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Coexpression cluster:C324: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.301048,1.89299,0.120617,1.43784,0.221108,0.565615,0.364109,0.0756189,0.00409537,0.00663942,0.065343,0.423679,0.729478,0.107542,0.219037,0.255671,0.24936,0.0531755,0.0149182,0.690758,0.532568,0.0272454,0.0744014,0.995936,0.16208,0.149282,0.609477,0.544467,0.0204299,0.729557,0.208451,0.275568,0.106828,0.339777,0.0137016,1.13086,0.332455,0.0781627,0.137127,0.135543,0.0640904,0.0513446,0.00166816,1.00653,0.0196833,0.147843,0.113901,0.220464,0.108076,0.0204558,0.476639,0.381471,0.485812,0.332931,0.455849,0.109009,1.05629,0.0931646,0.21952,0.0926959,0.305735,0.115115,0.0239092,0.651415,0.124509,0.207224,0.531141,0.866281,0.739123,0.715292,0.0469306,0.761281,0.00024273,0.454176,0.00167167,0.0788894,0.237766,0.218822,0.73378,4.31918,3.53538,0.229495,0.392644,0.315952,0.41169,5.77189e-07,0.00105469,0.0200622,0.173187,2.2057,0.613327,0.38983,1.42955,0.421183,0.0199598,0.267795,0.220942,0.319631,0.176016,4.45961,0.485935,0.28368,0.315407,1.29727,1.09736,0.227488,0.240891,0.344303,0.161835,0.0168178,0.13025,0.313317,0.517507,0.0690718,0.570763,1.55664,0.000147969,0.455139,0.205693,5.30795,0.447266,0.171704,0.0764997,0.811196,0.669724,0.219331,1.18596,0.291496,1.21331,0.00931421,0.390385,0.0581517,0.49533,0.803302,0.624847,0.00445148,1.18623,0.0737359,0.58705,1.40265,1.01074,0.554203,0.110997,0.316958,0.200866,1.04248,0.556347,1.24646,0.187744,0.00735813,0.00149602,2.18416e-05,0.390692,0.00357514,0.742309,0.743452,0.1634,0.388735,0.660952,0.0335878,0.553139,0.375879,0.26519,0.138231,0.211386,0.391559,0.00617318,1.20279,3.74142e-08
|tfbs_overrepresentation_for_novel_motifs=0.301048,1.89299,0.120617,1.43784,0.221108,0.565615,0.364109,0.0756189,0.00409537,0.00663942,0.065343,0.423679,0.729478,0.107542,0.219037,0.255671,0.24936,0.0531755,0.0149182,0.690758,0.532568,0.0272454,0.0744014,0.995936,0.16208,0.149282,0.609477,0.544467,0.0204299,0.729557,0.208451,0.275568,0.106828,0.339777,0.0137016,1.13086,0.332455,0.0781627,0.137127,0.135543,0.0640904,0.0513446,0.00166816,1.00653,0.0196833,0.147843,0.113901,0.220464,0.108076,0.0204558,0.476639,0.381471,0.485812,0.332931,0.455849,0.109009,1.05629,0.0931646,0.21952,0.0926959,0.305735,0.115115,0.0239092,0.651415,0.124509,0.207224,0.531141,0.866281,0.739123,0.715292,0.0469306,0.761281,0.00024273,0.454176,0.00167167,0.0788894,0.237766,0.218822,0.73378,4.31918,3.53538,0.229495,0.392644,0.315952,0.41169,5.77189e-07,0.00105469,0.0200622,0.173187,2.2057,0.613327,0.38983,1.42955,0.421183,0.0199598,0.267795,0.220942,0.319631,0.176016,4.45961,0.485935,0.28368,0.315407,1.29727,1.09736,0.227488,0.240891,0.344303,0.161835,0.0168178,0.13025,0.313317,0.517507,0.