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Coexpression cluster:C2556: Difference between revisions

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{{Coexpression_clusters
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342,0.284496,0.512545,0.512178,0.0515768,0.829402,0.684899,0.263302,0.552023,0.180735,0.0646927,0.216102,0.0355932,0.109605,0.397869,0.217863,0.226491,0.417131,0.463987,0.0782409,0.503881,0.454761,0.271678,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.0458396,0.438176,0.349112,8.43794e-05,0.0862349,0.0531591,0.461541,0.0135171,0.382854,0.598787,0.478745,0.611661,0.00716065,0.475047,0.557967,0.608127,0.282281,0.245336,0.2536,0.00307371,0.564333,0.0362483,0.387134,0.559969,0.358813,2.7525e-08,0.574252,0.493455,0.346636,0.125876,0.348802,0.476541,0.215342,0.447581,0.0187686,0.254628,0.0382032,0.0286377,0.416962,0.0806585,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.0383658,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.00397584,0.000302406,0.125087,0.00197745,0.321224,0.469461,0.325254,0.266651,0.00871319,0.00250962,0.249415,0.00479755,0.0453548,0.427316,0.00170225,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.000165013,0.290415,0.353147,0.112422,0.170886,0.00399713,0.00686166,0.284866,0.0887542,0.267811,0.00865954,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.0015944,0.15696,0.129351,0.141936,0.0786166,0.276997,0.00170949,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.000100809,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.00080978,0.262022,0.00433276,0.00394881,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.036547,0.181895,0.253768,0.30702,0.202977,0.00095279,0.327002,0.28543,0.222656,0.00239762,0.127111,0.259989,0.390754,0.355805,0.00461365,0.108118,0.0371525,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.0944985,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.000477314,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.00376397,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.00347609,0.362898,0.302133,0.40806,0.151361,0.279606,0.00499935,0.150674,0.251128,0.246177,0.0103202,0.35852,0.318525,0.000113915,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.000934607,0.132374,0.285122,0.22741,0.203996,0.00445319,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,1.42265,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,3.37992,0.809319,0.532789,0.559384,1.05593,0.471262,1.67497,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.285913,3.15145,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,1.31558,1.08066,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,2.42873,1.54953,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.17995,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,1.88833,0.632569,8.26246,0.594299,2.58439,1.40954,0.717043,1.46636,0.489254,2.51097,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,3.77577,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,1.73115,3.26642,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,2.26519,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,1.47036,0.997702,0.843324,0.423521,0.820225,1.4289|tfbs_overrepresentation_jaspar=MA0003.1;1.8989,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.896009,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;4.04183,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;1.30988,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.791759,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;1.80156,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;2.13662,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.656404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|full_id=C2556_Fibroblast_corpus_medulla_gastrointestinal_occipital_temporal_cerebellum
|id=C2556
}}

Latest revision as of 12:08, 17 September 2013


Full id: C2556_Fibroblast_corpus_medulla_gastrointestinal_occipital_temporal_cerebellum



Phase1 CAGE Peaks

Hg19::chr1:204797749..204797855,+p1@NFASC
Hg19::chr1:240255166..240255197,+p1@FMN2
Hg19::chr1:240255198..240255211,+p3@FMN2
Hg19::chr1:240255217..240255249,+p2@FMN2


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
fibroblast1.43e-1676
skin fibroblast2.31e-1123
non-terminally differentiated cell1.33e-09106
neurectodermal cell1.91e-0859
neural cell2.17e-0725
Uber Anatomy
Ontology termp-valuen
nervous system7.38e-3889
central nervous system2.06e-3681
neural tube2.72e-3456
neural rod2.72e-3456
future spinal cord2.72e-3456
neural keel2.72e-3456
neural plate6.49e-3382
presumptive neural plate6.49e-3382
regional part of nervous system2.63e-3253
regional part of brain2.63e-3253
brain2.67e-3168
future brain2.67e-3168
neurectoderm1.37e-2986
ectoderm-derived structure2.52e-29171
ectoderm2.52e-29171
presumptive ectoderm2.52e-29171
structure with developmental contribution from neural crest3.60e-29132
ecto-epithelium1.65e-28104
regional part of forebrain6.17e-2641
forebrain6.17e-2641
anterior neural tube6.17e-2641
future forebrain6.17e-2641
pre-chordal neural plate3.01e-2461
brain grey matter4.21e-2234
gray matter4.21e-2234
telencephalon4.82e-2234
cerebral hemisphere6.10e-2132
regional part of telencephalon8.47e-2132
adult organism2.08e-17114
cerebral cortex1.28e-1625
pallium1.28e-1625
multi-tissue structure2.65e-16342
regional part of cerebral cortex6.26e-1622
anatomical cluster4.85e-15373
organ system subdivision5.34e-15223
epithelium5.42e-15306
cell layer1.35e-14309
neocortex1.37e-1420
multi-cellular organism3.23e-12656
anatomical system5.99e-11624
anatomical group9.65e-11625
tube1.29e-10192
skin of body4.36e-1041
integument7.25e-1046
integumental system7.25e-1046
anatomical conduit1.44e-09240
organ part1.77e-09218
posterior neural tube2.11e-0915
chordal neural plate2.11e-0915
dense mesenchyme tissue8.31e-0873
segmental subdivision of nervous system1.09e-0713
segmental subdivision of hindbrain1.46e-0712
hindbrain1.46e-0712
presumptive hindbrain1.46e-0712
organ1.70e-07503
paraxial mesoderm1.99e-0772
presumptive paraxial mesoderm1.99e-0772
surface structure3.78e-0799
somite5.10e-0771
presomitic mesoderm5.10e-0771
presumptive segmental plate5.10e-0771
dermomyotome5.10e-0771
trunk paraxial mesoderm5.10e-0771
embryo5.43e-07592
basal ganglion5.99e-079
nuclear complex of neuraxis5.99e-079
aggregate regional part of brain5.99e-079
collection of basal ganglia5.99e-079
cerebral subcortex5.99e-079
neural nucleus6.20e-079
nucleus of brain6.20e-079


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)
MA0003.11.8989
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.10.577281
MA0019.10.873355
MA0024.14.04183
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.80156
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.12.13662
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.98562
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.22.43626
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.80246
MA0163.14.57046
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.72671
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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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