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Coexpression cluster:C2552: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,2.78539,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,1.18793,0.356737,0.635753,0.581762,0.975621,1.73475,0.528529,0.632849,0.892087,0.316693,0.728867,1.33003,0.297585,0.682839,1.09415,0.433165,0.911389,0.49475,0.0842336,0.491074,2.93742,2.0411,0.371755,0.493145,0.66492,0.539378,0.53106,1.59529,0.61613,1.92371,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,1.90242,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,1.96835,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.893276,0.321165,0.823598,1.00941,1.08,3.74841,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,3.54254,1.89266,1.51507,2.78853,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,5.50441,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.66252,1.00204,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,2.49031,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.91266
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,2.78539,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,1.18793,0.356737,0.635753,0.581762,0.975621,1.73475,0.528529,0.632849,0.892087,0.316693,0.728867,1.33003,0.297585,0.682839,1.09415,0.433165,0.911389,0.49475,0.0842336,0.491074,2.93742,2.0411,0.371755,0.493145,0.66492,0.539378,0.53106,1.59529,0.61613,1.92371,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,1.90242,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,1.96835,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.893276,0.321165,0.823598,1.00941,1.08,3.74841,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,3.54254,1.89266,1.51507,2.78853,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,5.50441,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.66252,1.00204,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,2.49031,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.91266
|tfbs_overrepresentation_jaspar=MA0003.1;0.233555,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;1.92746,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;1.30988,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;4.01633,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;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;5.15161,MA0115.1;3.20374,MA0116.1;0.457606,MA0117.1;2.78257,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;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,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;0.0247757,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;4.98884,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,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;1.90765,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;2.02192,MA0099.2;0.7872,MA0079.2;0.00910927,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:44, 22 January 2013


Full id: C2552_seminal_heart_ductus_mature_skeletal_corpus_medulla



Phase1 CAGE Peaks

Hg19::chr1:202317855..202317864,+p10@PPP1R12B
Hg19::chr1:202317869..202317884,+p2@PPP1R12B
Hg19::chr1:202317894..202317903,+p4@PPP1R12B
Hg19::chr1:202317923..202317936,+p5@PPP1R12B


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.45e-24114
neural tube4.65e-1656
neural rod4.65e-1656
future spinal cord4.65e-1656
neural keel4.65e-1656
central nervous system5.99e-1681
nervous system1.89e-1489
regional part of nervous system2.08e-1453
regional part of brain2.08e-1453
brain5.36e-1468
future brain5.36e-1468
regional part of forebrain2.76e-1341
forebrain2.76e-1341
anterior neural tube2.76e-1341
future forebrain2.76e-1341
telencephalon1.63e-1234
brain grey matter3.05e-1234
gray matter3.05e-1234
cerebral hemisphere3.32e-1132
regional part of telencephalon3.84e-1132
neural plate7.45e-1182
presumptive neural plate7.45e-1182
neurectoderm4.61e-1086
ecto-epithelium3.26e-08104
neocortex3.43e-0820
regional part of cerebral cortex4.73e-0822
pre-chordal neural plate1.31e-0761
neural nucleus2.52e-079
nucleus of brain2.52e-079
cerebral cortex3.68e-0725
pallium3.68e-0725


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)
MA0003.10.233555
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
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.14.01633
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
MA0073.10.00636811
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
MA0114.15.15161
MA0115.13.20374
MA0116.10.457606
MA0117.12.78257
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.25938
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.24.98884
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.22.02192
MA0099.20.7872
MA0079.20.00910927
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
ATF3#467422.46317452600873.92475754624726e-060.000127416149633981
BATF#10538424.35780179230362.83869198020713e-069.78449345613375e-05
BCLAF1#9774421.65264761012184.54636978835329e-060.000141736810246516
BRCA1#672420.18423064322386.02116732184487e-060.000179516041657481
CCNT2#90546.336201576962630.0006203100587215640.00512414476175128
CEBPB#105147.971147625824820.0002476385788090830.0026823403372995
CHD2#1106410.34402283411698.73193255208051e-050.0012911713206948
E2F1#186944.907389214879320.001724022357361790.0106528914318133
E2F4#1874412.66806031528443.88145892637771e-050.0007271312803802
ELF1#199744.258097958807540.003041525565781240.0160967816238283
ESR1#2099430.76860329615451.11467714392546e-064.60870016763384e-05
ETS1#211349.728760922202340.0001115955317418140.00154615624032678
FOS#235348.99795530889440.0001525147711168630.0019496316010617
GABPB1#255347.067683836182170.0004006876864423170.00390404154159428
GATA1#2623413.56030814380042.95627390049268e-050.00061393972935684
GATA2#2624412.7449317335543.78864877853583e-050.000722180488741566
HEY1#2346244.040111043105710.00375304636917980.0186179836484477
HMGN3#932448.178547723350590.0002234570284440470.00248167041617055
HNF4G#3174428.75342252644681.46167379934821e-065.67071879383833e-05
IRF1#365947.63716375356390.0002938853996185490.00307700223065279
IRF4#3662421.91451268674414.33289161192893e-060.000136507652204599
JUN#3725412.51282919233634.07770316866756e-050.00074349029544775
JUND#372746.994663941871030.000417684217818580.00391865990161289
MAX#414946.452555509007120.0005767613195645490.00485620569606594
MXI1#460149.96157162875930.0001015224754950450.00142473875547258
MYC#460945.22228187160940.001344309395272740.00888091143860392
NANOG#79923429.24477848101271.36586687657858e-065.33669175918409e-05
NFYA#4800418.42558069983058.67100748407158e-060.000234609158194029
NR2C2#7182432.61461090524098.82887529809196e-073.82288104169746e-05
NRF1#4899412.21027944771094.49717228915276e-050.000794183592673022
PAX5#507946.669565531177830.0005052774169483260.00444085400561021
REST#597849.650028716128020.0001152825614219170.00157118562342994
RFX5#5993412.04791082719514.74457429336527e-050.000827243062812647
RXRA#6256420.07461713913336.1537798808435e-060.000182376452036156
SIX5#147912417.0867153554591.17257016123224e-050.000297599161771406
SMARCB1#6598418.25271578115749.00423392720929e-060.000241622093300054
SP1#666745.69838137814090.0009482606065333980.00684607973771198
SPI1#668848.204323508522730.000220661881527680.00249547441741953
SRF#6722413.79717826216782.75840773062708e-050.000584707418264585
STAT1#6772420.70658749719925.43610708103893e-060.000165377683494502
STAT3#6774410.51946499715428.16377768286615e-050.00123174917281257
TAF1#687243.343046285745290.008005664898701650.0322434011937643
TAF7#6879411.43306940492395.85061525419808e-050.000969892708782846
TBP#690843.706770687096390.005296377814784350.0244399064462627
TCF7L2#6934410.77017656313737.42969445082454e-050.00115503104904683
TFAP2C#7022410.80922860986027.32289634782688e-050.0011457617553119
THAP1#55145431.36914460285131.03171810326891e-064.31870168285779e-05
TRIM28#10155418.59052504526258.36730015875654e-060.000230269423262286
USF1#739146.361499277207960.0006105011399140830.00508170308053614
USF2#7392412.99219738506963.50833029870167e-050.000681432970180591
YY1#752844.911170749853860.00171871838055440.0106903239203574
ZBTB7A#5134147.35190930787590.000342223540015990.00346802680921113
ZNF143#7702413.50087655222793.00867915035614e-050.000621240493839551
ZNF263#1012748.221841637010680.0002187871180958320.00249018175967857



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:C2552&oldid=2571063"