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Coexpression cluster:C415: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0737355,0.0835622,0.0704497,0.44898,0.762449,0.446495,0.193858,0.205635,0.201483,0.0241672,0.127781,0.635883,0.279201,0.18622,0.75795,0.484254,0.359143,0.923327,0.0572824,0.0867481,0.528893,0.15028,0.14085,1.60804,0.306895,0.239737,2.45585,0.139567,0.0544198,1.11239,0.115556,0.389116,0.260815,0.487921,0.0408246,0.122538,0.0397666,0.146177,0.131632,0.0657489,0.64612,0.106777,0.301276,0.193557,0.0548432,0.0845678,0.194588,0.38574,0.0384572,0.200595,0.250009,0.202536,0.121746,0.453481,0.587358,0.188158,0.787127,0.166937,0.089928,0.166299,0.423157,0.196176,0.391942,0.336984,0.208359,0.309988,0.667509,1.01514,0.380596,0.859886,0.328502,0.215242,0.00239942,0.585564,0.00922526,0.238638,0.0973823,0.323653,0.37794,0.298626,0.322532,0.336133,0.599262,0.210347,0.539768,3.60514e-05,0.00962642,0.0281108,0.269174,1.11136,0.753896,0.516018,1.04021,0.509424,0.197724,0.29887,0.520617,0.438691,0.272612,0.687221,0.13295,1.02999,0.433978,0.362101,0.301097,0.125207,0.349366,0.18395,0.306554,0.0472968,0.075464,0.431643,0.0680411,0.133204,0.70928,0.635439,7.36332e-05,0.368181,0.308176,0.517966,0.578146,0.267369,0.143829,0.215895,0.812657,0.324249,0.189628,1.04926,0.616494,0.126749,0.516623,0.752499,0.629526,0.612237,0.765929,0.00441261,0.112299,0.139902,0.726382,1.55835,1.16239,1.65307,0.190777,1.11129,0.302448,0.486671,0.289694,1.40098,0.697322,0.110545,0.100722,0.0143922,0.516957,0.188592,1.70289,2.05942,0.257209,0.181063,0.0919218,0.0781127,0.690731,0.500787,0.377296,0.079602,0.845352,0.207576,0.24603,0.563058,0.127529
|tfbs_overrepresentation_jaspar=MA0003.1;3.40323e-06,MA0004.1;0.130779,MA0006.1;0.194765,MA0007.1;0.120068,MA0009.1;0.480543,MA0014.1;0.00104451,MA0017.1;0.242343,MA0019.1;0.644268,MA0024.1;0.391254,MA0025.1;0.599238,MA0027.1;2.03861,MA0028.1;0.0589063,MA0029.1;0.407394,MA0030.1;0.397801,MA0031.1;0.912186,MA0038.1;0.195728,MA0040.1;0.412311,MA0041.1;1.38763,MA0042.1;0.778983,MA0043.1;0.480818,MA0046.1;0.47108,MA0048.1;0.0169194,MA0050.1;0.123567,MA0051.1;0.192868,MA0052.1;0.41557,MA0055.1;0.031139,MA0056.1;0,MA0057.1;0.0501,MA0058.1;0.274844,MA0059.1;0.273146,MA0060.1;0.079013,MA0061.1;0.0122325,MA0063.1;0,MA0066.1;0.570377,MA0067.1;0.769322,MA0068.1;0.394958,MA0069.1;0.467738,MA0070.1;0.458064,MA0071.1;0.170069,MA0072.1;0.454189,MA0073.1;8.68774e-07,MA0074.1;0.19236,MA0076.1;0.0879186,MA0077.1;0.44756,MA0078.1;0.263604,MA0081.1;0.575852,MA0083.1;0.487092,MA0084.1;0.947429,MA0087.1;1.14666,MA0088.1;0.0453304,MA0089.1;0,MA0090.1;0.0951695,MA0091.1;1.92403,MA0092.1;0.357807,MA0093.1;0.198309,MA0095.1;0,MA0098.1;0,MA0100.1;0.205224,MA0101.1;0.0550002,MA0103.1;0.411939,MA0105.1;0.0116264,MA0106.1;0.224407,MA0107.1;0.122976,MA0108.2;0.906703,MA0109.1;0,MA0111.1;0.102187,MA0113.1;0.236174,MA0114.1;0.0284198,MA0115.1;0.697973,MA0116.1;0.126338,MA0117.1;0.513502,MA0119.1;1.37522,MA0122.1;0.53644,MA0124.1;0.659634,MA0125.1;1.42551,MA0130.1;0,MA0131.1;0.277285,MA0132.1;0,MA0133.1;0,MA0135.1;0.507125,MA0136.1;0.200538,MA0139.1;0.489406,MA0140.1;0.168354,MA0141.1;0.96632,MA0142.1;0.319458,MA0143.1;0.236302,MA0144.1;0.104952,MA0145.1;0.0216393,MA0146.1;0.143735,MA0147.1;0.031895,MA0148.1;0.145617,MA0149.1;0.162171,MA0062.2;0.30369,MA0035.2;0.50217,MA0039.2;0.000430054,MA0138.2;0.264522,MA0002.2;0.359117,MA0137.2;0.221623,MA0104.2;0.0172311,MA0047.2;0.617535,MA0112.2;0.000629343,MA0065.2;0.00611619,MA0150.1;0.636869,MA0151.1;0,MA0152.1;0.172601,MA0153.1;0.567879,MA0154.1;0.31593,MA0155.1;0.441643,MA0156.1;0.487034,MA0157.1;0.807311,MA0158.1;0,MA0159.1;0.0320844,MA0160.1;0.470272,MA0161.1;0,MA0162.1;0.000165262,MA0163.1;0.0241537,MA0164.1;0.245213,MA0080.2;1.17211,MA0018.2;0.225392,MA0099.2;0.172833,MA0079.2;8.77048e-09,MA0102.2;0.983247,MA0258.1;0.0222068,MA0259.1;0.0344451,MA0442.1;0
}}
}}