0690718,0.570763,1.55664,0.000147969,0.455139,0.205693,5.30795,0.447266,0.171704,0.0764997,0.811196,0.669724,0.219331,1.18596,0.291496,1.21331,0.00931421,0.390385,0.0581517,0.49533,0.803302,0.624847,0.00445148,1.18623,0.0737359,0.58705,1.40265,1.01074,0.554203,0.110997,0.316958,0.200866,1.04248,0.556347,1.24646,0.187744,0.00735813,0.00149602,2.18416e-05,0.390692,0.00357514,0.742309,0.743452,0.1634,0.388735,0.660952,0.0335878,0.553139,0.375879,0.26519,0.138231,0.211386,0.391559,0.00617318,1.20279,3.74142e-08
|tfbs_overrepresentation_jaspar=MA0003.1;1.63988e-08,MA0004.1;0.0673987,MA0006.1;0.0866247,MA0007.1;0.474016,MA0009.1;0.357426,MA0014.1;2.46239e-06,MA0017.1;0.0281901,MA0019.1;0.139271,MA0024.1;0.27745,MA0025.1;0.466941,MA0027.1;1.88112,MA0028.1;0.0227941,MA0029.1;0.291715,MA0030.1;0.283226,MA0031.1;0.236975,MA0038.1;0.114772,MA0040.1;0.29608,MA0041.1;0.0750477,MA0042.1;0.0621361,MA0043.1;0.357676,MA0046.1;0.348837,MA0048.1;0.226506,MA0050.1;0.224248,MA0051.1;0.362128,MA0052.1;0.298977,MA0055.1;5.18683,MA0056.1;0,MA0057.1;0.120966,MA0058.1;0.0348447,MA0059.1;0.0344842,MA0060.1;0.00412118,MA0061.1;0.00249953,MA0063.1;0,MA0066.1;0.114994,MA0067.1;0.628098,MA0068.1;0.0010853,MA0069.1;0.34581,MA0070.1;0.337064,MA0071.1;0.316593,MA0072.1;0.333568,MA0073.1;3.56445e-10,MA0074.1;0.361112,MA0076.1;0.0394639,MA0077.1;1.5724,MA0078.1;0.168619,MA0081.1;0.588735,MA0083.1;0.363385,MA0084.1;0.800231,MA0087.1;1.58683,MA0088.1;0.0162957,MA0089.1;0,MA0090.1;0.679811,MA0091.1;0.887174,MA0092.1;0.199374,MA0093.1;0.0200604,MA0095.1;0,MA0098.1;0,MA0100.1;0.122079,MA0101.1;0.020732,MA0103.1;0.395384,MA0105.1;0.00139816,MA0106.1;0.13708,MA0107.1;0.00884185,MA0108.2;0.23485,MA0109.1;0,MA0111.1;0.18219,MA0113.1;0.14643,MA0114.1;0.00824813,MA0115.1;0.560015,MA0116.1;0.00926229,MA0117.1;0.387522,MA0119.1;0.0301744,MA0122.1;0.408619,MA0124.1;1.29994,MA0125.1;0.451839,MA0130.1;0,MA0131.1;0.179874,MA0132.1;0,MA0133.1;0,MA0135.1;0.381677,MA0136.1;0.118463,MA0139.1;0.103418,MA0140.1;0.0942076,MA0141.1;0.136712,MA0142.1;1.80962,MA0143.1;2.03919,MA0144.1;0.00672774,MA0145.1;0.00854129,MA0146.1;6.25803e-06,MA0147.1;0.00969958,MA0148.1;0.566098,MA0149.1;0.300852,MA0062.2;0.0142755,MA0035.2;0.644966,MA0039.2;5.8189e-11,MA0138.2;0.169371,MA0002.2;0.27078,MA0137.2;0.253969,MA0104.2;0.00406753,MA0047.2;0.130332,MA0112.2;0.805779,MA0065.2;5.35263e-05,MA0150.1;1.95201,MA0151.1;0,MA0152.1;0.0973462,MA0153.1;0.43772,MA0154.1;0.0185282,MA0155.1;2.67001e-05,MA0156.1;0.0247505,MA0157.1;0.197151,MA0158.1;0,MA0159.1;0.135583,MA0160.1;0.599432,MA0161.1;0,MA0162.1;1.57419e-07,MA0163.1;3.34912e-06,MA0164.1;2.09562,MA0080.2;0.0200778,MA0018.2;0.137859,MA0099.2;0.0975183,MA0079.2;0,MA0102.2;0.835136,MA0258.1;0.0942457,MA0259.1;0.503101,MA0442.1;0
}}
}}

