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Coexpression cluster:C598: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.172755,0.725063,0.501231,0.277483,0.847893,0.757608,0.899058,0.517403,0.510737,0.0781644,0.252096,0.980853,0.177832,0.329255,0.843993,0.153757,0.534852,0.33964,0.431744,0.587627,0.968262,1.92831,0.26993,0.833341,1.10105,0.395548,0.151052,0.268197,0.434999,0.131814,0.235027,0.568576,0.288446,0.180835,0.116543,0.00488944,0.114552,0.27709,0.32965,0.212026,0.370199,0.633281,0.118046,1.3579,0.136748,0.189598,0.901103,1.26597,0.0067887,0.8571,0.407934,0.349819,0.0893853,0.639823,0.784252,0.331716,0.442382,0.304469,1.74086,0.303639,0.606437,0.341844,0.512045,0.509653,0.357077,1.20368,0.869007,1.22829,0.559029,1.06908,0.212516,0.532685,0.420444,0.782342,0.171892,0.155706,1.33362,0.494371,0.556046,1.0831,0.443974,0.50868,0.356776,0.897002,0.733386,0.0363137,0.175802,0.126142,0.430803,1.32629,0.95934,0.70782,0.584068,0.0892066,0.431036,0.0967938,0.427968,0.623577,0.434875,0.108128,0.679229,0.578851,0.618385,0.538198,1.18153,0.694065,0.523764,0.326366,0.20048,0.128402,1.00057,0.61581,0.952135,2.04418,0.912801,0.364707,0.00237972,1.91084,1.19918,0.0908333,0.77444,0.428661,0.273941,0.366411,1.02031,2.1446,0.33358,0.588683,0.815183,1.62016,0.708473,1.24203,0.828971,0.953662,0.971853,0.0284956,0.230408,0.268649,0.930667,1.77777,1.3781,0.894557,0.335034,1.50374,0.469857,0.297516,0.454976,1.61933,0.627312,0.0873523,0.383495,0.0375843,0.708834,0.225902,1.6213,1.09904,0.41656,0.808193,0.200711,0.179634,0.893382,0.691354,0.555323,0.536459,0.48429,0.937181,0.275921,0.337803,0.371261
|tfbs_overrepresentation_jaspar=MA0003.1;0.000385441,MA0004.1;1.31328,MA0006.1;0.426713,MA0007.1;0.67744,MA0009.1;0.669377,MA0014.1;0.00275422,MA0017.1;1.52535,MA0019.1;0.38027,MA0024.1;0.570967,MA0025.1;0.796882,MA0027.1;2.25966,MA0028.1;0.148561,MA0029.1;0.588958,MA0030.1;0.578277,MA0031.1;0.518602,MA0038.1;0.34128,MA0040.1;0.594421,MA0041.1;0.27117,MA0042.1;0.245557,MA0043.1;0.669676,MA0046.1;0.659066,MA0048.1;0.23222,MA0050.1;0.246257,MA0051.1;0.337676,MA0052.1;0.598036,MA0055.1;0.120131,MA0056.1;0,MA0057.1;0.0873069,MA0058.1;1.03067,MA0059.1;2.31102,MA0060.1;0.877206,MA0061.1;0.43901,MA0063.1;0,MA0066.1;0.341645,MA0067.1;0.975379,MA0068.1;0.147451,MA0069.1;0.655419,MA0070.1;0.644843,MA0071.1;0.308534,MA0072.1;0.640598,MA0073.1;0.0372716,MA0074.1;0.894848,MA0076.1;0.194691,MA0077.1;0.633326,MA0078.1;1.08632,MA0081.1;0.18212,MA0083.1;0.676499,MA0084.1;1.15904,MA0087.1;0.63829,MA0088.1;0.94902,MA0089.1;0,MA0090.1;1.12017,MA0091.1;0.258318,MA0092.1;0.647316,MA0093.1;1.37484,MA0095.1;0,MA0098.1;0,MA0100.1;0.353174,MA0101.1;0.861002,MA0103.1;0.411001,MA0105.1;0.376193,MA0106.1;0.37688,MA0107.1;0.650533,MA0108.2;0.515791,MA0109.1;0,MA0111.1;0.215855,MA0113.1;0.39123,MA0114.1;1.06224,MA0115.1;0.900969,MA0116.1;0.320986,MA0117.1;0.705104,MA0119.1;1.55801,MA0122.1;0.729811,MA0124.1;0.860724,MA0125.1;0.779672,MA0130.1;0,MA0131.1;0.440395,MA0132.1;0,MA0133.1;0,MA0135.1;0.698212,MA0136.1;0.347318,MA0139.1;0.0481205,MA0140.1;0.30631,MA0141.1;0.180729,MA0142.1;0.489543,MA0143.1;0.391385,MA0144.1;0.284854,MA0145.1;0.00981909,MA0146.1;0.310147,MA0147.1;0.670164,MA0148.1;1.38762,MA0149.1;0.298252,MA0062.2;0.191053,MA0035.2;0.305721,MA0039.2;0.072333,MA0138.2;1.91075,MA0002.2;0.480166,MA0137.2;0.153033,MA0104.2;0.509661,MA0047.2;0.366327,MA0112.2;0.00868143,MA0065.2;0.287056,MA0150.1;0.201098,MA0151.1;0,MA0152.1;0.311809,MA0153.1;0.763487,MA0154.1;0.187751,MA0155.1;0.421308,MA0156.1;0.469333,MA0157.1;0.46471,MA0158.1;0,MA0159.1;0.327637,MA0160.1;0.288813,MA0161.1;0,MA0162.1;0.0243066,MA0163.1;0.257146,MA0164.1;0.402162,MA0080.2;0.139746,MA0018.2;0.378086,MA0099.2;0.839067,MA0079.2;0.00055716,MA0102.2;1.1957,MA0258.1;0.0785319,MA0259.1;0.340204,MA0442.1;0
}}
}}

