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Coexpression cluster:C1954: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.26722,0.452433,0.500341,0.654974,0.454983,0.653236,1.73914,0.866061,0.321368,0.345702,1.50573,0.778743,1.37937,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.969147,0.500405,0.121147,0.645033,0.44943,1.35492,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.94379,0.27659,0.417272,0.432883,0.413782,0.654459,0.388123,1.48009,0.415749,0.580638,0.132849,0.451846,0.218848,0.533483,0.734485,0.609718,0.124583,1.16046,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,2.26785,1.53343,0.566575,0.330474,0.554326,1.23387,0.269111,2.02182,0.240727,2.11876,0.987729,0.543014,0.796279,0.934302,0.755403,0.873042,1.18161,1.37242,2.19312,3.47992,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,4.06216,1.76107,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.11542,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,2.6759,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,1.55197,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,2.06113,0.680988,0.87256,2.09294,0.577088,0.953361,0.526389,0.398598,1.15522,2.31232,0.736459,1.56426,0.827475,0.439798,0.54968,1.2893,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
|tfbs_overrepresentation_for_novel_motifs=1.26722,0.452433,0.500341,0.654974,0.454983,0.653236,1.73914,0.866061,0.321368,0.345702,1.50573,0.778743,1.37937,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.969147,0.500405,0.121147,0.645033,0.44943,1.35492,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.94379,0.27659,0.417272,0.432883,0.413782,0.654459,0.388123,1.48009,0.415749,0.580638,0.132849,0.451846,0.218848,0.533483,0.734485,0.609718,0.124583,1.16046,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,2.26785,1.53343,0.566575,0.330474,0.554326,1.23387,0.269111,2.02182,0.240727,2.11876,0.987729,0.543014,0.796279,0.934302,0.755403,0.873042,1.18161,1.37242,2.19312,3.47992,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,4.06216,1.76107,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,1.11542,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,2.6759,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,1.55197,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,2.06113,0.680988,0.87256,2.09294,0.577088,0.953361,0.526389,0.398598,1.15522,2.31232,0.736459,1.56426,0.827475,0.439798,0.54968,1.2893,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
|tfbs_overrepresentation_jaspar=MA0003.1;0.136928,MA0004.1;0.626788,MA0006.1;1.14863,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;2.48957,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;1.55893,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;1.48918,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;1.5062,MA0056.1;0,MA0057.1;0.554727,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;0.692739,MA0069.1;4.04346,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;15.2955,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;1.2972,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.412364,MA0089.1;0,MA0090.1;1.36977,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;0.779931,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;0.277033,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;0.333008,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;1.12758,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;0.880827,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,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;5.73519,MA0163.1;6.71536,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;7.22083,MA0102.2;1.66336,MA0258.1;0.914277,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:18, 22 January 2013


Full id: C1954_occipital_parietal_temporal_duodenum_brain_Neurons_medulloblastoma



Phase1 CAGE Peaks

Hg19::chr5:146833190..146833201,-p10@DPYSL3
Hg19::chr5:146833206..146833217,-p9@DPYSL3
Hg19::chr5:146833222..146833261,-p1@DPYSL3
Hg19::chr5:146833451..146833484,-p5@DPYSL3
Hg19::chr5:146833803..146833825,-p14@DPYSL3


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>

Uber Anatomy
Ontology termp-valuen
central nervous system1.03e-2981
nervous system2.88e-2889
anatomical cluster3.65e-26373
neural plate6.10e-2382
presumptive neural plate6.10e-2382
structure with developmental contribution from neural crest3.02e-22132
brain1.84e-2168
future brain1.84e-2168
neural tube4.00e-2156
neural rod4.00e-2156
future spinal cord4.00e-2156
neural keel4.00e-2156
neurectoderm1.84e-2086
ectoderm-derived structure6.56e-20171
ectoderm6.56e-20171
presumptive ectoderm6.56e-20171
adult organism1.32e-19114
tube1.50e-19192
regional part of nervous system2.79e-1953
regional part of brain2.79e-1953
multi-cellular organism9.23e-17656
anatomical conduit2.69e-16240
embryo2.83e-15592
regional part of forebrain3.92e-1541
forebrain3.92e-1541
anterior neural tube3.92e-1541
future forebrain3.92e-1541
multi-tissue structure6.93e-15342
pre-chordal neural plate8.56e-1561
ecto-epithelium1.18e-14104
germ layer1.56e-14560
germ layer / neural crest1.56e-14560
embryonic tissue1.56e-14560
presumptive structure1.56e-14560
germ layer / neural crest derived structure1.56e-14560
epiblast (generic)1.56e-14560
embryonic structure2.19e-14564
organ system subdivision2.39e-14223
brain grey matter2.96e-1434
gray matter2.96e-1434
telencephalon5.78e-1434
regional part of telencephalon3.52e-1332
developing anatomical structure4.12e-13581
cerebral hemisphere5.05e-1332
anatomical group2.52e-12625
epithelium2.53e-12306
anatomical system4.01e-12624
cell layer5.90e-12309
splanchnic layer of lateral plate mesoderm1.42e-1083
cerebral cortex4.91e-1025
pallium4.91e-1025
artery1.38e-0942
arterial blood vessel1.38e-0942
arterial system1.38e-0942
organ part4.01e-09218
regional part of cerebral cortex1.45e-0822
organ4.89e-08503
neocortex1.46e-0720
systemic artery2.13e-0733
systemic arterial system2.13e-0733
epithelial tube open at both ends2.76e-0759
blood vessel2.76e-0759
blood vasculature2.76e-0759
vascular cord2.76e-0759
posterior neural tube2.84e-0715
chordal neural plate2.84e-0715
heart3.30e-0724
primitive heart tube3.30e-0724
primary heart field3.30e-0724
anterior lateral plate mesoderm3.30e-0724
heart tube3.30e-0724
heart primordium3.30e-0724
cardiac mesoderm3.30e-0724
cardiogenic plate3.30e-0724
heart rudiment3.30e-0724
primary circulatory organ9.47e-0727


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)
MA0003.10.136928
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.12.48957
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
MA0041.11.55893
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.11.48918
MA0051.10.731787
MA0052.11.03442
MA0055.11.5062
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.14.04346
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.115.2955
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.11.36977
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
MA0106.10.779931
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
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.15.73519
MA0163.16.71536
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.27.22083
MA0102.21.66336
MA0258.10.914277
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
CTCF#1066455.360256373075030.0002259278299937090.00250192732867277
EGR1#195843.990543275848110.0067800983001440.0287754667737621
RAD21#5885510.35503389545638.39503550283973e-060.000229881781038563
SMC3#9126515.04493284493281.29633924985553e-065.16749522578862e-05
YY1#752854.911170749853860.00034993140821360.00353106148235943
ZNF143#770238.100525931336740.003624870512090980.0183366197526044



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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