Revision as of 19:04, 22 January 2013


Full id: C324_tongue_salivary_oral_Prostate_amniotic_chorionic_small



Phase1 CAGE Peaks

Hg19::chr6:7562948..7562964,+p@chr6:7562948..7562964
+
Hg19::chr6:7565679..7565698,+p@chr6:7565679..7565698
+
Hg19::chr6:7567611..7567625,+p@chr6:7567611..7567625
+
Hg19::chr6:7568048..7568061,+p@chr6:7568048..7568061
+
Hg19::chr6:7569493..7569505,+p@chr6:7569493..7569505
+
Hg19::chr6:7569519..7569533,+p@chr6:7569519..7569533
+
Hg19::chr6:7574968..7574981,+p@chr6:7574968..7574981
+
Hg19::chr6:7576594..7576615,+p@chr6:7576594..7576615
+
Hg19::chr6:7578024..7578041,+p@chr6:7578024..7578041
+
Hg19::chr6:7578075..7578092,+p@chr6:7578075..7578092
+
Hg19::chr6:7578682..7578706,+p@chr6:7578682..7578706
+
Hg19::chr6:7578714..7578725,+p@chr6:7578714..7578725
+
Hg19::chr6:7579504..7579515,+p13@DSP
Hg19::chr6:7579521..7579530,+p23@DSP
Hg19::chr6:7579533..7579588,+p8@DSP
Hg19::chr6:7579595..7579685,+p5@DSP
Hg19::chr6:7579686..7579739,+p6@DSP
Hg19::chr6:7579922..7579931,+p17@DSP
Hg19::chr6:7579938..7579968,+p10@DSP
Hg19::chr6:7580331..7580352,+p@chr6:7580331..7580352
+
Hg19::chr6:7580647..7580666,+p@chr6:7580647..7580666
+
Hg19::chr6:7580693..7580711,+p@chr6:7580693..7580711
+
Hg19::chr6:7580738..7580758,+p@chr6:7580738..7580758
+
Hg19::chr6:7580760..7580789,+p@chr6:7580760..7580789
+
Hg19::chr6:7580800..7580825,+p@chr6:7580800..7580825
+
Hg19::chr6:7581295..7581322,+p@chr6:7581295..7581322
+
Hg19::chr6:7581399..7581431,+p@chr6:7581399..7581431
+
Hg19::chr6:7581480..7581493,+p@chr6:7581480..7581493
+
Hg19::chr6:7581522..7581546,+p@chr6:7581522..7581546
+
Hg19::chr6:7581717..7581735,+p@chr6:7581717..7581735
+
Hg19::chr6:7582860..7582909,+p@chr6:7582860..7582909
+
Hg19::chr6:7582954..7583016,+p@chr6:7582954..7583016
+
Hg19::chr6:7583024..7583048,+p@chr6:7583024..7583048
+
Hg19::chr6:7583081..7583107,+p@chr6:7583081..7583107
+
Hg19::chr6:7584615..7584630,+p11@DSP
Hg19::chr6:7584673..7584685,+p18@DSP