Revision as of 19:18, 22 January 2013


Full id: C598_fibrosarcoma_osteoclastoma_fibrous_astrocytoma_large_liposarcoma_embryonic



Phase1 CAGE Peaks

Hg19::chr15:65536787..65536794,-p@chr15:65536787..65536794
-
Hg19::chr16:1756807..1756810,+p@chr16:1756807..1756810
+
Hg19::chr18:45109430..45109434,+p@chr18:45109430..45109434
+
Hg19::chr1:23519975..23519983,-p@chr1:23519975..23519983
-
Hg19::chr1:23520006..23520019,-p@chr1:23520006..23520019
-
Hg19::chr1:23520445..23520450,-p4@HTR1D
Hg19::chr1:23520457..23520462,-p6@HTR1D
Hg19::chr1:2382521..2382522,-p@chr1:2382521..2382522
-
Hg19::chr5:135378735..135378744,+p@chr5:135378735..135378744
+
Hg19::chr5:135378750..135378757,+p@chr5:135378750..135378757
+
Hg19::chr5:135378786..135378804,+p@chr5:135378786..135378804
+
Hg19::chr7:36362212..36362214,+p@chr7:36362212..36362214
+
Hg19::chrX:132231123..132231140,-p1@USP26
Hg19::chrX:45477349..45477359,+p@chrX:45477349..45477359
+
Hg19::chrX:45488121..45488123,+p@chrX:45488121..45488123
+


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

GO IDGO nameFDR corrected p-value
GO:0004993serotonin receptor activity0.0474424610434464



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
sarcoma2.29e-1120


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)
MA0003.10.000385441
MA0004.11.31328
MA0006.10.426713
MA0007.10.67744
MA0009.10.669377
MA0014.10.00275422
MA0017.11.52535
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.120131
MA0056.10
MA0057.10.0873069
MA0058.11.03067
MA0059.12.31102
MA0060.10.877206
MA0061.10.43901
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.147451
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.0372716
MA0074.10.894848
MA0076.10.194691
MA0077.10.633326
MA0078.11.08632
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.94902
MA0089.10
MA0090.11.12017
MA0091.10.258318
MA0092.10.647316
MA0093.11.37484
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.861002
MA0103.10.411001
MA0105.10.376193
MA0106.10.37688
MA0107.10.650533
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.11.06224
MA0115.10.900969
MA0116.10.320986
MA0117.10.705104
MA0119.11.55801
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.0481205
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.284854
MA0145.10.00981909
MA0146.10.310147
MA0147.10.670164
MA0148.11.38762
MA0149.10.298252
MA0062.20.191053
MA0035.20.305721
MA0039.20.072333
MA0138.21.91075
MA0002.20.480166
MA0137.20.153033
MA0104.20.509661
MA0047.20.366327
MA0112.20.00868143
MA0065.20.287056
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.187751
MA0155.10.421308
MA0156.10.469333
MA0157.10.46471
MA0158.10
MA0159.10.327637
MA0160.10.288813
MA0161.10
MA0162.10.0243066
MA0163.10.257146
MA0164.10.402162
MA0080.20.139746
MA0018.20.378086
MA0099.20.839067
MA0079.20.00055716
MA0102.21.1957
MA0258.10.0785319
MA0259.10.340204
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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