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Coexpression cluster:C553: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.157827,0.438932,0.152819,0.258928,1.86757,0.25764,0.318839,0.215354,0.211907,0.268189,0.234283,0.355038,1.00162,0.309388,0.786056,0.431887,0.511522,0.639388,0.388593,0.520625,0.464958,0.765208,0.251588,0.387475,0.542899,0.374311,0.566593,0.249905,0.127478,0.509928,0.217756,0.544857,0.552347,0.363901,0.694555,0.159992,0.102549,0.258546,0.299553,0.419472,0.338389,0.205653,0.097714,0.123709,1.16726,0.173971,0.319738,0.226038,0.18831,0.12756,0.386472,0.878028,0.625622,0.615394,0.758742,0.311792,1.31612,0.2852,0.274137,0.284391,0.582323,0.321692,0.0585016,0.48664,0.336598,0.456015,0.843028,1.20113,0.535417,1.04233,0.19602,0.0621482,0.0158491,0.756844,0.0383048,1.3125,0.288432,0.471562,0.532468,0.18023,0.400226,0.48568,0.893218,0.82567,0.70821,0.00106305,0.30235,0.10849,0.408949,1.29895,0.932961,0.68283,1.37726,0.571383,0.12599,0.0858933,0.684177,0.599297,0.412954,0.229879,0.0899484,0.555021,0.594155,0.514828,0.445845,0.230832,0.500571,0.306566,0.18443,0.115618,0.938911,0.591605,0.149112,0.241506,0.886618,0.101627,0.0385455,0.216858,0.453946,0.977584,0.748992,0.406842,0.255485,0.345739,0.993708,0.472239,0.313614,0.564749,0.78949,0.291925,0.683478,0.219902,0.803201,0.342946,0.945426,0.101403,0.21329,0.250344,0.904406,1.74999,1.35069,0.868456,0.845643,0.596045,0.447394,0.278424,0.432737,1.59165,1.74369,0.0770919,0.336018,0.00537053,0.683836,0.0546497,0.321292,1.07219,0.394947,1.23019,0.184652,0.164414,0.867287,0.66649,0.531753,0.166635,1.1672,0.335644,1.36088,0.317742,0.568601
|tfbs_overrepresentation_jaspar=MA0003.1;0.000901175,MA0004.1;0.238283,MA0006.1;0.392773,MA0007.1;0.223897,MA0009.1;0.644692,MA0014.1;0.111471,MA0017.1;0.150184,MA0019.1;0.359322,MA0024.1;0.547222,MA0025.1;0.771296,MA0027.1;2.23171,MA0028.1;0.134741,MA0029.1;0.565022,MA0030.1;0.554453,MA0031.1;0.495474,MA0038.1;0.321141,MA0040.1;0.570428,MA0041.1;0.252793,MA0042.1;0.227947,MA0043.1;0.644989,MA0046.1;0.634468,MA0048.1;0.0172925,MA0050.1;0.647665,MA0051.1;1.53688,MA0052.1;0.574006,MA0055.1;0.324189,MA0056.1;0,MA0057.1;0.0733461,MA0058.1;0.5014,MA0059.1;0.499176,MA0060.1;0.212419,MA0061.1;0.0461955,MA0063.1;0,MA0066.1;0.860141,MA0067.1;0.948938,MA0068.1;0.128042,MA0069.1;0.630852,MA0070.1;0.620368,MA0071.1;0.289163,MA0072.1;0.616162,MA0073.1;0.000310801,MA0074.1;0.316991,MA0076.1;0.528959,MA0077.1;1.47997,MA0078.1;1.83296,MA0081.1;2.19686,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;0.0965118,MA0089.1;0,MA0090.1;0.189305,MA0091.1;0.240316,MA0092.1;0.211423,MA0093.1;0.397767,MA0095.1;0,MA0098.1;0,MA0100.1;0.332778,MA0101.1;0.128426,MA0103.1;0.377626,MA0105.1;0.0129929,MA0106.1;0.355999,MA0107.1;0.0842574,MA0108.2;1.23385,MA0109.1;0,MA0111.1;0.199239,MA0113.1;1.72141,MA0114.1;0.584594,MA0115.1;0.874839,MA0116.1;0.607827,MA0117.1;0.680135,MA0119.1;0.471628,MA0122.1;0.70466,MA0124.1;0.834787,MA0125.1;0.75419,MA0130.1;0,MA0131.1;0.418384,MA0132.1;0,MA0133.1;0,MA0135.1;0.673296,MA0136.1;1.57044,MA0139.1;0.159457,MA0140.1;0.286995,MA0141.1;0.165463,MA0142.1;0.4668,MA0143.1;1.72194,MA0144.1;0.0738381,MA0145.1;0.039861,MA0146.1;0.0427873,MA0147.1;0.0881384,MA0148.1;0.257816,MA0149.1;0.279141,MA0062.2;0.382208,MA0035.2;0.286421,MA0039.2;0.0116984,MA0138.2;0.403517,MA0002.2;1.16356,MA0137.2;0.138998,MA0104.2;0.0580852,MA0047.2;0.345656,MA0112.2;0.22067,MA0065.2;0.246686,MA0150.1;0.185024,MA0151.1;0,MA0152.1;0.292357,MA0153.1;0.738108,MA0154.1;0.0600612,MA0155.1;0.0948197,MA0156.1;0.433955,MA0157.1;0.442323,MA0158.1;0,MA0159.1;0.29763,MA0160.1;0.743405,MA0161.1;0,MA0162.1;0.0005964,MA0163.1;0.0267068,MA0164.1;2.64221,MA0080.2;0.397909,MA0018.2;0.357181,MA0099.2;0.292649,MA0079.2;9.76624e-07,MA0102.2;1.16862,MA0258.1;0.520754,MA0259.1;0.309645,MA0442.1;0
}}
}}

