97e-0715
germ layer8.47e-07560
germ layer / neural crest8.47e-07560
embryonic tissue8.47e-07560
presumptive structure8.47e-07560
germ layer / neural crest derived structure8.47e-07560
epiblast (generic)8.47e-07560


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.12.54431
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.12.94475
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.12.47057
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.12.05538
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.20937
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
CTBP2#1488462.71700033932816.45042639894877e-083.95814384653238e-06
EGR1#195844.988179094810140.001615011500076050.0101467957682995
ELF1#199744.258097958807540.003041525565781240.0160935195341284
EP300#203346.77394172622320.0004748459821442640.00434449754964212
HEY1#2346244.040111043105710.00375304636917980.0186135630045954
MAFK#7975427.10073313782991.85228494563408e-066.85266693011258e-05
REST#597849.650028716128020.0001152825614219170.00157077565979695
SIN3A#2594245.408884726815140.001168172384885160.00796622629481037
SP1#666745.69838137814090.0009482606065333980.00684466027270313
TAF1#687243.343046285745290.008005664898701650.0322346995279321
TBP#690843.706770687096390.005296377814784350.02443127081835
USF1#739146.361499277207960.0006105011399140830.00508089318284221
YY1#752844.911170749853860.00171871838055440.0106890507322528
ZBTB7A#5134147.35190930787590.000342223540015990.00346668130899418



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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