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 cell2.76e-29253
endodermal cell1.02e-1458
endo-epithelial cell1.90e-1342
epithelial cell of alimentary canal4.78e-1320
germ line cell9.00e-077
germ cell9.00e-077
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.67e-15160
endoderm3.67e-15160
presumptive endoderm3.67e-15160
digestive system2.60e-13145
digestive tract2.60e-13145
primitive gut2.60e-13145
subdivision of digestive tract5.43e-12118
respiratory system9.38e-1174
foregut1.73e-1087
respiratory tract1.07e-0754
upper respiratory tract2.30e-0719
larynx3.45e-079
Disease
Ontology termp-valuen
carcinoma2.79e-26106
cell type cancer1.19e-19143
cancer2.95e-11235
disease of cellular proliferation1.86e-10239
squamous cell carcinoma1.09e-0714


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)
MA0003.11.63988e-08
MA0004.10.0673987
MA0006.10.0866247
MA0007.10.474016
MA0009.10.357426
MA0014.12.46239e-06
MA0017.10.0281901
MA0019.10.139271
MA0024.10.27745
MA0025.10.466941
MA0027.11.88112
MA0028.10.0227941
MA0029.10.291715
MA0030.10.283226
MA0031.10.236975
MA0038.10.114772
MA0040.10.29608
MA0041.10.0750477
MA0042.10.0621361
MA0043.10.357676
MA0046.10.348837
MA0048.10.226506
MA0050.10.224248
MA0051.10.362128
MA0052.10.298977
MA0055.15.18683
MA0056.10
MA0057.10.120966
MA0058.10.0348447
MA0059.10.0344842
MA0060.10.00412118
MA0061.10.00249953
MA0063.10
MA0066.10.114994
MA0067.10.628098
MA0068.10.0010853
MA0069.10.34581
MA0070.10.337064
MA0071.10.316593
MA0072.10.333568
MA0073.13.56445e-10
MA0074.10.361112
MA0076.10.0394639
MA0077.11.5724
MA0078.10.168619
MA0081.10.588735
MA0083.10.363385
MA0084.10.800231
MA0087.11.58683
MA0088.10.0162957
MA0089.10
MA0090.10.679811
MA0091.10.887174
MA0092.10.199374
MA0093.10.0200604
MA0095.10
MA0098.10
MA0100.10.122079
MA0101.10.020732
MA0103.10.395384
MA0105.10.00139816
MA0106.10.13708
MA0107.10.00884185
MA0108.20.23485
MA0109.10
MA0111.10.18219
MA0113.10.14643
MA0114.10.00824813
MA0115.10.560015
MA0116.10.00926229
MA0117.10.387522
MA0119.10.0301744
MA0122.10.408619
MA0124.11.29994
MA0125.10.451839
MA0130.10
MA0131.10.179874
MA0132.10
MA0133.10
MA0135.10.381677
MA0136.10.118463
MA0139.10.103418
MA0140.10.0942076
MA0141.10.136712
MA0142.11.80962
MA0143.12.03919
MA0144.10.00672774
MA0145.10.00854129
MA0146.16.25803e-06
MA0147.10.00969958
MA0148.10.566098
MA0149.10.300852
MA0062.20.0142755
MA0035.20.644966
MA0039.25.8189e-11
MA0138.20.169371
MA0002.20.27078
MA0137.20.253969
MA0104.20.00406753
MA0047.20.130332
MA0112.20.805779
MA0065.25.35263e-05
MA0150.11.95201
MA0151.10
MA0152.10.0973462
MA0153.10.43772
MA0154.10.0185282
MA0155.12.67001e-05
MA0156.10.0247505
MA0157.10.197151
MA0158.10
MA0159.10.135583
MA0160.10.599432
MA0161.10
MA0162.11.57419e-07
MA0163.13.34912e-06
MA0164.12.09562
MA0080.20.0200778
MA0018.20.137859
MA0099.20.0975183
MA0079.20
MA0102.20.835136
MA0258.10.0942457
MA0259.10.503101
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

No analysis results for this cluster

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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