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Coexpression cluster:C252: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.3629,0.281638,0.683946,0.134936,0.331192,0.573585,2.20545,0.182417,2.01984,0.482224,0.110041,0.248453,0.0974018,1.1453,0.180672,0.102854,0.473612,0.0131866,1.09046,0.392281,0.254552,0.0625187,0.301832,0.0259181,0.577546,2.0018,1.02462,0.869405,0.338935,0.681359,0.445823,0.177715,3.30653,0.0505398,0.0176946,0.964449,1.13927,0.134535,0.0995547,0.36684,0.0562647,0.99196,0.0885886,0.761381,0.147132,0.313984,0.055621,0.102164,0.165125,0.0859695,0.0858169,0.471573,0.0197471,0.641329,0.3341,0.0524224,0.555625,0.372713,0.875958,0.0420799,0.202848,0.453762,0.292785,0.435283,0.224892,0.123014,0.402704,0.720274,0.171563,0.575342,0.379093,0.0499082,0.000102787,0.332593,0.160691,0.13264,0.935167,1.32733,0.169657,0.0629316,0.126368,0.140452,0.840335,1.4217,0.294608,0.000458702,0.0010676,0.833434,0.32136,0.811794,0.479041,0.2753,0.18786,2.9689,0.00494039,0.0108878,4.82471,0.214593,0.326994,0.88477,0.335245,3.09337,1.14146,0.930504,0.117242,0.106715,0.149529,0.737605,0.344514,0.0705241,1.78439,0.209243,1.28307,0.281382,0.439341,0.126207,0.0129981,0.0214019,0.386209,1.15713,0.326377,0.0961449,2.24093,0.509153,0.532117,0.132442,1.63622,0.19092,6.74469,0.185378,0.275788,0.0221808,0.369895,2.38235,0.489841,0.211077,0.0205074,0.126043,0.454492,1.24681,0.860735,1.90637,0.438691,1.7937,3.14398,1.90788,0.720049,1.09233,0.400899,0.0298676,0.0294413,4.10603e-06,0.276058,0.0854674,0.205929,3.64458,0.301888,0.0232319,0.868583,0.140641,0.423004,3.76662,0.50535,0.144238,1.87361,0.838037,0.378356,0.201611,0.00282251
|tfbs_overrepresentation_for_novel_motifs=1.3629,0.281638,0.683946,0.134936,0.331192,0.573585,2.20545,0.182417,2.01984,0.482224,0.110041,0.248453,0.0974018,1.1453,0.180672,0.102854,0.473612,0.0131866,1.09046,0.392281,0.254552,0.0625187,0.301832,0.0259181,0.577546,2.0018,1.02462,0.869405,0.338935,0.681359,0.445823,0.177715,3.30653,0.0505398,0.0176946,0.964449,1.13927,0.134535,0.0995547,0.36684,0.0562647,0.99196,0.0885886,0.761381,0.147132,0.313984,0.055621,0.102164,0.165125,0.0859695,0.0858169,0.471573,0.0197471,0.641329,0.3341,0.0524224,0.555625,0.372713,0.875958,0.0420799,0.202848,0.453762,0.292785,0.435283,0.224892,0.123014,0.402704,0.720274,0.171563,0.575342,0.379093,0.0499082,0.000102787,0.332593,0.160691,0.13264,0.935167,1.32733,0.169657,0.0629316,0.126368,0.140452,0.840335,1.4217,0.294608,0.000458702,0.0010676,0.833434,0.32136,0.811794,0.479041,0.2753,0.18786,2.9689,0.00494039,0.0108878,4.82471,0.214593,0.326994,0.88477,0.335245,3.09337,1.14146,0.930504,0.117242,0.106715,0.149529,0.737605,0.344514,0.0705241,1.78439,0.209243,1.28307,0.281382