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Coexpression cluster:C1713: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=2.1885,0.452433,1.25018,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.345702,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.501863,0.500405,0.770467,0.645033,0.44943,0.549618,0.802434,0.25115,1.55072,2.02225,0.659743,0.598009,1.00172,0.359091,0.758594,2.81341,0.432883,3.81581,0.654459,0.388123,0.815792,0.415749,0.580638,0.821929,0.451846,0.218848,1.32072,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.880217,1.66643,1.23387,0.741483,0.255232,0.675933,0.917983,0.987729,1.34093,0.293154,0.934302,0.755403,0.327263,1.18161,1.37242,0.49825,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.99322,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,1.49565,3.5944,0.717647,0.549347,1.11542,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.597842,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.177807,1.87689,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,1.29666,0.906429,0.754576,0.35004,0.731946,0.233587
|tfbs_overrepresentation_for_novel_motifs=2.1885,0.452433,1.25018,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.345702,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.501863,0.500405,0.770467,0.645033,0.44943,0.549618,0.802434,0.25115,1.55072,2.02225,0.659743,0.598009,1.00172,0.359091,0.758594,2.81341,0.432883,3.81581,0.654459,0.388123,0.815792,0.415749,0.580638,0.821929,0.451846,0.218848,1.32072,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.880217,1.66643,1.23387,0.741483,0.255232,0.675933,0.917983,0.987729,1.34093,0.293154,0.934302,0.755403,0.327263,1.18161,1.37242,0.49825,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.99322,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,1.49565,3.5944,0.717647,0.549347,1.11542,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.597842,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.177807,1.87689,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,1.29666,0.906429,0.754576,0.35004,0.731946,0.233587
|tfbs_overrepresentation_jaspar=MA0003.1;1.40197,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;1.9468,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;2.29497,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;1.7452,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.569896,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.288856,MA0056.1;0,MA0057.1;1.66737,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;5.26847,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.692739,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.362215,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.818263,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.520776,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;1.40074,MA0113.1;0.797251,MA0114.1;0.973423,MA0115.1;1.35895,MA0116.1;4.68138,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;1.39016,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;0.946108,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;1.50246,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.98952,MA0155.1;0.409315,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;1.23503,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;1.27276,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:07, 22 January 2013


Full id: C1713_Alveolar_Renal_Hodgkin_chronic_MCF7_Placental_Melanocyte



Phase1 CAGE Peaks

Hg19::chr14:104181771..104181827,-p1@XRCC3
Hg19::chr16:3030386..3030400,-p2@PKMYT1
Hg19::chr16:3030407..3030489,-p1@PKMYT1
Hg19::chr19:12917364..12917407,+p2@RNASEH2A
Hg19::chr19:14247387..14247409,-p1@ASF1B


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:0006259DNA metabolic process0.0279660708108065



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 cell4.78e-23253
animal cell5.26e-16679
eukaryotic cell5.26e-16679
native cell2.12e-11722
embryonic cell1.63e-10250
migratory neural crest cell5.70e-0941
epithelial cell of nephron7.32e-0715
neurectodermal cell9.82e-0759
Uber Anatomy
Ontology termp-valuen
larynx2.89e-079
nephron epithelium7.32e-0715
renal tubule7.32e-0715
nephron tubule7.32e-0715
nephron7.32e-0715
uriniferous tubule7.32e-0715
nephrogenic mesenchyme7.32e-0715
Disease
Ontology termp-valuen
cancer6.75e-38235
disease of cellular proliferation5.77e-37239
cell type cancer9.89e-19143
organ system cancer8.91e-18137
hematologic cancer2.32e-1751
immune system cancer2.32e-1751
carcinoma1.96e-15106
leukemia4.45e-1439
myeloid leukemia1.40e-1031


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)
MA0003.11.40197
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.9468
MA0017.10.496101
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.11.7452
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.11.66737
MA0058.10.523638
MA0059.10.522232
MA0060.15.26847
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.362215
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.14.68138
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.946108
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.21.50246
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.23503
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.27276
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
CCNT2#90556.336201576962639.78880505817628e-050.00138960583318047
E2F1#186954.907389214879320.0003512818099256460.00352459611363479
E2F4#1874512.66806031528443.06319883889696e-060.000103399296553187
E2F6#187655.017155731697390.0003144978599297790.0032261901574704
EGR1#195854.988179094810140.0003237398000590710.00330605856833571
ELF1#199754.258097958807540.0007142416939776840.00572791893398874
GABPB1#255345.654147068945740.001776696502096670.0109067422548918
HEY1#2346254.040111043105710.0009288852205177990.00673927360511694
HMGN3#932446.542838178680470.00100801277768350.00721957526323462
IRF1#365957.63716375356393.84754333311872e-050.000723633312025187
IRF3#3661218.79278088459580.004339629777121510.0205853020072123
MAX#414956.452555509007128.93743970843928e-050.00130620943984004
MXI1#460135.976942977255580.008653004889366880.0329472885500962
MYC#460944.177825497287520.005691969036823440.0256754439699738
NFKB1#479044.390450739355070.004707732692524960.0222003384058615
NRF1#489937.326167668626540.004839689817117540.0226873901346532
PAX5#507945.335652424942260.002223389586187790.0127776693441846
SIN3A#2594255.408884726815140.0002159522671657270.00247871621392696
SMARCB1#6598310.95162946869440.001511872848343180.00965149684646171
SP1#666755.69838137814090.000166391843712550.00204132476982204
SP2#6668210.46141219753790.01353191183347140.04777591494459
SREBF1#6720218.80233977619530.004335312729587370.0205779087472333
TAF1#687253.343046285745290.002394600090870310.013525670031931
TBP#690853.706770687096390.001428755106721120.00918206600152897
TFAP2C#702248.647382887888180.0003390518878174050.00344826566479325
USF1#739145.089199421766370.00266867775360040.0147156301957905
YY1#752854.911170749853860.00034993140821360.00352595140785529



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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