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Coexpression cluster:C1245: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.247072,0.384703,1.31224,0.343148,0.52784,0.604235,0.226729,0.224331,0.0544999,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,1.43406,0.19568,0.0986842,0.384762,0.0646572,0.520063,0.338096,0.430372,0.670692,0.164928,1.28759,0.346214,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.442372,0.305874,0.529001,0.282922,0.207499,0.307642,0.459366,0.541549,0.340293,5.01707,0.415364,0.60533,0.486696,3.71358,0.346342,0.684981,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,0.562713,2.07128,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,1.78001,1.0929,0.179863,0.503161,0.156354,0.782748,0.850825,0.424224,3.23447,0.798651,0.625403,0.229431,1.04131,0.131619,0.097572,0.146388,1.69317,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,3.87933,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,1.42509,0.474472,0.762789,0.26701,1.0846,2.83562,0.525076,1.53817,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,5.97124,0.469685,1.28879,1.24743,2.10682,1.70417,1.21002,1.4603,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.703388,0.241704,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.00626991
|tfbs_overrepresentation_for_novel_motifs=0.392069,0.247072,0.384703,1.31224,0.343148,0.52784,0.604235,0.226729,0.224331,0.0544999,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,1.43406,0.19568,0.0986842,0.384762,0.0646572,0.520063,0.338096,0.430372,0.670692,0.164928,1.28759,0.346214,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.442372,0.305874,0.529001,0.282922,0.207499,0.307642,0.459366,0.541549,0.340293,5.01707,0.415364,0.60533,0.486696,3.71358,0.346342,0.684981,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,0.562713,2.07128,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,1.78001,1.0929,0.179863,0.503161,0.156354,0.782748,0.850825,0.424224,3.23447,0.798651,0.625403,0.229431,1.04131,0.131619,0.097572,0.146388,1.69317,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,3.87933,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,1.42509,0.474472,0.762789,0.26701,1.0846,2.83562,0.525076,1.53817,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,5.97124,0.469685,1.28879,1.24743,2.10682,1.70417,1.21002,1.4603,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.703388,0.241704,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.00626991
|tfbs_overrepresentation_jaspar=MA0003.1;0.358813,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0156227,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.120314,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.362619,MA0056.1;0,MA0057.1;0.115382,MA0058.1;0.406232,MA0059.1;2.75581,MA0060.1;0.224688,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;2.88073,MA0068.1;0.946606,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.0282921,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.252594,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;4.99343,MA0101.1;0.347695,MA0103.1;1.58817,MA0105.1;0.104569,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;1.8902,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;1.36091,MA0115.1;1.21667,MA0116.1;1.39213,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;2.87791,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;1.04059,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.0807715,MA0146.1;0.0610556,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.0553061,MA0138.2;0.704862,MA0002.2;1.15032,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;1.41281,MA0065.2;2.65697,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;6.09516,MA0155.1;1.36741,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.0249953,MA0163.1;3.79643,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;2.64985,MA0099.2;0.572,MA0079.2;0.0441319,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;3.04904,MA0442.1;0
}}
}}

Revision as of 19:48, 22 January 2013


Full id: C1245_normal_Neurons_parietal_temporal_neuroectodermal_occipital_basal



Phase1 CAGE Peaks

Hg19::chr19:9964647..9964684,-p@chr19:9964647..9964684
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Hg19::chr19:9964687..9964698,-p@chr19:9964687..9964698
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Hg19::chr19:9964700..9964741,-p@chr19:9964700..9964741
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Hg19::chr19:9964743..9964754,-p@chr19:9964743..9964754
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Hg19::chr19:9964757..9964786,-p@chr19:9964757..9964786
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Hg19::chr19:9964795..9964828,-p@chr19:9964795..9964828
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Hg19::chr19:9965051..9965063,-p@chr19:9965051..9965063
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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
neuronal stem cell3.96e-088
fat cell1.56e-0715
neuron7.28e-076
neuroblast7.28e-076
electrically signaling cell7.28e-076
Uber Anatomy
Ontology termp-valuen
nervous system2.78e-4189
central nervous system4.27e-4081
neural tube1.16e-3656
neural rod1.16e-3656
future spinal cord1.16e-3656
neural keel1.16e-3656
regional part of nervous system2.19e-3453
regional part of brain2.19e-3453
brain2.01e-3068
future brain2.01e-3068
regional part of forebrain7.14e-2941
forebrain7.14e-2941
anterior neural tube7.14e-2941
future forebrain7.14e-2941
neurectoderm1.72e-2886
neural plate1.51e-2582
presumptive neural plate1.51e-2582
brain grey matter1.77e-2534
gray matter1.77e-2534
telencephalon9.21e-2534
cerebral hemisphere5.03e-2432
regional part of telencephalon7.15e-2432
ectoderm-derived structure1.33e-21171
ectoderm1.33e-21171
presumptive ectoderm1.33e-21171
cerebral cortex1.08e-1925
pallium1.08e-1925
ecto-epithelium3.99e-19104
pre-chordal neural plate1.39e-1861
adult organism1.47e-18114
regional part of cerebral cortex1.39e-1722
neocortex4.70e-1620
organ system subdivision3.68e-15223
structure with developmental contribution from neural crest4.98e-15132
posterior neural tube6.58e-0915
chordal neural plate6.58e-0915
segmental subdivision of nervous system1.85e-0713
basal ganglion2.55e-079
nuclear complex of neuraxis2.55e-079
aggregate regional part of brain2.55e-079
collection of basal ganglia2.55e-079
cerebral subcortex2.55e-079
neural nucleus3.17e-079
nucleus of brain3.17e-079
temporal lobe7.48e-076
segmental subdivision of hindbrain7.63e-0712
hindbrain7.63e-0712
presumptive hindbrain7.63e-0712


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)
MA0003.10.358813
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.12.75581
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.12.88073
MA0068.10.946606
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0282921
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.14.99343
MA0101.10.347695
MA0103.11.58817
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.21.8902
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.11.36091
MA0115.11.21667
MA0116.11.39213
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.12.87791
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.11.04059
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.0610556
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.0553061
MA0138.20.704862
MA0002.21.15032
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.21.41281
MA0065.22.65697
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.16.09516
MA0155.11.36741
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.13.79643
MA0164.10.678332
MA0080.20.344472
MA0018.22.64985
MA0099.20.572
MA0079.20.0441319
MA0102.21.51913
MA0258.10.245543
MA0259.13.04904
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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