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Coexpression cluster:C714: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;5.44997,MA0004.1;0.32225,MA0006.1;0.188769,MA0007.1;0.305951,MA0009.1;0.756202,MA0014.1;0.898798,MA0017.1;1.8359,MA0019.1;0.45566,MA0024.1;0.654931,MA0025.1;0.886436,MA0027.1;2.35633,MA0028.1;0.583404,MA0029.1;0.673506,MA0030.1;0.662482,MA0031.1;0.600685,MA0038.1;1.06455,MA0040.1;0.67914,MA0041.1;0.338572,MA0042.1;0.310552,MA0043.1;0.756508,MA0046.1;0.745626,MA0048.1;1.00007,MA0050.1;0.311321,MA0051.1;0.410316,MA0052.1;0.682867,MA0055.1;0.107116,MA0056.1;0,MA0057.1;1.85243,MA0058.1;0.240796,MA0059.1;0.239727,MA0060.1;0.103131,MA0061.1;2.07346,MA0063.1;0,MA0066.1;0.414559,MA0067.1;1.06751,MA0068.1;0.491198,MA0069.1;0.741884,MA0070.1;0.731026,MA0071.1;0.379038,MA0072.1;0.726666,MA0073.1;1.45819,MA0074.1;0.40963,MA0076.1;0.706813,MA0077.1;0.719193,MA0078.1;0.502027,MA0081.1;0.239862,MA0083.1;0.763502,MA0084.1;1.25286,MA0087.1;0.724294,MA0088.1;0.0178242,MA0089.1;0,MA0090.1;0.266215,MA0091.1;0.324543,MA0092.1;0.291716,MA0093.1;0.191154,MA0095.1;0,MA0098.1;0,MA0100.1;0.426863,MA0101.1;0.564934,MA0103.1;0.181541,MA0105.1;10.1515,MA0106.1;0.452066,MA0107.1;1.3641,MA0108.2;0.597764,MA0109.1;0,MA0111.1;0.277713,MA0113.1;0.467266,MA0114.1;1.34132,MA0115.1;0.992167,MA0116.1;0.854781,MA0117.1;4.46185,MA0119.1;0.226505,MA0122.1;0.818044,MA0124.1;0.951337,MA0125.1;0.868909,MA0130.1;0,MA0131.1;3.2772,MA0132.1;0,MA0133.1;0,MA0135.1;0.785738,MA0136.1;0.420617,MA0139.1;0.268952,MA0140.1;0.376643,MA0141.1;0.238287,MA0142.1;0.570448,MA0143.1;0.467429,MA0144.1;0.124153,MA0145.1;0.0212759,MA0146.1;2.39218,MA0147.1;0.143012,MA0148.1;0.344198,MA0149.1;0.367947,MA0062.2;0.280813,MA0035.2;0.376007,MA0039.2;2.09733,MA0138.2;0.503176,MA0002.2;0.0954816,MA0137.2;0.20663,MA0104.2;0.102626,MA0047.2;0.440861,MA0112.2;2.29615,MA0065.2;0.096411,MA0150.1;0.261236,MA0151.1;0,MA0152.1;0.382565,MA0153.1;0.852412,MA0154.1;0.30107,MA0155.1;5.78116,MA0156.1;0.208455,MA0157.1;0.544523,MA0158.1;0,MA0159.1;0.441451,MA0160.1;0.357736,MA0161.1;0,MA0162.1;2.30081,MA0163.1;8.13708,MA0164.1;0.478818,MA0080.2;0.191221,MA0018.2;0.453345,MA0099.2;1.76576,MA0079.2;5.08071,MA0102.2;1.28978,MA0258.1;0.117513,MA0259.1;0.455773,MA0442.1;0
}}
}}

