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Coexpression cluster:C2696: Difference between revisions

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{{Coexpression_clusters
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,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,0.534346,1.75218,0.821651,1.02453,1.01802,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,1.67497,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,1.72987,1.33003,0.806311,1.63433,1.09415,1.10579,0.344471,1.23824,2.05579,0.491074,0.740899,0.463978,0.371755,1.23481,0.66492,0.183156,0.53106,2.82841,0.61613,1.92371,1.65941,0.173425,0.538016,2.09659,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,4.83082,0.248021,1.32819,0.336329,0.321165,0.823598,1.00941,1.08,2.5716,0.95118,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,3.99585,0.934646,1.89266,1.51507,2.78853,1.11156,0.441618,0.535192,11.8096,0.934671,1.15558,0.939507,0.272395,0.465545,2.50078,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,1.22649,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,1.90732,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.175846,1.24902,2.65458,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.4289|tfbs_overrepresentation_jaspar=MA0003.1;0.233555,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.524262,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;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;1.98521,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;0.214613,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;1.4709,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;0.521546,MA0105.1;0.232357,MA0106.1;2.01886,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;1.94315,MA0139.1;2.47057,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;1.09982,MA0145.1;1.08195,MA0146.1;0.221129,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;7.30181,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.483275,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;0.199162,MA0150.1;2.59564,MA0151.1;0,MA0152.1;3.08195,MA0153.1;1.30799,MA0154.1;0.649108,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;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;1.32578,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;1.38179,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2696_Alveolar_Amniotic_Mesenchymal_Mallassezderived_Placental_Adipocyte_Urothelial
|id=C2696
}}

Latest revision as of 12:11, 17 September 2013


Full id: C2696_Alveolar_Amniotic_Mesenchymal_Mallassezderived_Placental_Adipocyte_Urothelial



Phase1 CAGE Peaks

Hg19::chr2:24307635..24307660,-p1@TP53I3
Hg19::chr2:24307664..24307682,-p6@TP53I3
Hg19::chr2:24307692..24307711,-p3@TP53I3
Hg19::chr2:24307712..24307742,-p2@TP53I3


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
embryonic cell1.86e-30250
mesodermal cell1.06e-24121
animal cell8.50e-22679
eukaryotic cell8.50e-22679
somatic cell6.72e-20588
epithelial cell4.62e-14253
fibroblast5.06e-1376
lining cell2.35e-1258
barrier cell2.35e-1258
contractile cell2.58e-1259
muscle precursor cell8.39e-1258
myoblast8.39e-1258
multi-potent skeletal muscle stem cell8.39e-1258
meso-epithelial cell1.80e-1145
endothelial cell5.33e-1136
muscle cell1.08e-1055
non-terminally differentiated cell1.61e-10106
electrically responsive cell2.55e-1061
electrically active cell2.55e-1061
smooth muscle cell1.80e-0943
smooth muscle myoblast1.80e-0943
native cell2.23e-09722
endothelial cell of vascular tree7.98e-0924
blood vessel endothelial cell1.23e-0718
embryonic blood vessel endothelial progenitor cell1.23e-0718
vascular associated smooth muscle cell7.08e-0732
preadipocyte7.75e-0712
Uber Anatomy
Ontology termp-valuen
multi-cellular organism8.15e-18656
organism subdivision2.68e-17264
vasculature3.02e-1778
vascular system3.02e-1778
anatomical system7.34e-16624
anatomical group1.12e-15625
trunk3.84e-15199
epithelial tube4.66e-14117
unilaminar epithelium4.84e-14148
epithelial vesicle8.01e-1478
vessel9.57e-1468
multilaminar epithelium1.32e-1383
mesenchyme2.54e-13160
entire embryonic mesenchyme2.54e-13160
splanchnic layer of lateral plate mesoderm6.12e-1383
epithelial tube open at both ends4.67e-1259
blood vessel4.67e-1259
blood vasculature4.67e-1259
vascular cord4.67e-1259
trunk mesenchyme1.06e-11122
somite8.29e-1171
presomitic mesoderm8.29e-1171
presumptive segmental plate8.29e-1171
dermomyotome8.29e-1171
trunk paraxial mesoderm8.29e-1171
cardiovascular system1.27e-10109
dense mesenchyme tissue2.27e-1073
skeletal muscle tissue2.67e-1062
striated muscle tissue2.67e-1062
myotome2.67e-1062
paraxial mesoderm2.90e-1072
presumptive paraxial mesoderm2.90e-1072
developing anatomical structure3.29e-10581
artery4.18e-1042
arterial blood vessel4.18e-1042
arterial system4.18e-1042
muscle tissue4.23e-1064
musculature4.23e-1064
musculature of body4.23e-1064
circulatory system6.55e-10112
embryo8.98e-10592
anatomical cluster4.11e-09373
cell layer7.87e-09309
epithelium1.08e-08306
embryonic structure1.71e-08564
mesoderm2.13e-08315
mesoderm-derived structure2.13e-08315
presumptive mesoderm2.13e-08315
subdivision of trunk2.45e-08112
simple squamous epithelium4.01e-0822
multi-tissue structure7.94e-08342
systemic artery9.73e-0833
systemic arterial system9.73e-0833
squamous epithelium1.07e-0725
blood vessel endothelium1.23e-0718
endothelium1.23e-0718
cardiovascular system endothelium1.23e-0718
germ layer1.32e-07560
germ layer / neural crest1.32e-07560
embryonic tissue1.32e-07560
presumptive structure1.32e-07560
germ layer / neural crest derived structure1.32e-07560
epiblast (generic)1.32e-07560
urinary system structure4.94e-0747


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
MA0014.10.524262
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
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.98521
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
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
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
MA0103.10.521546
MA0105.10.232357
MA0106.12.01886
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
MA0136.11.94315
MA0139.12.47057
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.11.08195
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.17.30181
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.05083
MA0065.20.199162
MA0150.12.59564
MA0151.10
MA0152.13.08195
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
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
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.21.38179
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
CCNT2#90546.336201576962630.0006203100587215640.00513023140820569
CTCF#1066445.360256373075030.001211145381643620.00818604792347129
CTCFL#140690419.74647435897446.5732084880439e-060.000193271205316108
EBF1#187948.9064668465690.00015887907472010.00199869569798754
ELF1#199744.258097958807540.003041525565781240.0161147467818906
EP300#203346.77394172622320.0004748459821442640.00434640136101357
ETS1#211349.728760922202340.0001115955317418140.0015469771355964
HEY1#2346244.040111043105710.00375304636917980.0186383456847727
HMGN3#932448.178547723350590.0002234570284440470.00248431217731189
IRF1#365947.63716375356390.0002938853996185490.00307916304682601
JUNB#3726430.61063265982111.13787152942193e-064.6621484763161e-05
RAD21#5885410.35503389545638.6948481184721e-050.00129670318812667
SMARCB1#6598418.25271578115749.00423392720929e-060.000241932901241011
SP2#6668426.15353049384462.13562021071447e-067.75259086502638e-05
TAF1#687243.343046285745290.008005664898701650.0322770088154533
TAF7#6879411.43306940492395.85061525419808e-050.000970663076303722
TBP#690843.706770687096390.005296377814784350.0244647679167741
THAP1#55145431.36914460285131.03171810326891e-064.32043331945877e-05
YY1#752844.911170749853860.00171871838055440.0106973318800191
ZBTB7A#5134147.35190930787590.000342223540015990.00347072094540007



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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