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Coexpression cluster:C2327: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,0.462021,1.68405,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,1.63433,1.09415,0.433165,0.911389,0.49475,0.598278,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.648765,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,1.28263,1.32819,0.336329,0.859396,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.17995,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.749003,0.465545,1.1057,2.59018,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,1.00204,1.24902,0.383416,0.824835,1.65997,0.917558,1.28873,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,0.359498
|tfbs_overrepresentation_jaspar=MA0003.1;0.720743,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;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;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.946082,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;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;1.22348,MA0106.1;0.869173,MA0107.1;1.1497,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;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;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;1.09982,MA0145.1;0.195821,MA0146.1;0.481,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.10559,MA0138.2;0.928035,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;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;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.06783,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;1.38179,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:34, 22 January 2013


Full id: C2327_Hepatocyte_spinal_liver_normal_optic_tubular_corpus



Phase1 CAGE Peaks

Hg19::chr15:102029900..102029917,-p1@PCSK6
Hg19::chr1:155099927..155099964,+p4@EFNA1
Hg19::chr3:133493719..133493723,+p11@TF
Hg19::chr3:133497553..133497587,+p@chr3:133497553..133497587
+


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

GO IDGO nameFDR corrected p-value
GO:0007267cell-cell signaling0.000805307766608751
GO:0015682ferric iron transport0.00267131755563405
GO:0015091ferric iron transmembrane transporter activity0.00267131755563405
GO:0031643positive regulation of myelination0.00267131755563405
GO:0031641regulation of myelination0.00854746129459153
GO:0005381iron ion transmembrane transporter activity0.00915745506820525
GO:0046875ephrin receptor binding0.00915745506820525
GO:0031646positive regulation of neurological process0.0106830685655978
GO:0014070response to organic cyclic substance0.0130559306666949
GO:0030139endocytic vesicle0.021351044647696
GO:0031644regulation of neurological process0.021351044647696
GO:0042552myelination0.021351044647696
GO:0046915transition metal ion transmembrane transporter activity0.021351044647696
GO:0007272ensheathment of neurons0.021351044647696
GO:0006953acute-phase response0.021351044647696
GO:0008366axon ensheathment0.021351044647696
GO:0004289subtilase activity0.0219408985330224
GO:0008199ferric iron binding0.0219408985330224
GO:0001508regulation of action potential0.0224694898948729
GO:0001666response to hypoxia0.024322277194695
GO:0007154cell communication0.024322277194695
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.024322277194695
GO:0055072iron ion homeostasis0.024322277194695
GO:0006879cellular iron ion homeostasis0.024322277194695
GO:0006826iron ion transport0.024322277194695
GO:0010033response to organic substance0.0254345330902621
GO:0002526acute inflammatory response0.0311925781763437
GO:0000041transition metal ion transport0.0388092979149681
GO:0048503GPI anchor binding0.0462550364175995



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>disease_data<br>

Cell Type
Ontology termp-valuen
endodermal cell2.08e-1158
epithelial cell3.71e-07253
epithelial cell of alimentary canal4.52e-0720
Uber Anatomy
Ontology termp-valuen
adult organism8.51e-46114
neural tube4.74e-3756
neural rod4.74e-3756
future spinal cord4.74e-3756
neural keel4.74e-3756
regional part of nervous system7.92e-3453
regional part of brain7.92e-3453
organ system subdivision2.78e-33223
regional part of forebrain5.18e-3041
forebrain5.18e-3041
anterior neural tube5.18e-3041
future forebrain5.18e-3041
brain grey matter1.42e-2634
gray matter1.42e-2634
telencephalon3.41e-2634
brain7.01e-2668
future brain7.01e-2668
anatomical cluster3.59e-25373
central nervous system7.21e-2581
regional part of telencephalon2.18e-2432
cerebral hemisphere4.71e-2432
neural plate6.95e-2482
presumptive neural plate6.95e-2482
anatomical conduit1.79e-23240
multi-tissue structure9.98e-23342
neurectoderm7.13e-2286
nervous system9.61e-2289
ecto-epithelium9.69e-22104
tube1.00e-19192
pre-chordal neural plate3.47e-1961
structure with developmental contribution from neural crest1.85e-18132
regional part of cerebral cortex1.45e-1722
cerebral cortex1.55e-1725
pallium1.55e-1725
neocortex1.17e-1520
organ part7.86e-15218
organ8.86e-15503
endoderm-derived structure1.65e-13160
endoderm1.65e-13160
presumptive endoderm1.65e-13160
epithelium1.77e-13306
cell layer4.88e-13309
subdivision of digestive tract7.90e-13118
digestive system8.85e-13145
digestive tract8.85e-13145
primitive gut8.85e-13145
ectoderm-derived structure1.83e-12171
ectoderm1.83e-12171
presumptive ectoderm1.83e-12171
multi-cellular organism3.70e-12656
anatomical system6.99e-11624
neural nucleus8.29e-119
nucleus of brain8.29e-119
anatomical group8.81e-11625
embryo1.45e-10592
foregut2.28e-1087
basal ganglion2.71e-109
nuclear complex of neuraxis2.71e-109
aggregate regional part of brain2.71e-109
collection of basal ganglia2.71e-109
cerebral subcortex2.71e-109
developing anatomical structure6.04e-10581
embryonic structure1.35e-08564
telencephalic nucleus1.37e-087
posterior neural tube2.74e-0815
chordal neural plate2.74e-0815
germ layer2.91e-08560
germ layer / neural crest2.91e-08560
embryonic tissue2.91e-08560
presumptive structure2.91e-08560
germ layer / neural crest derived structure2.91e-08560
epiblast (generic)2.91e-08560
brainstem7.44e-086
temporal lobe2.14e-076
gyrus3.67e-076
epithelium of foregut-midgut junction4.57e-0725
anatomical boundary4.57e-0725
hepatobiliary system4.57e-0725
foregut-midgut junction4.57e-0725
septum transversum4.57e-0725
digestive tract diverticulum8.00e-0723
endo-epithelium9.70e-0782
Disease
Ontology termp-valuen
carcinoma9.66e-09106


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
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
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
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
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
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
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.481
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
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
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.38179
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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2327&oldid=2570838"