Revision as of 19:23, 22 January 2013


Full id: C714_Smooth_Fibroblast_Mesenchymal_mesenchymal_Myoblast_leiomyoma_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr6:130686664..130686693,+p7@TMEM200A
Hg19::chr6:130686698..130686732,+p8@TMEM200A
Hg19::chr6:130686856..130686885,+p11@TMEM200A
Hg19::chr6:130687103..130687170,+p1@TMEM200A
Hg19::chr6:130687172..130687179,+p10@TMEM200A
Hg19::chr6:130687198..130687218,+p3@TMEM200A
Hg19::chr6:130687449..130687474,+p5@TMEM200A
Hg19::chr6:130687521..130687535,+p6@TMEM200A
Hg19::chr6:130687547..130687569,+p2@TMEM200A
Hg19::chr6:130687570..130687594,+p4@TMEM200A
Hg19::chr6:130687599..130687610,+p9@TMEM200A
Hg19::chr6:130687612..130687617,+p13@TMEM200A


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
dense mesenchyme tissue1.79e-2073
muscle tissue3.63e-2064
musculature3.63e-2064
musculature of body3.63e-2064
skeletal muscle tissue5.01e-2062
striated muscle tissue5.01e-2062
myotome5.01e-2062
somite5.25e-2071
presomitic mesoderm5.25e-2071
presumptive segmental plate5.25e-2071
dermomyotome5.25e-2071
trunk paraxial mesoderm5.25e-2071
paraxial mesoderm6.58e-2072
presumptive paraxial mesoderm6.58e-2072
multilaminar epithelium2.41e-1883
epithelial vesicle3.56e-1778
artery1.89e-1242
arterial blood vessel1.89e-1242
arterial system1.89e-1242
trunk mesenchyme4.35e-11122
systemic artery5.14e-1133
systemic arterial system5.14e-1133
organism subdivision2.05e-09264
vasculature4.31e-0978
vascular system4.31e-0978
smooth muscle tissue4.57e-0915
mesenchyme7.59e-09160
entire embryonic mesenchyme7.59e-09160
surface structure1.66e-0899
blood vessel smooth muscle2.21e-0810
arterial system smooth muscle2.21e-0810
artery smooth muscle tissue2.21e-0810
aorta smooth muscle tissue2.21e-0810
unilaminar epithelium8.61e-08148
epithelial tube open at both ends1.31e-0759
blood vessel1.31e-0759
blood vasculature1.31e-0759
vascular cord1.31e-0759
trunk1.83e-07199
Disease
Ontology termp-valuen
ovarian cancer1.95e-0814


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)
MA0003.15.44997
MA0004.10.32225
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.10.898798
MA0017.11.8359
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.583404
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.11.06455
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.11.00007
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.107116
MA0056.10
MA0057.11.85243
MA0058.10.240796
MA0059.10.239727
MA0060.10.103131
MA0061.12.07346
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.491198
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.11.45819
MA0074.10.40963
MA0076.10.706813
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.0178242
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.564934
MA0103.10.181541
MA0105.110.1515
MA0106.10.452066
MA0107.11.3641
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.11.34132
MA0115.10.992167
MA0116.10.854781
MA0117.14.46185
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.13.2772
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.268952
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.10.0212759
MA0146.12.39218
MA0147.10.143012
MA0148.10.344198
MA0149.10.367947
MA0062.20.280813
MA0035.20.376007
MA0039.22.09733
MA0138.20.503176
MA0002.20.0954816
MA0137.20.20663
MA0104.20.102626
MA0047.20.440861
MA0112.22.29615
MA0065.20.096411
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.30107
MA0155.15.78116
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.441451
MA0160.10.357736
MA0161.10
MA0162.12.30081
MA0163.18.13708
MA0164.10.478818
MA0080.20.191221
MA0018.20.453345
MA0099.21.76576
MA0079.25.08071
MA0102.21.28978
MA0258.10.117513
MA0259.10.455773
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#10664125.360256373075031.77458566542848e-091.54704467705914e-07
NANOG#7992337.311194620253160.006971199585208680.0294822884583766
TCF7L2#693465.385088281568670.0003605763085939490.00360538335023872



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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