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Coexpression cluster:C1789: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=2.1885,1.20042,1.25018,0.654974,0.454983,0.653236,0.733342,0.324142,0.859849,1.70183,0.621241,0.778743,0.752887,0.721271,1.14971,0.478935,3.63308,0.395009,0.784337,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,1.16016,0.233785,0.598009,1.00172,1.68319,0.27659,2.81341,0.432883,8.5602,0.654459,0.388123,0.815792,0.415749,0.580638,0.132849,0.451846,2.90891,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,1.22844,0.688844,2.37491,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,21.1054,1.23387,7.98498,0.709554,0.240727,2.11876,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,11.6455,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,10.3853,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,2.32322,0.437618,0.512457,1.05402,0.494368,1.52665,1.37132,0.412056,10.1935,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,1.18046,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.526389,13.8832,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,1.73625,0.443702
|tfbs_overrepresentation_for_novel_motifs=2.1885,1.20042,1.25018,0.654974,0.454983,0.653236,0.733342,0.324142,0.859849,1.70183,0.621241,0.778743,0.752887,0.721271,1.14971,0.478935,3.63308,0.395009,0.784337,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,1.16016,0.233785,0.598009,1.00172,1.68319,0.27659,2.81341,0.432883,8.5602,0.654459,0.388123,0.815792,0.415749,0.580638,0.132849,0.451846,2.90891,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,1.22844,0.688844,2.37491,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,21.1054,1.23387,7.98498,0.709554,0.240727,2.11876,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,11.6455,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,10.3853,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,2.32322,0.437618,0.512457,1.05402,0.494368,1.52665,1.37132,0.412056,10.1935,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,1.18046,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.526389,13.8832,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,1.73625,0.443702
|tfbs_overrepresentation_jaspar=MA0003.1;16.6523,MA0004.1;0.626788,MA0006.1;4.0459,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;3.07977,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,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;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;1.05691,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;3.88786,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;3.31872,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;0.175503,MA0106.1;3.06034,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,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;3.87914,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;1.35428,MA0147.1;2.66688,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;6.53669,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;3.24989,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;5.79564,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;7.37801,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;9.40685,MA0102.2;1.66336,MA0258.1;2.47453,MA0259.1;1.80881,MA0442.1;0
}}
}}

Revision as of 20:11, 22 January 2013


Full id: C1789_Small_MCF7_occipital_temporal_parietal_duodenum_brain



Phase1 CAGE Peaks

Hg19::chr17:61043561..61043617,+p@chr17:61043561..61043617
+
Hg19::chr17:61043618..61043648,+p@chr17:61043618..61043648
+
Hg19::chr17:61043653..61043672,+p@chr17:61043653..61043672
+
Hg19::chr17:61043790..61043869,+p@chr17:61043790..61043869
+
Hg19::chr17:61043870..61043902,+p@chr17:61043870..61043902
+


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
respiratory epithelial cell9.65e-0813
Uber Anatomy
Ontology termp-valuen
neural tube1.72e-2356
neural rod1.72e-2356
future spinal cord1.72e-2356
neural keel1.72e-2356
regional part of nervous system2.32e-2253
regional part of brain2.32e-2253
central nervous system4.21e-2281
nervous system5.57e-2289
brain2.17e-2168
future brain2.17e-2168
regional part of forebrain1.71e-1941
forebrain1.71e-1941
anterior neural tube1.71e-1941
future forebrain1.71e-1941
telencephalon1.67e-1834
brain grey matter3.34e-1834
gray matter3.34e-1834
ecto-epithelium6.86e-18104
cerebral hemisphere7.68e-1832
ectoderm-derived structure1.41e-17171
ectoderm1.41e-17171
presumptive ectoderm1.41e-17171
regional part of telencephalon1.53e-1732
anatomical system1.71e-16624
anatomical group4.12e-16625
multi-cellular organism8.19e-16656
neural plate5.78e-1582
presumptive neural plate5.78e-1582
cerebral cortex8.10e-1425
pallium8.10e-1425
regional part of cerebral cortex2.16e-1322
neurectoderm7.93e-1386
neocortex1.08e-1220
organ1.30e-12503
pre-chordal neural plate7.21e-1261
structure with developmental contribution from neural crest2.46e-11132
organ system subdivision1.28e-10223
embryonic structure4.65e-10564
developing anatomical structure5.54e-10581
organ part2.11e-09218
germ layer2.56e-09560
germ layer / neural crest2.56e-09560
embryonic tissue2.56e-09560
presumptive structure2.56e-09560
germ layer / neural crest derived structure2.56e-09560
epiblast (generic)2.56e-09560
embryo5.25e-09592
epithelium1.43e-08306
cell layer3.89e-08309
tube3.19e-07192
anatomical conduit7.66e-07240
multi-tissue structure9.03e-07342


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)
MA0003.116.6523
MA0004.10.626788
MA0006.14.0459
MA0007.10.606704
MA0009.11.11255
MA0014.13.07977
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.13.88786
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.13.31872
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
MA0105.10.175503
MA0106.13.06034
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
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
MA0139.13.87914
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.11.35428
MA0147.12.66688
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.26.53669
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.23.24989
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.15.79564
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.17.37801
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.29.40685
MA0102.21.66336
MA0258.12.47453
MA0259.11.80881
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-050.00139036177270621
CTCF#1066455.360256373075030.0002259278299937090.00249768991602762
CTCFL#140690519.74647435897443.32745051287657e-071.6572036438451e-05
E2F1#186954.907389214879320.0003512818099256460.00352730708074459
E2F6#187655.017155731697390.0003144978599297790.00322777535310595
EGR1#195854.988179094810140.0003237398000590710.00330767569735564
HMGN3#932458.178547723350592.73180911341838e-050.000581903756875998
NR3C1#2908514.9730233311731.32777388277837e-065.2427741604344e-05
TRIM28#10155311.15431502715750.001433159271529250.00920187637767388
ZBTB7A#5134157.35190930787594.65425347594289e-050.000815716695375062



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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