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Coexpression cluster:C2622: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.0938548,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;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;1.28333,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.946082,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.841508,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;5.01475,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;2.31225,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;2.29123,MA0103.1;0.521546,MA0105.1;1.90157,MA0106.1;0.869173,MA0107.1;2.98058,MA0108.2;1.03412,MA0109.1;0,MA0111.1;1.57689,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;4.07269,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;0.569905,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;1.13403,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;0.199162,MA0150.1;1.53138,MA0151.1;0,MA0152.1;1.84959,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;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;1.85039,MA0079.2;3.97967,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:47, 22 January 2013


Full id: C2622_Osteoblast_Chondrocyte_meningioma_Fibroblast_mesenchymal_Smooth_tenocyte



Phase1 CAGE Peaks

Hg19::chr20:57090346..57090361,-p6@APCDD1L
Hg19::chr20:57090369..57090380,-p7@APCDD1L
Hg19::chr20:57090389..57090412,-p3@APCDD1L
Hg19::chr20:57090438..57090462,-p1@APCDD1L


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>

Uber Anatomy
Ontology termp-valuen
multilaminar epithelium9.03e-2383
somite2.99e-2271
presomitic mesoderm2.99e-2271
presumptive segmental plate2.99e-2271
dermomyotome2.99e-2271
trunk paraxial mesoderm2.99e-2271
dense mesenchyme tissue3.35e-2273
paraxial mesoderm1.17e-2172
presumptive paraxial mesoderm1.17e-2172
epithelial vesicle4.05e-2178
muscle tissue1.92e-1864
musculature1.92e-1864
musculature of body1.92e-1864
skeletal muscle tissue5.29e-1862
striated muscle tissue5.29e-1862
myotome5.29e-1862
mesenchyme6.63e-14160
entire embryonic mesenchyme6.63e-14160
systemic artery2.13e-1333
systemic arterial system2.13e-1333
artery2.46e-1342
arterial blood vessel2.46e-1342
arterial system2.46e-1342
trunk mesenchyme2.06e-12122
mesoderm4.27e-12315
mesoderm-derived structure4.27e-12315
presumptive mesoderm4.27e-12315
surface structure2.28e-0999
musculoskeletal system3.30e-09167
smooth muscle tissue5.42e-0915
integument9.54e-0946
integumental system9.54e-0946
blood vessel smooth muscle2.21e-0810
arterial system smooth muscle2.21e-0810
artery smooth muscle tissue2.21e-0810
aorta smooth muscle tissue2.21e-0810
skin of body5.52e-0841
epithelial tube open at both ends1.14e-0759
blood vessel1.14e-0759
blood vasculature1.14e-0759
vascular cord1.14e-0759
unilaminar epithelium2.51e-07148
splanchnic layer of lateral plate mesoderm3.08e-0783
connective tissue7.10e-07371
trunk9.01e-07199
Disease
Ontology termp-valuen
ovarian cancer5.41e-1014
female reproductive organ cancer5.74e-0727


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
MA0007.10.6918
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
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.15.01475
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.12.31225
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.12.29123
MA0103.10.521546
MA0105.11.90157
MA0106.10.869173
MA0107.12.98058
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.14.07269
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
MA0145.10.569905
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.11.53138
MA0151.10
MA0152.11.84959
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
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.21.85039
MA0079.23.97967
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
MYC#460945.22228187160940.001344309395272740.00888315905934131
USF1#739146.361499277207960.0006105011399140830.00508372895483072



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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