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Coexpression cluster:C2484: Difference between revisions

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{{Coexpression_clusters
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0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,1.59529,1.49501,0.822818,0.694903,0.173425,0.538016,2.09659,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,1.46445,0.776148,1.13655,1.92893,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,2.35456,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.793068,2.1528,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,2.93824,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,3.61007,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,2.02143,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,1.92786,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.4289|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;0.244769,MA0017.1;1.41335,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;1.12718,MA0055.1;0.396851,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;3.18358,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;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;1.6149,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;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;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;6.60408,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;0.8309,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;2.35208,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;0.649108,MA0155.1;0.180766,MA0156.1;1.37856,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;1.32578,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.122011,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2484_Alveolar_Mallassezderived_Urothelial_epidermoid_Esophageal_Corneal_endometrial
|id=C2484
|ontology_enrichment_celltype=CL:0000066!1.05e-32!254;CL:0002076!7.16e-14!43;CL:0000223!4.44e-10!59;CL:0002368!4.21e-07!13
|ontology_enrichment_disease=DOID:305!1.50e-20!106;DOID:0050687!2.56e-15!143;DOID:1749!2.42e-08!14;DOID:299!8.58e-08!25
|ontology_enrichment_uberon=UBERON:0004119!2.63e-19!169;UBERON:0000925!2.63e-19!169;UBERON:0006595!2.63e-19!169;UBERON:0000064!2.31e-15!219;UBERON:0000464!8.79e-15!104;UBERON:0001007!9.60e-15!155;UBERON:0001555!9.60e-15!155;UBERON:0007026!9.60e-15!155;UBERON:0004921!2.31e-14!129;UBERON:0004185!2.31e-14!129;UBERON:0001004!3.38e-14!72;UBERON:0000466!7.85e-14!126;UBERON:0000077!5.72e-13!130;UBERON:0000481!1.73e-12!347;UBERON:0000065!5.14e-12!53;UBERON:0001041!8.13e-12!98;UBERON:0005177!4.07e-11!107;UBERON:0000062!6.10e-11!511;UBERON:0001048!6.58e-11!168;UBERON:0008947!3.26e-10!38;UBERON:0003258!3.26e-10!38;UBERON:0000072!1.82e-09!46;UBERON:0005157!3.06e-09!51;UBERON:0001008!5.29e-09!45;UBERON:0006554!6.18e-09!44;UBERON:0005911!7.12e-09!82;UBERON:0000063!9.29e-09!97;UBERON:0002553!1.14e-08!70;UBERON:0009569!1.24e-08!113;UBERON:0000475!4.81e-08!365;UBERON:0005153!8.76e-08!37;UBERON:0005156!1.38e-07!59;UBERON:0000990!1.38e-07!59;UBERON:0003064!1.58e-07!37;UBERON:0003104!1.67e-07!238;UBERON:0009142!1.67e-07!238;UBERON:0003886!2.13e-07!63;UBERON:0005181!2.39e-07!35;UBERON:0005178!2.87e-07!34;UBERON:0002224!2.87e-07!34;UBERON:0007023!5.38e-07!115;UBERON:0003103!7.14e-07!69
}}

Latest revision as of 12:06, 17 September 2013


Full id: C2484_Alveolar_Mallassezderived_Urothelial_epidermoid_Esophageal_Corneal_endometrial



Phase1 CAGE Peaks

Hg19::chr19:36001122..36001196,-p6@DMKN
Hg19::chr19:36001304..36001382,-p1@DMKN
Hg19::chr19:36001386..36001429,-p4@DMKN
Hg19::chr19:36001433..36001463,-p7@DMKN


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell1.20e-31253
endo-epithelial cell3.02e-1442
endodermal cell8.13e-1058
respiratory epithelial cell2.94e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.70e-18160
endoderm6.70e-18160
presumptive endoderm6.70e-18160
organ part6.08e-16218
respiratory system6.46e-1474
digestive system7.88e-14145
digestive tract7.88e-14145
primitive gut7.88e-14145
subdivision of digestive tract1.24e-13118
respiratory tract9.62e-1254
foregut1.61e-1187
multi-tissue structure2.19e-11342
trunk region element7.65e-11101
anatomical space1.45e-1095
respiratory primordium2.55e-1038
endoderm of foregut2.55e-1038
organ3.04e-10503
immaterial anatomical entity9.48e-10117
organ system subdivision1.05e-09223
segment of respiratory tract2.43e-0947
primordium4.51e-09160
organ segment5.94e-0998
renal system6.00e-0948
urinary system structure6.59e-0947
subdivision of trunk1.16e-08112
organism subdivision4.59e-08264
endo-epithelium5.92e-0882
epithelial fold1.36e-0747
adult organism1.46e-07114
thoracic segment organ2.81e-0735
thoracic cavity element3.44e-0734
thoracic cavity3.44e-0734
epithelial bud3.68e-0737
compound organ9.01e-0768
Disease
Ontology termp-valuen
carcinoma5.27e-19106
cell type cancer5.63e-14143
squamous cell carcinoma6.28e-0814
adenocarcinoma2.15e-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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.11.41335
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
MA0052.11.12718
MA0055.10.396851
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
MA0074.13.18358
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.11.6149
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
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.16.60408
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.22.35208
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
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
CEBPB#105147.971147625824820.0002476385788090830.00268150601682133
CTBP2#1488462.71700033932816.45042639894877e-083.95581962818444e-06
CTCF#1066445.360256373075030.001211145381643620.00817335309598593
CTCFL#140690419.74647435897446.5732084880439e-060.000192945284227885
EGR1#195844.988179094810140.001615011500076050.0101449648776881
HEY1#2346244.040111043105710.00375304636917980.0186073776288046
NANOG#79923429.24477848101271.36586687657858e-065.33270170927068e-05
PAX5#507946.669565531177830.0005052774169483260.00443861284789858
RAD21#5885410.35503389545638.6948481184721e-050.00129393166521104
RXRA#6256420.07461713913336.1537798808435e-060.000182221326049167
SMC3#9126415.04493284493281.95092670935632e-050.000437989756230578
SP1#666745.69838137814090.0009482606065333980.00684182310782325
STAT1#6772420.70658749719925.43610708103893e-060.000165329524588417
STAT3#6774410.51946499715428.16377768286615e-050.0012315712515107
TAF1#687243.343046285745290.008005664898701650.0322260025575449
TAF7#6879411.43306940492395.85061525419808e-050.000969123563097848
TBP#690843.706770687096390.005296377814784350.0244247981012171
TCF12#6938410.63446490218647.8163066689251e-050.00120065782055577
ZBTB7A#5134147.35190930787590.000342223540015990.0034653368524074
ZEB1#6935416.88843201754391.22862303393937e-050.000304210908111887
ZNF143#7702413.50087655222793.00867915035614e-050.000620994944237243
ZNF263#1012748.221841637010680.0002187871180958320.00248909671316019



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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