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{{Coexpression_clusters
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A0027.1;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;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,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;3.06856,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;1.51122,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;1.02755,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;1.33363,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;2.66544,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;3.64588,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;2.1393,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;1.53138,MA0151.1;0,MA0152.1;1.84959,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;2.98688,MA0161.1;0,MA0162.1;0.640035,MA0163.1;0.0725493,MA0164.1;3.43559,MA0080.2;0.535868,MA0018.2;2.02192,MA0099.2;1.85039,MA0079.2;0.00910927,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2091_Hepatic_spleen_Endothelial_lung_lymph_adipose_acute
|id=C2091
}}

Latest revision as of 11:58, 17 September 2013


Full id: C2091_Hepatic_spleen_Endothelial_lung_lymph_adipose_acute



Phase1 CAGE Peaks

Hg19::chr11:10590118..10590129,-p5@LYVE1
Hg19::chr11:10590144..10590159,-p3@LYVE1
Hg19::chr11:10590173..10590191,-p1@LYVE1
Hg19::chr11:10590198..10590230,-p2@LYVE1


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 organism6.29e-66114
neural tube9.55e-2656
neural rod9.55e-2656
future spinal cord9.55e-2656
neural keel9.55e-2656
regional part of nervous system9.56e-2453
regional part of brain9.56e-2453
anatomical conduit3.02e-23240
anatomical cluster2.34e-22373
tube6.52e-22192
regional part of forebrain2.12e-2041
forebrain2.12e-2041
anterior neural tube2.12e-2041
future forebrain2.12e-2041
brain2.69e-2068
future brain2.69e-2068
central nervous system1.29e-1981
neural plate2.45e-1882
presumptive neural plate2.45e-1882
neurectoderm1.95e-1786
nervous system7.76e-1789
telencephalon4.23e-1634
brain grey matter4.26e-1634
gray matter4.26e-1634
structure with developmental contribution from neural crest1.25e-15132
regional part of telencephalon6.58e-1532
cerebral hemisphere8.61e-1532
organ system subdivision1.24e-14223
regional part of cerebral cortex6.20e-1322
cell layer1.60e-12309
ecto-epithelium1.70e-12104
blood vessel endothelium1.91e-1218
endothelium1.91e-1218
cardiovascular system endothelium1.91e-1218
pre-chordal neural plate7.32e-1261
epithelium1.04e-11306
neocortex1.21e-1120
multi-tissue structure7.59e-11342
cerebral cortex1.07e-1025
pallium1.07e-1025
multi-cellular organism3.40e-10656
anatomical system2.59e-09624
anatomical group3.20e-09625
simple squamous epithelium3.24e-0922
squamous epithelium1.95e-0825
embryonic structure2.68e-08564
germ layer3.15e-08560
germ layer / neural crest3.15e-08560
embryonic tissue3.15e-08560
presumptive structure3.15e-08560
germ layer / neural crest derived structure3.15e-08560
epiblast (generic)3.15e-08560
ectoderm-derived structure9.41e-08171
ectoderm9.41e-08171
presumptive ectoderm9.41e-08171
developing anatomical structure1.01e-07581
embryo1.22e-07592
basal ganglion2.40e-079
nuclear complex of neuraxis2.40e-079
aggregate regional part of brain2.40e-079
collection of basal ganglia2.40e-079
cerebral subcortex2.40e-079
neural nucleus3.87e-079
nucleus of brain3.87e-079
splanchnic layer of lateral plate mesoderm5.27e-0783
vessel5.71e-0768
organ6.64e-07503
vasculature9.35e-0778
vascular system9.35e-0778


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
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
MA0071.13.06856
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.12.66544
MA0113.10.886811
MA0114.10.447443
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
MA0141.13.64588
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.22.1393
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.11.53138
MA0151.10
MA0152.11.84959
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.12.98688
MA0161.10
MA0162.10.640035
MA0163.10.0725493
MA0164.13.43559
MA0080.20.535868
MA0018.22.02192
MA0099.21.85039
MA0079.20.00910927
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235348.99795530889440.0001525147711168630.00194534564981364
GATA2#2624412.7449317335543.78864877853583e-050.000719684775884874
JUN#3725412.51282919233634.07770316866756e-050.000741677536106707
JUND#372746.994663941871030.000417684217818580.00390952877081508
MAFF#23764456.31535648994529.92458849374232e-085.83294371242518e-06
MAFK#7975427.10073313782991.85228494563408e-066.84297090332784e-05
SPI1#668848.204323508522730.000220661881527680.00249008171203343



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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