Revision as of 19:09, 22 January 2013


Full id: C415_neuroectodermal_eye_retina_thyroid_acute_adult_lymphoma



Phase1 CAGE Peaks

Hg19::chr11:89956461..89956473,-p4@CHORDC1
Hg19::chr11:89975228..89975231,+p@chr11:89975228..89975231
+
Hg19::chr11:89984365..89984381,+p1@EU302123
Hg19::chr11:90054231..90054236,+p@chr11:90054231..90054236
+
Hg19::chr11:90055651..90055654,+p@chr11:90055651..90055654
+
Hg19::chr11:90285400..90285405,+p@chr11:90285400..90285405
+
Hg19::chr11:90298500..90298504,+p@chr11:90298500..90298504
+
Hg19::chr11:90469497..90469501,+p@chr11:90469497..90469501
+
Hg19::chr17:33805303..33805307,-p@chr17:33805303..33805307
-
Hg19::chr18:3742564..3742580,-p24@DLGAP1
Hg19::chr18:616690..616703,+p2@CLUL1
Hg19::chr18:616711..616720,+p3@CLUL1
Hg19::chr1:60314072..60314088,+p@chr1:60314072..60314088
+
Hg19::chr3:131736573..131736580,-p15@CPNE4
Hg19::chr3:131736593..131736606,-p6@CPNE4
Hg19::chr7:150745614..150745621,+p7@ACCN3
Hg19::chr8:126527331..126527334,+p@chr8:126527331..126527334
+
Hg19::chr8:128902523..128902539,+p12@PVT1
Hg19::chr8:128902571..128902583,+p15@PVT1
Hg19::chr8:128902610..128902630,+p17@PVT1
Hg19::chr8:129056472..129056485,+p@chr8:129056472..129056485
+
Hg19::chr8:37374492..37374499,-p1@ENST00000521989
Hg19::chrX:2715113..2715130,+p@chrX:2715113..2715130
+
Hg19::chrX:2715135..2715149,+p@chrX:2715135..2715149
+
Hg19::chrX:2715202..2715214,+p@chrX:2715202..2715214
+


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><br><br>disease_data<br>

Disease
Ontology termp-valuen
neuroectodermal tumor2.00e-4010
germ cell and embryonal cancer3.41e-1922
germ cell cancer3.41e-1922


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)
MA0003.13.40323e-06
MA0004.10.130779
MA0006.10.194765
MA0007.10.120068
MA0009.10.480543
MA0014.10.00104451
MA0017.10.242343
MA0019.10.644268
MA0024.10.391254
MA0025.10.599238
MA0027.12.03861
MA0028.10.0589063
MA0029.10.407394
MA0030.10.397801
MA0031.10.912186
MA0038.10.195728
MA0040.10.412311
MA0041.11.38763
MA0042.10.778983
MA0043.10.480818
MA0046.10.47108
MA0048.10.0169194
MA0050.10.123567
MA0051.10.192868
MA0052.10.41557
MA0055.10.031139
MA0056.10
MA0057.10.0501
MA0058.10.274844
MA0059.10.273146
MA0060.10.079013
MA0061.10.0122325
MA0063.10
MA0066.10.570377
MA0067.10.769322
MA0068.10.394958
MA0069.10.467738
MA0070.10.458064
MA0071.10.170069
MA0072.10.454189
MA0073.18.68774e-07
MA0074.10.19236
MA0076.10.0879186
MA0077.10.44756
MA0078.10.263604
MA0081.10.575852
MA0083.10.487092
MA0084.10.947429
MA0087.11.14666
MA0088.10.0453304
MA0089.10
MA0090.10.0951695
MA0091.11.92403
MA0092.10.357807
MA0093.10.198309
MA0095.10
MA0098.10
MA0100.10.205224
MA0101.10.0550002
MA0103.10.411939
MA0105.10.0116264
MA0106.10.224407
MA0107.10.122976
MA0108.20.906703
MA0109.10
MA0111.10.102187
MA0113.10.236174
MA0114.10.0284198
MA0115.10.697973
MA0116.10.126338
MA0117.10.513502
MA0119.11.37522
MA0122.10.53644
MA0124.10.659634
MA0125.11.42551
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.10.200538
MA0139.10.489406
MA0140.10.168354
MA0141.10.96632
MA0142.10.319458
MA0143.10.236302
MA0144.10.104952
MA0145.10.0216393
MA0146.10.143735
MA0147.10.031895
MA0148.10.145617
MA0149.10.162171
MA0062.20.30369
MA0035.20.50217
MA0039.20.000430054
MA0138.20.264522
MA0002.20.359117
MA0137.20.221623
MA0104.20.0172311
MA0047.20.617535
MA0112.20.000629343
MA0065.20.00611619
MA0150.10.636869
MA0151.10
MA0152.10.172601
MA0153.10.567879
MA0154.10.31593
MA0155.10.441643
MA0156.10.487034
MA0157.10.807311
MA0158.10
MA0159.10.0320844
MA0160.10.470272
MA0161.10
MA0162.10.000165262
MA0163.10.0241537
MA0164.10.245213
MA0080.21.17211
MA0018.20.225392
MA0099.20.172833
MA0079.28.77048e-09
MA0102.20.983247
MA0258.10.0222068
MA0259.10.0344451
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
ESR1#209944.922976527384720.008164341820144850.0322372663649946



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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