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Coexpression cluster:C2709: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,1.44778,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.911389,1.23824,1.00622,2.13139,0.740899,0.463978,1.72725,0.493145,0.66492,0.539378,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,1.5667,0.402607,1.28263,1.32819,1.6033,0.859396,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.72726,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,1.15724,0.354969,1.15558,0.939507,0.749003,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,2.51097,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,0.521611,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.359498
|tfbs_overrepresentation_jaspar=MA0003.1;1.05935,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.524262,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;0.791759,MA0056.1;0,MA0057.1;1.28333,MA0058.1;0.605914,MA0059.1;0.604454,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;0.0343867,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;2.31225,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;1.90157,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;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;0.569905,MA0146.1;0.481,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.931615,MA0035.2;0.778873,MA0039.2;0.257871,MA0138.2;0.928035,MA0002.2;0.98779,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.577908,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;2.64806,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;1.1691,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.57817,MA0163.1;1.90765,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.869502,MA0102.2;1.75932,MA0258.1;1.07498,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:51, 22 January 2013


Full id: C2709_pituitary_pineal_retinoblastoma_argyrophil_carcinoid_cerebellum_iPS



Phase1 CAGE Peaks

Hg19::chr2:98962946..98962963,+p1@CNGA3
Hg19::chr3:19189589..19189626,+p5@KCNH8
Hg19::chr5:89854580..89854593,+p4@GPR98
Hg19::chr5:89854867..89854899,+p@chr5:89854867..89854899
+


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:0005249voltage-gated potassium channel activity0.00354585496442826
GO:0005267potassium channel activity0.00354585496442826
GO:0007601visual perception0.00354585496442826
GO:0050953sensory perception of light stimulus0.00354585496442826
GO:0022843voltage-gated cation channel activity0.00354585496442826
GO:0006813potassium ion transport0.00354585496442826
GO:0022832voltage-gated channel activity0.00423142055570313
GO:0005244voltage-gated ion channel activity0.00423142055570313
GO:0048496maintenance of organ identity0.00494481231918518
GO:0005261cation channel activity0.00571673838554059
GO:0046873metal ion transmembrane transporter activity0.00687851363887805
GO:0022836gated channel activity0.00687851363887805
GO:0015672monovalent inorganic cation transport0.00693836414094316
GO:0019002GMP binding0.00785864363720596
GO:0030553cGMP binding0.00785864363720596
GO:0005216ion channel activity0.00785864363720596
GO:0030001metal ion transport0.00785864363720596
GO:0022838substrate specific channel activity0.00785864363720596
GO:0022803passive transmembrane transporter activity0.00785864363720596
GO:0015267channel activity0.00785864363720596
GO:0045494photoreceptor cell maintenance0.00794444668596613
GO:0000155two-component sensor activity0.00978554135310251
GO:0006812cation transport0.00978554135310251
GO:0008324cation transmembrane transporter activity0.00978554135310251
GO:0000160two-component signal transduction system (phosphorelay)0.00978554135310251
GO:0030551cyclic nucleotide binding0.0106912991966847
GO:0007600sensory perception0.0107332785924815
GO:0004673protein histidine kinase activity0.0111179690311578
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.012266658879953
GO:0007165signal transduction0.0145568394445184
GO:0050877neurological system process0.0165785386159458
GO:0007154cell communication0.0168591289326561
GO:0015075ion transmembrane transporter activity0.0168591289326561
GO:0006811ion transport0.0174311980338561
GO:0045596negative regulation of cell differentiation0.0203214149269298
GO:0022891substrate-specific transmembrane transporter activity0.0203214149269298
GO:0003008system process0.0203214149269298
GO:0022857transmembrane transporter activity0.0219192063984734
GO:0051093negative regulation of developmental process0.0219192063984734
GO:0016021integral to membrane0.023466445814658
GO:0031224intrinsic to membrane0.023466445814658
GO:0022892substrate-specific transporter activity0.023466445814658
GO:0050954sensory perception of mechanical stimulus0.032925205536912
GO:0007605sensory perception of sound0.032925205536912
GO:0044425membrane part0.032925205536912
GO:0030955potassium ion binding0.0339473491586143
GO:0045595regulation of cell differentiation0.0339473491586143
GO:0009986cell surface0.0341594209964774
GO:0015276ligand-gated ion channel activity0.0363211010183369
GO:0022834ligand-gated channel activity0.0363211010183369
GO:0007218neuropeptide signaling pathway0.0364731310049928
GO:0031420alkali metal ion binding0.0471945555141875
GO:0050793regulation of developmental process0.0492038426264123



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
neural cell1.33e-1225
neuronal stem cell2.14e-128
neuron1.08e-096
neuroblast1.08e-096
electrically signaling cell1.08e-096
embryonic stem cell1.46e-085
neurectodermal cell5.53e-0759
Uber Anatomy
Ontology termp-valuen
central nervous system3.79e-4981
nervous system4.34e-4489
neural tube3.74e-4056
neural rod3.74e-4056
future spinal cord3.74e-4056
neural keel3.74e-4056
regional part of nervous system1.27e-3653
regional part of brain1.27e-3653
brain2.12e-3568
future brain2.12e-3568
neural plate5.61e-3082
presumptive neural plate5.61e-3082
neurectoderm3.73e-2986
organ system subdivision1.43e-28223
regional part of forebrain1.11e-2641
forebrain1.11e-2641
anterior neural tube1.11e-2641
future forebrain1.11e-2641
adult organism3.22e-26114
ecto-epithelium5.63e-23104
ectoderm-derived structure6.59e-22171
ectoderm6.59e-22171
presumptive ectoderm6.59e-22171
pre-chordal neural plate2.28e-2161
telencephalon3.55e-2034
brain grey matter6.05e-2034
gray matter6.05e-2034
cerebral hemisphere3.14e-1832
regional part of telencephalon4.86e-1832
cerebral cortex4.93e-1725
pallium4.93e-1725
structure with developmental contribution from neural crest1.21e-15132
posterior neural tube1.26e-1415
chordal neural plate1.26e-1415
regional part of cerebral cortex3.83e-1422
anatomical cluster4.39e-14373
neocortex9.14e-1420
segmental subdivision of hindbrain3.78e-1112
hindbrain3.78e-1112
presumptive hindbrain3.78e-1112
segmental subdivision of nervous system4.29e-1013
brainstem7.03e-096
tube2.14e-08192
diencephalon2.82e-087
future diencephalon2.82e-087
gland of diencephalon4.78e-084
neuroendocrine gland4.78e-084
embryo1.26e-07592
regional part of metencephalon2.44e-079
metencephalon2.44e-079
future metencephalon2.44e-079
anatomical conduit3.05e-07240
multi-tissue structure3.57e-07342
epithelium3.91e-07306
testis4.02e-078
cell layer6.65e-07309


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)
MA0003.11.05935
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
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
MA0055.10.791759
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
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
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.12.31225
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
MA0105.11.90157
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
MA0119.10.586221
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
MA0145.10.569905
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.12.64806
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.869502
MA0102.21.75932
MA0258.11.07498
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
REST#597837.237521537096020.004104697304192610.0195865345525916
ZNF263#1012736.166381227758010.006539814347975980.027983106796471



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:C2709&oldid=2571220"