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Coexpression cluster:C2418: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.44014,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,2.45508,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.223552,0.581762,0.505745,0.731221,0.528529,2.59358,0.892087,0.316693,0.728867,1.33003,0.806311,0.682839,1.09415,1.10579,0.344471,3.16804,2.05579,3.15145,1.75478,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.0946706,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,1.82985,0.806003,0.776148,1.13655,1.92893,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,2.45549,1.62905,0.650393,0.402607,1.28263,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,3.02769,0.221873,1.44378,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,8.03095,2.04634,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,1.63159,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,1.00204,1.24902,2.65458,0.824835,1.65997,0.917558,1.28873,0.632914,1.4628,1.44595,1.23002,1.07918,1.47036,0.997702,0.843324,0.423521,0.820225,0.156682
|tfbs_overrepresentation_jaspar=MA0003.1;0.0938548,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;1.65296,MA0009.1;1.20602,MA0014.1;1.86845,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;1.35734,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;1.30988,MA0050.1;0.69864,MA0051.1;1.91805,MA0052.1;1.12718,MA0055.1;5.70469,MA0056.1;0,MA0057.1;2.77736,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;1.52107,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.380957,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;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;4.42006,MA0106.1;0.869173,MA0107.1;1.1497,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;1.08195,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.931615,MA0035.2;0.778873,MA0039.2;9.51044,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.577908,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;2.30186,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;0.870662,MA0099.2;0.7872,MA0079.2;8.14977,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:39, 22 January 2013


Full id: C2418_Renal_Urothelial_salivary_Corneal_Bronchial_Mammary_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr17:48133330..48133349,+p2@ITGA3
Hg19::chr17:48133352..48133363,+p4@ITGA3
Hg19::chr17:48133424..48133443,+p3@ITGA3
Hg19::chr17:48133459..48133486,+p1@ITGA3


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 cell4.76e-39253
embryonic cell4.47e-33250
mesodermal cell3.69e-16121
squamous epithelial cell1.71e-1363
endo-epithelial cell2.10e-1242
kidney cell2.83e-1017
kidney epithelial cell2.83e-1017
animal cell8.57e-10679
eukaryotic cell8.57e-10679
epithelial cell of nephron1.38e-0915
endodermal cell2.49e-0958
mesothelial cell4.98e-0919
ecto-epithelial cell5.78e-0834
respiratory epithelial cell5.91e-0813
kidney tubule cell8.21e-0810
nephron tubule epithelial cell8.21e-0810
kidney cortical cell9.49e-0812
renal cortical epithelial cell9.49e-0812
lining cell1.03e-0758
barrier cell1.03e-0758
contractile cell1.22e-0759
non-terminally differentiated cell1.41e-07106
columnar/cuboidal epithelial cell2.34e-0727
muscle precursor cell4.30e-0758
myoblast4.30e-0758
multi-potent skeletal muscle stem cell4.30e-0758
ectodermal cell5.70e-0772
Uber Anatomy
Ontology termp-valuen
organism subdivision2.29e-19264
multi-tissue structure1.19e-15342
cell layer1.91e-15309
epithelium3.32e-15306
trunk2.24e-14199
anatomical system2.98e-12624
anatomical cluster3.51e-12373
anatomical group4.19e-12625
mesenchyme8.63e-12160
entire embryonic mesenchyme8.63e-12160
multi-cellular organism1.37e-11656
epithelial tube4.11e-11117
unilaminar epithelium6.57e-10148
nephron epithelium1.38e-0915
renal tubule1.38e-0915
nephron tubule1.38e-0915
nephron1.38e-0915
uriniferous tubule1.38e-0915
nephrogenic mesenchyme1.38e-0915
trunk mesenchyme1.92e-09122
epithelial vesicle2.06e-0978
multilaminar epithelium2.21e-0983
vasculature3.94e-0978
vascular system3.94e-0978
excretory tube4.11e-0916
kidney epithelium4.11e-0916
primordium6.92e-09160
trunk region element1.00e-08101
parenchyma1.22e-0815
surface structure3.31e-0899
endoderm-derived structure5.36e-08160
endoderm5.36e-08160
presumptive endoderm5.36e-08160
anatomical conduit6.00e-08240
cortex6.07e-0815
anatomical space7.08e-0895
nephron tubule epithelium8.21e-0810
cortex of kidney9.49e-0812
renal parenchyma9.49e-0812
ectodermal placode9.71e-0831
organ part1.18e-07218
embryo1.30e-07592
urinary system structure1.81e-0747
vessel2.88e-0768
renal system3.27e-0748
female organism3.84e-0741
somite4.21e-0771
presomitic mesoderm4.21e-0771
presumptive segmental plate4.21e-0771
dermomyotome4.21e-0771
trunk paraxial mesoderm4.21e-0771
developing anatomical structure5.37e-07581
paraxial mesoderm5.64e-0772
presumptive paraxial mesoderm5.64e-0772
immaterial anatomical entity5.68e-07117
dense mesenchyme tissue5.71e-0773
Disease
Ontology termp-valuen
reproductive organ cancer8.92e-0829
female reproductive organ cancer9.15e-0827


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0048.11.30988
MA0050.10.69864
MA0051.11.91805
MA0052.11.12718
MA0055.15.70469
MA0056.10
MA0057.12.77736
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.380957
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
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.14.42006
MA0106.10.869173
MA0107.11.1497
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
MA0145.11.08195
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.29.51044
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.12.30186
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
MA0018.20.870662
MA0099.20.7872
MA0079.28.14977
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
CTCF#1066445.360256373075030.001211145381643620.00816965785141628
CTCFL#140690419.74647435897446.5732084880439e-060.000192836888000791
EP300#203346.77394172622320.0004748459821442640.0043399351998919
STAT3#6774410.51946499715428.16377768286615e-050.00123086008000701
TAF1#687243.343046285745290.008005664898701650.0321999397810792
TCF7L2#6934410.77017656313737.42969445082454e-050.00115365723870006
YY1#752844.911170749853860.00171871838055440.0106788761346137
ZBTB7A#5134147.35190930787590.000342223540015990.00346365774742998



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:C2418&oldid=2570929"