,0.439341,0.126207,0.0129981,0.0214019,0.386209,1.15713,0.326377,0.0961449,2.24093,0.509153,0.532117,0.132442,1.63622,0.19092,6.74469,0.185378,0.275788,0.0221808,0.369895,2.38235,0.489841,0.211077,0.0205074,0.126043,0.454492,1.24681,0.860735,1.90637,0.438691,1.7937,3.14398,1.90788,0.720049,1.09233,0.400899,0.0298676,0.0294413,4.10603e-06,0.276058,0.0854674,0.205929,3.64458,0.301888,0.0232319,0.868583,0.140641,0.423004,3.76662,0.50535,0.144238,1.87361,0.838037,0.378356,0.201611,0.00282251
|tfbs_overrepresentation_jaspar=MA0003.1;0.000104715,MA0004.1;1.18532,MA0006.1;1.05505,MA0007.1;0.0232257,MA0009.1;0.247013,MA0014.1;0.0938253,MA0017.1;0.247253,MA0019.1;0.0728369,MA0024.1;0.179268,MA0025.1;0.344113,MA0027.1;1.7227,MA0028.1;0.367984,MA0029.1;0.191103,MA0030.1;0.184045,MA0031.1;0.146399,MA0038.1;0.205745,MA0040.1;0.194748,MA0041.1;0.557737,MA0042.1;0.103967,MA0043.1;0.24723,MA0046.1;0.239588,MA0048.1;0.314896,MA0050.1;0.0244947,MA0051.1;0.444523,MA0052.1;0.197173,MA0055.1;0.0253044,MA0056.1;0,MA0057.1;0.399875,MA0058.1;0.295688,MA0059.1;1.07971,MA0060.1;0.000516773,MA0061.1;1.11588,MA0063.1;0,MA0066.1;0.20618,MA0067.1;0.492893,MA0068.1;7.92234,MA0069.1;0.236979,MA0070.1;0.229464,MA0071.1;0.16802,MA0072.1;0.22647,MA0073.1;2.86803,MA0074.1;0.0545051,MA0076.1;0.164591,MA0077.1;0.221371,MA0078.1;0.0938727,MA0081.1;2.30314,MA0083.1;0.252183,MA0084.1;0.656589,MA0087.1;0.224848,MA0088.1;0.00651444,MA0089.1;0,MA0090.1;0.182672,MA0091.1;0.115952,MA0092.1;0.0887874,MA0093.1;1.07299,MA0095.1;0,MA0098.1;0,MA0100.1;0.220108,MA0101.1;1.09255,MA0103.1;1.00086,MA0105.1;0.581123,MA0106.1;0.249701,MA0107.1;3.58005,MA0108.2;0.144705,MA0109.1;0,MA0111.1;0.0171834,MA0113.1;0.0778665,MA0114.1;0.291105,MA0115.1;0.42937,MA0116.1;0.950918,MA0117.1;0.273271,MA0119.1;0.453467,MA0122.1;0.291885,MA0124.1;0.395861,MA0125.1;0.330489,MA0130.1;0,MA0131.1;0.102211,MA0132.1;0,MA0133.1;0,MA0135.1;0.268144,MA0136.1;1.22844,MA0139.1;0.0213304,MA0140.1;0.043016,MA0141.1;0.0520676,MA0142.1;0.129252,MA0143.1;1.43349,MA0144.1;0.252381,MA0145.1;0.46481,MA0146.1;0.000109415,MA0147.1;0.718004,MA0148.1;0.033106,MA0149.1;0.15676,MA0062.2;0.0246103,MA0035.2;0.0428087,MA0039.2;0.000541227,MA0138.2;1.593,MA0002.2;0.391462,MA0137.2;0.385218,MA0104.2;0.837452,MA0047.2;0.0666578,MA0112.2;0.00105426,MA0065.2;0.189072,MA0150.1;0.87076,MA0151.1;0,MA0152.1;0.0449747,MA0153.1;0.317813,MA0154.1;0.0502066,MA0155.1;6.61129,MA0156.1;0.221329,MA0157.1;0.115269,MA0158.1;0,MA0159.1;1.27129,MA0160.1;0.146686,MA0161.1;0,MA0162.1;0.000932191,MA0163.1;0.0349484,MA0164.1;0.0830315,MA0080.2;1.4084,MA0018.2;0.0718527,MA0099.2;0.0450826,MA0079.2;0.0368681,MA0102.2;0.690195,MA0258.1;0.0232716,MA0259.1;1.02864,MA0442.1;0
}}
}}