Revision as of 19:15, 22 January 2013


Full id: C553_acute_non_choriocarcinoma_endometrial_hepatoblastoma_signet_rhabdomyosarcoma



Phase1 CAGE Peaks

Hg19::chr10:130077036..130077085,+p@chr10:130077036..130077085
+
Hg19::chr10:49667817..49667824,-p@chr10:49667817..49667824
-
Hg19::chr10:49667833..49667844,-p@chr10:49667833..49667844
-
Hg19::chr10:49667987..49667997,-p@chr10:49667987..49667997
-
Hg19::chr10:73497583..73497595,-p6@C10orf105
Hg19::chr10:73497602..73497612,-p7@C10orf105
Hg19::chr21:16281272..16281275,-p@chr21:16281272..16281275
-
Hg19::chr21:16426559..16426566,-p@chr21:16426559..16426566
-
Hg19::chr2:11821544..11821577,+p1@ENST00000455754
p1@uc002rbr.2
Hg19::chr2:11821601..11821611,+p1@ENST00000435175
Hg19::chr2:62592016..62592063,+p@chr2:62592016..62592063
+
Hg19::chr3:152258355..152258360,+p@chr3:152258355..152258360
+
Hg19::chr4:116236647..116236690,+p@chr4:116236647..116236690
+
Hg19::chr9:100686938..100686967,+p@chr9:100686938..100686967
+
Hg19::chr9:117701714..117701725,+p@chr9:117701714..117701725
+
Hg19::chrX:87129212..87129221,-p@chrX:87129212..87129221
-


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
myeloid leukemia3.79e-2031
leukemia2.93e-1639
hematologic cancer1.06e-1251
immune system cancer1.06e-1251


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)
MA0003.10.000901175
MA0004.10.238283
MA0006.10.392773
MA0007.10.223897
MA0009.10.644692
MA0014.10.111471
MA0017.10.150184
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.10.0172925
MA0050.10.647665
MA0051.11.53688
MA0052.10.574006
MA0055.10.324189
MA0056.10
MA0057.10.0733461
MA0058.10.5014
MA0059.10.499176
MA0060.10.212419
MA0061.10.0461955
MA0063.10
MA0066.10.860141
MA0067.10.948938
MA0068.10.128042
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.000310801
MA0074.10.316991
MA0076.10.528959
MA0077.11.47997
MA0078.11.83296
MA0081.12.19686
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.0965118
MA0089.10
MA0090.10.189305
MA0091.10.240316
MA0092.10.211423
MA0093.10.397767
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.128426
MA0103.10.377626
MA0105.10.0129929
MA0106.10.355999
MA0107.10.0842574
MA0108.21.23385
MA0109.10
MA0111.10.199239
MA0113.11.72141
MA0114.10.584594
MA0115.10.874839
MA0116.10.607827
MA0117.10.680135
MA0119.10.471628
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.11.57044
MA0139.10.159457
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.11.72194
MA0144.10.0738381
MA0145.10.039861
MA0146.10.0427873
MA0147.10.0881384
MA0148.10.257816
MA0149.10.279141
MA0062.20.382208
MA0035.20.286421
MA0039.20.0116984
MA0138.20.403517
MA0002.21.16356
MA0137.20.138998
MA0104.20.0580852
MA0047.20.345656
MA0112.20.22067
MA0065.20.246686
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.0600612
MA0155.10.0948197
MA0156.10.433955
MA0157.10.442323
MA0158.10
MA0159.10.29763
MA0160.10.743405
MA0161.10
MA0162.10.0005964
MA0163.10.0267068
MA0164.12.64221
MA0080.20.397909
MA0018.20.357181
MA0099.20.292649
MA0079.29.76624e-07
MA0102.21.16862
MA0258.10.520754
MA0259.10.309645
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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