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Coexpression cluster:C2080: Difference between revisions

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{{Coexpression_clusters
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09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,1.08066,1.49501,0.822818,0.694903,0.173425,0.538016,2.09659,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,6.36983,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.6318,0.291738,3.54254,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,2.04634,2.50078,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,1.52945,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,2.24704,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987|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;0.244769,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;1.66718,MA0051.1;0.820063,MA0052.1;4.13471,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;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;0.182167,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;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;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.10559,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;3.96014,MA0065.2;1.09513,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;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.000248021,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2080_mucinous_Fibroblast_epithelioid_Preadipocyte_Olfactory_prostate_acantholytic
|id=C2080
}}

Latest revision as of 11:58, 17 September 2013


Full id: C2080_mucinous_Fibroblast_epithelioid_Preadipocyte_Olfactory_prostate_acantholytic



Phase1 CAGE Peaks

Hg19::chr10:95241966..95241996,-p4@MYOF
Hg19::chr10:95242030..95242041,-p6@MYOF
Hg19::chr10:95242044..95242072,-p1@MYOF
Hg19::chr10:95242083..95242098,-p2@MYOF


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
fibroblast4.42e-1676
embryonic cell1.28e-15250
mesodermal cell2.53e-15121
squamous epithelial cell1.05e-1363
epithelial cell9.83e-13253
animal cell1.34e-10679
eukaryotic cell1.34e-10679
skin fibroblast4.51e-1023
lining cell4.08e-0858
barrier cell4.08e-0858
muscle precursor cell1.25e-0758
myoblast1.25e-0758
multi-potent skeletal muscle stem cell1.25e-0758
muscle cell5.20e-0755
Uber Anatomy
Ontology termp-valuen
organism subdivision3.25e-17264
multi-cellular organism2.08e-15656
surface structure2.76e-1599
trunk7.86e-14199
anatomical system9.08e-14624
anatomical group1.91e-13625
unilaminar epithelium3.39e-11148
mesenchyme2.92e-10160
entire embryonic mesenchyme2.92e-10160
vasculature4.33e-1078
vascular system4.33e-1078
skin of body5.68e-1041
multilaminar epithelium9.96e-1083
organ component layer1.74e-0966
integument1.89e-0946
integumental system1.89e-0946
dense mesenchyme tissue3.52e-0973
somite3.52e-0971
presomitic mesoderm3.52e-0971
presumptive segmental plate3.52e-0971
dermomyotome3.52e-0971
trunk paraxial mesoderm3.52e-0971
trunk mesenchyme6.00e-09122
paraxial mesoderm7.58e-0972
presumptive paraxial mesoderm7.58e-0972
epithelial vesicle7.72e-0978
vessel8.24e-0868
splanchnic layer of lateral plate mesoderm1.79e-0783
epithelial tube open at both ends1.99e-0759
blood vessel1.99e-0759
blood vasculature1.99e-0759
vascular cord1.99e-0759
muscle tissue5.30e-0764
musculature5.30e-0764
musculature of body5.30e-0764
skeletal muscle tissue6.80e-0762
striated muscle tissue6.80e-0762
myotome6.80e-0762


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
MA0014.10.244769
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
MA0050.11.66718
MA0051.10.820063
MA0052.14.13471
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
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
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
MA0125.11.32534
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
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.23.96014
MA0065.21.09513
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
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
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
BCL11A#53335428.36945510360711.542446414682e-065.88140055140466e-05
CTCF#1066445.360256373075030.001211145381643620.00815385886117955
EP300#203346.77394172622320.0004748459821442640.00433424572008082
ESR1#2099430.76860329615451.11467714392546e-064.59233791851798e-05
GTF2B#2959431.94382993432429.59435337635006e-074.07824449439408e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000716187200692898
JUN#3725412.51282919233634.07770316866756e-050.00074141929183926
JUND#372735.245997956403270.01043432751748420.0386628372808676
MAX#414946.452555509007120.0005767613195645490.00484332037098994
MEF2A#4205418.74323090964418.0978922767748e-060.000224154723428063
MEF2C#4208441.31135449262413.42889182145094e-071.69720394758538e-05
MXI1#460149.96157162875930.0001015224754950450.00142072970899464
RAD21#5885410.35503389545638.6948481184721e-050.00129043803132742
SMARCC1#6599443.66335931963152.74744977017458e-071.40519542873293e-05
SMC3#9126415.04493284493281.95092670935632e-050.000436956539992418
SPI1#668848.204323508522730.000220661881527680.00248981268851225
STAT1#6772420.70658749719925.43610708103893e-060.000164897353307181
STAT3#6774410.51946499715428.16377768286615e-050.00122837743469364
TAF1#687243.343046285745290.008005664898701650.0321121341304875
TBP#690843.706770687096390.005296377814784350.0243409638107046
TFAP2A#7020416.5186343730451.34240829060362e-050.000325742982022192
TFAP2C#7022410.80922860986027.32289634782688e-050.00114319278276636
TRIM28#10155418.59052504526258.36730015875654e-060.000229603904697944



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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