Revision as of 18:52, 22 January 2013


Full id: C252_hepatic_Olfactory_sacrococcigeal_leiomyoma_normal_Synoviocyte_glioblastoma



Phase1 CAGE Peaks

Hg19::chr13:60923837..60923842,+p@chr13:60923837..60923842
+
Hg19::chr2:217536828..217536834,+p@chr2:217536828..217536834
+
Hg19::chr2:217536938..217536983,+p@chr2:217536938..217536983
+
Hg19::chr2:217536997..217537017,+p@chr2:217536997..217537017
+
Hg19::chr2:217537650..217537688,-p7@IGFBP5
Hg19::chr2:217538410..217538421,-p41@IGFBP5
Hg19::chr2:217538489..217538501,-p30@IGFBP5
Hg19::chr2:217539038..217539095,-p@chr2:217539038..217539095
-
Hg19::chr2:217539159..217539181,-p@chr2:217539159..217539181
-
Hg19::chr2:217539667..217539679,-p@chr2:217539667..217539679
-
Hg19::chr2:217540148..217540164,-p@chr2:217540148..217540164
-
Hg19::chr2:217540173..217540184,-p@chr2:217540173..217540184
-
Hg19::chr2:217540186..217540197,-p@chr2:217540186..217540197
-
Hg19::chr2:217540204..217540217,-p@chr2:217540204..217540217
-
Hg19::chr2:217540397..217540408,-p47@IGFBP5
Hg19::chr2:217540482..217540541,-p3@IGFBP5
Hg19::chr2:217540844..217540856,-p17@IGFBP5
Hg19::chr2:217540885..217540897,-p40@IGFBP5
Hg19::chr2:217540938..217540949,-p42@IGFBP5
Hg19::chr2:217541024..217541035,-p21@IGFBP5
Hg19::chr2:217541074..217541178,+p@chr2:217541074..217541178
+
Hg19::chr2:217541219..217541237,-p22@IGFBP5
Hg19::chr2:217541242..217541256,-p32@IGFBP5
Hg19::chr2:217541259..217541290,-p16@IGFBP5
Hg19::chr2:217541295..217541337,-p4@IGFBP5
Hg19::chr2:217541338..217541373,-p10@IGFBP5
Hg19::chr2:217541386..217541454,-p@chr2:217541386..217541454
-
Hg19::chr2:217541453..217541486,+p@chr2:217541453..217541486
+
Hg19::chr2:217541501..217541514,+p@chr2:217541501..217541514
+
Hg19::chr2:217541503..217541520,-p@chr2:217541503..217541520
-
Hg19::chr2:217541580..217541591,-p@chr2:217541580..217541591
-
Hg19::chr2:217542874..217542895,-p@chr2:217542874..217542895
-
Hg19::chr2:217542897..217542920,-p@chr2:217542897..217542920
-
Hg19::chr2:217542923..217542939,-p@chr2:217542923..217542939
-
Hg19::chr2:217542944..217542963,-p@chr2:217542944..217542963
-
Hg19::chr2:217543623..217543642,-p@chr2:217543623..217543642
-
Hg19::chr2:217543637..217543648,+p@chr2:217543637..217543648
+
Hg19::chr2:217543669..217543701,+p@chr2:217543669..217543701
+
Hg19::chr2:217543717..217543731,-p@chr2:217543717..217543731
-
Hg19::chr2:217543738..217543773,+p@chr2:217543738..217543773
+
Hg19::chr2:217559189..217559207,-p29@IGFBP5
Hg19::chr2:217559232..217559274,-p6@IGFBP5
Hg19::chr2:217559547..217559566,-p13@IGFBP5
Hg19::chr2:217559626..217559641,-p9@IGFBP5
Hg19::chr2:217559705..217559716,-p23@IGFBP5
Hg19::chr2:217559768..217559787,-p12@IGFBP5
Hg19::chr2:217559807..217559818,-p19@IGFBP5
Hg19::chr2:217559893..217559904,-p39@IGFBP5
Hg19::chr2:217559980..217559987,-p37@IGFBP5
Hg19::chr2:217560017..217560035,-p26@IGFBP5
Hg19::chr2:217560039..217560069,-p2@IGFBP5
Hg19::chr2:217560263..217560278,-p1@IGFBP5


