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Coexpression cluster:C2790: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,3.43272,1.42265,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,2.07992,1.68405,0.867962,3.37992,0.809319,0.532789,1.37557,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,2.33254,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,3.16804,0.598278,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,1.59529,0.61613,1.92371,0.694903,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,0.62601,1.69485,2.33882,0.844168,0.399165,2.84439,0.353274,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,1.12407,2.27689,1.15724,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,1.88833,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,3.22553,0.681522,0.988625,2.94144,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,3.98771,1.47036,0.997702,0.843324,0.423521,0.820225,1.4289
|tfbs_overrepresentation_for_novel_motifs=0.590005,3.43272,1.42265,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,2.07992,1.68405,0.867962,3.37992,0.809319,0.532789,1.37557,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,2.33254,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,3.16804,0.598278,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,1.59529,0.61613,1.92371,0.694903,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,0.62601,1.69485,2.33882,0.844168,0.399165,2.84439,0.353274,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,1.12407,2.27689,1.15724,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,1.88833,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,3.22553,0.681522,0.988625,2.94144,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,3.98771,1.47036,0.997702,0.843324,0.423521,0.820225,1.4289
|tfbs_overrepresentation_jaspar=MA0003.1;1.05935,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;2.02223,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,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;2.83685,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;1.02755,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;1.29536,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;1.57689,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;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;12.9082,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;1.09982,MA0145.1;0.569905,MA0146.1;1.25938,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;1.5472,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;1.37305,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,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;0.309472,MA0163.1;5.3466,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;7.57064,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0
}}
}}

Revision as of 20:54, 22 January 2013


Full id: C2790_anaplastic_mesothelioma_corpus_optic_substantia_thalamus_granulosa



Phase1 CAGE Peaks

Hg19::chr4:41216492..41216550,-p1@APBB2
Hg19::chr4:41216552..41216567,-p2@APBB2
Hg19::chr4:41216580..41216594,-p5@APBB2
Hg19::chr4:41216619..41216637,-p3@APBB2


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 layer4.68e-29309
epithelium1.35e-28306
anatomical cluster1.13e-25373
multi-tissue structure5.73e-24342
anatomical conduit7.47e-24240
tube4.55e-23192
structure with developmental contribution from neural crest9.66e-22132
multi-cellular organism2.44e-18656
neural plate1.94e-1582
presumptive neural plate1.94e-1582
brain2.61e-1568
future brain2.61e-1568
anatomical system3.55e-15624
anatomical group6.54e-15625
neural tube9.35e-1556
neural rod9.35e-1556
future spinal cord9.35e-1556
neural keel9.35e-1556
vasculature1.10e-1478
vascular system1.10e-1478
ecto-epithelium1.82e-14104
organism subdivision2.48e-14264
unilaminar epithelium2.88e-14148
regional part of nervous system1.49e-1353
regional part of brain1.49e-1353
central nervous system1.93e-1381
neurectoderm2.00e-1386
embryo3.14e-13592
splanchnic layer of lateral plate mesoderm9.96e-1383
nervous system2.29e-1289
embryonic structure2.31e-12564
ectoderm-derived structure3.37e-12171
ectoderm3.37e-12171
presumptive ectoderm3.37e-12171
pre-chordal neural plate5.32e-1261
germ layer6.55e-12560
germ layer / neural crest6.55e-12560
embryonic tissue6.55e-12560
presumptive structure6.55e-12560
germ layer / neural crest derived structure6.55e-12560
epiblast (generic)6.55e-12560
developing anatomical structure6.87e-12581
epithelial tube open at both ends1.10e-1159
blood vessel1.10e-1159
blood vasculature1.10e-1159
vascular cord1.10e-1159
vessel1.10e-1168
epithelial tube2.40e-11117
regional part of forebrain2.58e-1141
forebrain2.58e-1141
anterior neural tube2.58e-1141
future forebrain2.58e-1141
trunk5.41e-11199
trunk mesenchyme7.03e-11122
telencephalon1.65e-1034
brain grey matter1.81e-1034
gray matter1.81e-1034
paraxial mesoderm2.79e-1072
presumptive paraxial mesoderm2.79e-1072
artery3.99e-1042
arterial blood vessel3.99e-1042
arterial system3.99e-1042
dense mesenchyme tissue5.89e-1073
somite5.99e-1071
presomitic mesoderm5.99e-1071
presumptive segmental plate5.99e-1071
dermomyotome5.99e-1071
trunk paraxial mesoderm5.99e-1071
mesenchyme6.62e-10160
entire embryonic mesenchyme6.62e-10160
epithelial vesicle1.85e-0978
skeletal muscle tissue1.97e-0962
striated muscle tissue1.97e-0962
myotome1.97e-0962
regional part of telencephalon2.02e-0932
cerebral hemisphere2.34e-0932
organ system subdivision2.82e-09223
muscle tissue3.12e-0964
musculature3.12e-0964
musculature of body3.12e-0964
cardiovascular system3.26e-09109
circulatory system4.55e-09112
adult organism6.46e-09114
regional part of cerebral cortex2.94e-0822
organ part5.28e-08218
organ6.63e-08503
systemic artery9.73e-0833


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)
MA0003.11.05935
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
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
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
MA0073.12.83685
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.112.9082
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.569905
MA0146.11.25938
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
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
MA0162.10.309472
MA0163.15.3466
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.27.57064
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
BRCA1#672420.18423064322386.02116732184487e-060.00017966991255033
CHD2#1106410.34402283411698.73193255208051e-050.00129263544125689
CTCF#1066445.360256373075030.001211145381643620.00819241013688331
CTCFL#140690419.74647435897446.5732084880439e-060.000193380090502202
E2F1#186944.907389214879320.001724022357361790.0106730984576472
ELF1#199744.258097958807540.003041525565781240.0161196533322149
EP300#203346.77394172622320.0004748459821442640.00434983242953818
GATA3#2625427.2365163572061.81561517799785e-066.78429458228684e-05
HEY1#2346244.040111043105710.00375304636917980.0186480998025962
JUND#372746.994663941871030.000417684217818580.00392288867129089
MXI1#460149.96157162875930.0001015224754950450.0014262719690916
MYC#460945.22228187160940.001344309395272740.00889159777915702
NR3C1#2908414.9730233311731.98868032687801e-050.000443889259796564
NRF1#4899412.21027944771094.49717228915276e-050.000795124727792154
PAX5#507946.669565531177830.0005052774169483260.00444684150574418
RAD21#5885410.35503389545638.6948481184721e-050.0012980006327117
SMC3#9126415.04493284493281.95092670935632e-050.000439217147226697
SP1#666745.69838137814090.0009482606065333980.00685413450659157
TAF1#687243.343046285745290.008005664898701650.0323044446470714
TAF7#6879411.43306940492395.85061525419808e-050.000971125884509207
TBP#690843.706770687096390.005296377814784350.0244831763200222



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:C2790&oldid=2571301"