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Coexpression cluster:C2752: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;4.74396,MA0004.1;2.8475,MA0006.1;2.26728,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;4.49713,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,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;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;1.28887,MA0056.1;0,MA0057.1;1.28333,MA0058.1;3.66086,MA0059.1;1.47051,MA0060.1;0.393285,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;0.100363,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,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;4.51906,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;4.80079,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;2.17614,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.70272,MA0146.1;0.8309,MA0147.1;7.75267,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;2.01147,MA0138.2;0.928035,MA0002.2;0.98779,MA0137.2;0.558189,MA0104.2;9.60872,MA0047.2;0.856092,MA0112.2;1.65877,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.533581,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;2.03616,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.06783,MA0163.1;1.37853,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;5.41326,MA0102.2;1.75932,MA0258.1;1.07498,MA0259.1;2.06681,MA0442.1;0
}}
}}

Revision as of 20:53, 22 January 2013


Full id: C2752_pineal_duodenum_occipital_Fibroblast_lung_amygdala_insula



Phase1 CAGE Peaks

Hg19::chr3:74663774..74663788,-p@chr3:74663774..74663788
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Hg19::chr3:74663803..74663825,-p@chr3:74663803..74663825
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Hg19::chr3:74663830..74663873,-p@chr3:74663830..74663873
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Hg19::chr3:74663957..74663973,-p@chr3:74663957..74663973
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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>

Uber Anatomy
Ontology termp-valuen
adult organism6.62e-30114
neural tube1.27e-2956
neural rod1.27e-2956
future spinal cord1.27e-2956
neural keel1.27e-2956
regional part of nervous system1.43e-2853
regional part of brain1.43e-2853
regional part of forebrain9.72e-2741
forebrain9.72e-2741
anterior neural tube9.72e-2741
future forebrain9.72e-2741
central nervous system1.07e-2681
neural plate4.85e-2682
presumptive neural plate4.85e-2682
neurectoderm1.69e-2486
ecto-epithelium6.09e-24104
nervous system3.22e-2389
structure with developmental contribution from neural crest5.36e-23132
brain8.83e-2368
future brain8.83e-2368
telencephalon1.70e-2234
brain grey matter2.51e-2234
gray matter2.51e-2234
ectoderm-derived structure7.28e-22171
ectoderm7.28e-22171
presumptive ectoderm7.28e-22171
cerebral hemisphere1.12e-2132
regional part of telencephalon2.51e-2132
pre-chordal neural plate3.20e-2161
regional part of cerebral cortex1.98e-1822
tube3.41e-18192
cerebral cortex4.06e-1825
pallium4.06e-1825
epithelium7.86e-18306
cell layer3.78e-17309
neocortex7.45e-1720
anatomical conduit1.31e-16240
anatomical cluster1.94e-15373
multi-tissue structure3.39e-15342
multi-cellular organism4.05e-15656
systemic artery1.80e-1333
systemic arterial system1.80e-1333
anatomical system2.68e-13624
anatomical group3.84e-13625
artery9.66e-1342
arterial blood vessel9.66e-1342
arterial system9.66e-1342
organ system subdivision3.84e-11223
embryonic structure7.78e-09564
tissue8.64e-09773
embryo9.32e-09592
developing anatomical structure1.67e-08581
germ layer2.64e-08560
germ layer / neural crest2.64e-08560
embryonic tissue2.64e-08560
presumptive structure2.64e-08560
germ layer / neural crest derived structure2.64e-08560
epiblast (generic)2.64e-08560
organ7.22e-08503
muscle tissue7.61e-0864
musculature7.61e-0864
musculature of body7.61e-0864
epithelial tube open at both ends1.23e-0759
blood vessel1.23e-0759
blood vasculature1.23e-0759
vascular cord1.23e-0759
paraxial mesoderm1.60e-0772
presumptive paraxial mesoderm1.60e-0772
organ part2.10e-07218
skeletal muscle tissue2.57e-0762
striated muscle tissue2.57e-0762
myotome2.57e-0762
dense mesenchyme tissue3.12e-0773
somite4.61e-0771
presomitic mesoderm4.61e-0771
presumptive segmental plate4.61e-0771
dermomyotome4.61e-0771
trunk paraxial mesoderm4.61e-0771
aorta9.91e-0721
aortic system9.91e-0721


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)
MA0003.14.74396
MA0004.12.8475
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.14.49713
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.11.28333
MA0058.13.66086
MA0059.11.47051
MA0060.10.393285
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
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
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
MA0093.14.51906
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.14.80079
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
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
MA0145.11.70272
MA0146.10.8309
MA0147.17.75267
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.22.01147
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.29.60872
MA0047.20.856092
MA0112.21.65877
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.25.41326
MA0102.21.75932
MA0258.11.07498
MA0259.12.06681
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
TAF1#687243.343046285745290.008005664898701650.0322919680347405



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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