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><br>

Cell Type
Ontology termp-valuen
stromal cell1.19e-0728
fibroblast9.90e-0776
Uber Anatomy
Ontology termp-valuen
adult organism1.13e-12114
reproductive structure6.27e-0959
reproductive system6.27e-0959
reproductive organ1.88e-0748


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)
MA0003.10.000104715
MA0004.11.18532
MA0006.11.05505
MA0007.10.0232257
MA0009.10.247013
MA0014.10.0938253
MA0017.10.247253
MA0019.10.0728369
MA0024.10.179268
MA0025.10.344113
MA0027.11.7227
MA0028.10.367984
MA0029.10.191103
MA0030.10.184045
MA0031.10.146399
MA0038.10.205745
MA0040.10.194748
MA0041.10.557737
MA0042.10.103967
MA0043.10.24723
MA0046.10.239588
MA0048.10.314896
MA0050.10.0244947
MA0051.10.444523
MA0052.10.197173
MA0055.10.0253044
MA0056.10
MA0057.10.399875
MA0058.10.295688
MA0059.11.07971
MA0060.10.000516773
MA0061.11.11588
MA0063.10
MA0066.10.20618
MA0067.10.492893
MA0068.17.92234
MA0069.10.236979
MA0070.10.229464
MA0071.10.16802
MA0072.10.22647
MA0073.12.86803
MA0074.10.0545051
MA0076.10.164591
MA0077.10.221371
MA0078.10.0938727
MA0081.12.30314
MA0083.10.252183
MA0084.10.656589
MA0087.10.224848
MA0088.10.00651444
MA0089.10
MA0090.10.182672
MA0091.10.115952
MA0092.10.0887874
MA0093.11.07299
MA0095.10
MA0098.10
MA0100.10.220108
MA0101.11.09255
MA0103.11.00086
MA0105.10.581123
MA0106.10.249701
MA0107.13.58005
MA0108.20.144705
MA0109.10
MA0111.10.0171834
MA0113.10.0778665
MA0114.10.291105
MA0115.10.42937
MA0116.10.950918
MA0117.10.273271
MA0119.10.453467
MA0122.10.291885
MA0124.10.395861
MA0125.10.330489
MA0130.10
MA0131.10.102211
MA0132.10
MA0133.10
MA0135.10.268144
MA0136.11.22844
MA0139.10.0213304
MA0140.10.043016
MA0141.10.0520676
MA0142.10.129252
MA0143.11.43349
MA0144.10.252381
MA0145.10.46481
MA0146.10.000109415
MA0147.10.718004
MA0148.10.033106
MA0149.10.15676
MA0062.20.0246103
MA0035.20.0428087
MA0039.20.000541227
MA0138.21.593
MA0002.20.391462
MA0137.20.385218
MA0104.20.837452
MA0047.20.0666578
MA0112.20.00105426
MA0065.20.189072
MA0150.10.87076
MA0151.10
MA0152.10.0449747
MA0153.10.317813
MA0154.10.0502066
MA0155.16.61129
MA0156.10.221329
MA0157.10.115269
MA0158.10
MA0159.11.27129
MA0160.10.146686
MA0161.10
MA0162.10.000932191
MA0163.10.0349484
MA0164.10.0830315
MA0080.21.4084
MA0018.20.0718527
MA0099.20.0450826
MA0079.20.0368681
MA0102.20.690195
MA0258.10.0232716
MA0259.11.02864
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

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